diff --git a/.github/workflows/check_tpv_config.yml b/.github/workflows/check_tpv_config.yml
index a94e5320a..fe78f44b9 100644
--- a/.github/workflows/check_tpv_config.yml
+++ b/.github/workflows/check_tpv_config.yml
@@ -31,9 +31,9 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
- pip install total-perspective-vortex==$TPV_VERSION pyyaml galaxy-app==22.1.1
+ pip install total-perspective-vortex==$TPV_VERSION pyyaml galaxy-app==23.1.1
env:
- TPV_VERSION: '2.3.0'
+ TPV_VERSION: '2.3.2'
- name: Check TPV files and job conf
env:
SETTING: github
diff --git a/files/galaxy/config/local_tool_conf_dev.xml b/files/galaxy/config/local_tool_conf_dev.xml
index 328bb1801..1736e4705 100644
--- a/files/galaxy/config/local_tool_conf_dev.xml
+++ b/files/galaxy/config/local_tool_conf_dev.xml
@@ -19,6 +19,6 @@
diff --git a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/production_tools.yml b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/production_tools.yml
new file mode 120000
index 000000000..8c87a0031
--- /dev/null
+++ b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/production_tools.yml
@@ -0,0 +1 @@
+../../production/total_perspective_vortex/tools.yml
\ No newline at end of file
diff --git a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_config.yml b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_config.yml
index 03a4a2bb5..5a5ca9801 100644
--- a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_config.yml
+++ b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_config.yml
@@ -35,7 +35,7 @@ tools:
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*:
cores: 2
scheduling:
- prefer:
+ require:
- pulsar
rules:
- if: 0.01 <= input_size < 2
@@ -129,38 +129,3 @@ tools:
- if: 0.05 <= input_size
cores: 8
mem: 30.7
-
-users:
- jenkins_bot@usegalaxy.org.au:
- cores: 1
- mem: cores * 3.8
- params:
- nativeSpecification: "--nodes=1 --ntasks={cores} --ntasks-per-node={cores} --mem={round(mem*1024)} --partition=main"
- scheduling:
- require:
- - slurm
- pulsar_paw_user@usegalaxy.org.au:
- rules:
- - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
- scheduling:
- accept:
- - pulsar
- - offline
- require:
- - pulsar-paw
- pqld@usegalaxy.org.au:
- rules:
- - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
- scheduling:
- accept:
- - pulsar
- - offline
- require:
- - pulsar-QLD
- pulsar_nci_test_user@usegalaxy.org.au:
- rules:
- - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
- scheduling:
- require:
- - pulsar
- - pulsar-nci-test
diff --git a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_default_tool.yml b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_default_tool.yml
new file mode 100644
index 000000000..56dee75ef
--- /dev/null
+++ b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_default_tool.yml
@@ -0,0 +1,18 @@
+global:
+ default_inherits: default
+
+tools:
+ default:
+ context:
+ partition: main
+ test_cores: 1
+ cores: 1
+ mem: cores * 3.8
+ params: {}
+ env: {}
+ scheduling:
+ reject:
+ - offline
+ rules: []
+ rank: |
+ helpers.weighted_random_sampling(candidate_destinations)
diff --git a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_destinations.yml.j2 b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_destinations.yml.j2
index b6cd3e738..310ea099e 100644
--- a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_destinations.yml.j2
+++ b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_destinations.yml.j2
@@ -61,8 +61,8 @@ destinations:
slurm:
inherits: _slurm_destination
runner: slurm
- max_accepted_cores: 32
- max_accepted_mem: 122.86
+ max_cores: 32
+ max_mem: 122.86
tags: {{ job_conf_limits.environments['slurm'].tags }}
scheduling:
accept:
@@ -110,8 +110,8 @@ destinations:
pulsar-QLD:
inherits: _pulsar_destination
runner: pulsar-QLD_runner
- max_accepted_cores: 16
- max_accepted_mem: 62.72
+ max_cores: 16
+ max_mem: 62.4
tags: {{ job_conf_limits.environments['pulsar-QLD'].tags }}
params:
jobs_directory: /mnt/tmp/files/staging
@@ -119,6 +119,7 @@ destinations:
scheduling:
accept:
- pulsar-QLD
+ - pulsar-blast
require:
- pulsar
diff --git a/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_users.yml b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_users.yml
new file mode 100644
index 000000000..4851db0cd
--- /dev/null
+++ b/files/galaxy/dynamic_job_rules/load-testing/total_perspective_vortex/testing_tpv_users.yml
@@ -0,0 +1,52 @@
+users:
+ test_user:
+ rules:
+ - id: singularity_test_user_rule
+ if: |
+ enable_singularity = False
+ if tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed'):
+ try:
+ enable_singularity = 'singularity' in [hta.user_tname for hta in job.history.tags]
+ except:
+ pass
+ enable_singularity
+ params:
+ singularity_enabled: True
+ dependency_resolution: none
+ jenkins_bot@usegalaxy.org.au:
+ inherits: test_user
+ cores: test_cores
+ mem: cores * 3.8
+ params:
+ nativeSpecification: "--nodes=1 --ntasks={cores} --ntasks-per-node={cores} --mem={round(mem*1024)} --partition=main"
+ scheduling:
+ require:
+ - slurm
+ pulsar_paw_user@usegalaxy.org.au:
+ inherits: test_user
+ rules:
+ - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
+ scheduling:
+ accept:
+ - pulsar
+ - offline
+ require:
+ - pulsar-paw
+ pqld@usegalaxy.org.au:
+ inherits: test_user
+ rules:
+ - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
+ scheduling:
+ accept:
+ - pulsar
+ - offline
+ require:
+ - pulsar-QLD
+ pulsar_nci_test_user@usegalaxy.org.au:
+ inherits: test_user
+ rules:
+ - if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
+ scheduling:
+ require:
+ - pulsar
+ - pulsar-nci-test
diff --git a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/destinations.yml.j2 b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/destinations.yml.j2
index a3df198b2..b1a6800cb 100644
--- a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/destinations.yml.j2
+++ b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/destinations.yml.j2
@@ -120,7 +120,6 @@ destinations:
require:
- pulsar-paw
- pulsar
- - offline # on loan to etca
pulsar-mel3:
inherits: _pulsar_destination
runner: pulsar-mel3_runner
@@ -159,6 +158,7 @@ destinations:
require:
- pulsar
- pulsar-quick # tag given to tools where jobs are bound to complete in less than a day
+ - offline
pulsar-qld-high-mem0:
inherits: _pulsar_destination
runner: pulsar-qld-high-mem0_runner
@@ -236,7 +236,7 @@ destinations:
require:
- pulsar
- pulsar-quick # tag given to tools where jobs are bound to complete in less than a day
- - offline # etca testing
+ - offline # volume migration
pulsar-azure:
inherits: _pulsar_destination
runner: pulsar_azure_0_runner
diff --git a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
index 0f3a237f6..94b100036 100644
--- a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
+++ b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
@@ -1,17 +1,4 @@
tools:
- ### Tools with resource updates being tested due to OOM errors ###
- toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/.*:
- mem: 12
- toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft_add/.*:
- mem: 12
- toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/.*:
- cores: 2
- mem: 10
- toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/.*:
- mem: 12
- toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/.*:
- mem: 12
- ### ###
testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/htseqsams2mxlocal/.*:
cores: 3
mem: 11.5
@@ -29,6 +16,8 @@ tools:
testtoolshed.g2.bx.psu.edu/repos/simon-gladman/phyloseq_ordination_plot/phyloseq_ordinate/.*:
cores: 16
mem: 61.4
+ toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/.*:
+ mem: 8
toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
cores: 8
mem: 30.7
@@ -71,8 +60,6 @@ tools:
cores: 2
mem: 7.6
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/.*:
- cores: 1
- mem: 3.8
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/.*:
@@ -80,7 +67,7 @@ tools:
mem: 61.4
params:
docker_enabled: true
- toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/.*: #
+ toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/.*:
@@ -90,9 +77,6 @@ tools:
accept:
- pulsar
- pulsar-training-large
- toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/.*:
- params:
- singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/.*:
cores: 1
mem: 3.8
@@ -113,6 +97,12 @@ tools:
mem: 3.8
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/bgruening/circexplorer/circexplorer/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/.*:
cores: 8
mem: 30.7
@@ -132,8 +122,8 @@ tools:
- pulsar
- pulsar-quick
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*:
- cores: 10
- mem: 90 # TODO: delete this and get cores/mem from shared db if they are adjusted to 10c90g
+ cores: 10
+ mem: 90
params:
singularity_enabled: true
scheduling:
@@ -162,11 +152,18 @@ tools:
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/.*:
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/.*:
+ mem: 8
+ toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
context:
test_cores: 2
cores: 120
mem: 1922
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -186,9 +183,13 @@ tools:
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/.*:
cores: 10
mem: 38.3
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/.*:
cores: 120
mem: 1922
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -242,23 +243,29 @@ tools:
scheduling:
accept:
- pulsar
- toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
- cores: 5
- mem: 19.1
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/.*:
cores: 4
mem: 15.3
+ scheduling:
+ accept:
+ - pulsar
rules:
- id: sailfish_small_input_rule
if: input_size < 0.2
cores: 1
mem: 3.8
- scheduling:
- accept:
- - pulsar
+ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
+ cores: 5
+ mem: 19.1
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/.*:
+ mem: 10
params:
- tmp_dir: true
+ tmp_dir: true
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/.*:
cores: 1
mem: 3.8
@@ -318,6 +325,8 @@ tools:
if: input_size >= 0.03
fail: Too much data, Prokka is designed to annotate bacterial/virus genomes
only. Prokka will not annotate eukaryotic genomes nor metagenomes.
+ toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/.*:
+ mem: 12
toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/.*:
cores: 8
mem: 30.7
@@ -451,13 +460,11 @@ tools:
scheduling:
accept:
- pulsar
+ toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS.*:
+ mem: 10
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/.*:
cores: 2
mem: 7.6
- # scheduling: # 9/9/23: removing from pulsar due to large output files compared to inputs
- # accept:
- # - pulsar
- # - pulsar-quick
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/.*:
cores: 8
mem: 30.7
@@ -501,8 +508,8 @@ tools:
cores: 8
mem: 30.7
env:
- _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+ _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
scheduling:
accept:
- pulsar
@@ -521,6 +528,9 @@ tools:
if: 0.01 <= input_size < 2
cores: 4
mem: 15.3
+ toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/.*:
params:
singularity_enabled: true
@@ -649,8 +659,8 @@ tools:
cores: 3
mem: 11.5
env:
- _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+ _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
scheduling:
accept:
- pulsar
@@ -668,6 +678,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/.*:
cores: 3
mem: 11.5
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/devteam/samtools.*:
params:
singularity_enabled: true
@@ -692,6 +704,9 @@ tools:
if: input_size < 0.5
cores: 1
mem: 3.8
+ toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/.*:
cores: 8
mem: 30.7
@@ -703,9 +718,25 @@ tools:
if: input_size < 0.5
cores: 1
mem: 3.8
+ toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy.*:
- cores: 1
- mem: 3.8
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*:
@@ -713,9 +744,10 @@ tools:
cores: 8
mem: 69
params:
- tmp_dir: true
docker_enabled: true
- docker_volumes: $job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro
+ docker_volumes:
+ $job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro
+ tmp_dir: true
rules:
- if: |
user and 'Alphafold' in [role.name for role in user.all_roles() if not role.deleted] and not (
@@ -744,39 +776,43 @@ tools:
)])
fail: |
This tool is currently being beta-tested on GPUs and your account has not been given access. Contact help@genome.edu.au if you think this is in error.
-
toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.*:
+ inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
params:
- docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env
+ docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=5 --env
ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data/v2.1
- inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.3.*:
+ inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
params:
- docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env
+ docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=5 --env
ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data/v2.3
rules:
- - if: |
- min_version = '2.3.1+galaxy2'
- helpers.tool_version_gte(tool, min_version)
- params:
- docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data
- inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
-
+ - if: |
+ min_version = '2.3.1+galaxy2'
+ helpers.tool_version_gte(tool, min_version)
+ params:
+ docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=5 --env
+ ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_cactus/cactus_cactus/.*:
context:
test_cores: 10
- cores: 60
- mem: 961
+ cores: 24
+ mem: 200
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/.*:
- cores: 1
- mem: 3.8
+ context:
+ test_cores: 10
+ cores: 24
+ mem: 200
params:
singularity_enabled: true
+ scheduling:
+ accept:
+ - pulsar
toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/.*:
cores: 12
mem: 46.0
@@ -885,6 +921,18 @@ tools:
scheduling:
accept:
- pulsar
+ toolshed.g2.bx.psu.edu/repos/galaxyp/rawtools/rawtools/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
+ cores: 6
+ mem: 4
+ params:
+ singularity_container_id_override: docker://teambraker/braker3:v.1.0.4
+ singularity_enabled: true
+ scheduling:
+ require:
+ - pulsar
toolshed.g2.bx.psu.edu/repos/iracooke/protk_proteogenomics/.*:
cores: 1
mem: 3.8
@@ -917,7 +965,7 @@ tools:
mem: 3.8
scheduling:
prefer:
- - slurm
+ - slurm
- id: abricate_medium_input_rule
if: 0.005 <= input_size < 0.02
cores: 4
@@ -977,10 +1025,14 @@ tools:
if: input_size < 0.5
cores: 1
mem: 3.8
+ toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/.*:
+ mem: 8
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/.*:
scheduling:
accept:
- pulsar
+ toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/.*:
+ mem: 12
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.*:
cores: 2
mem: 7.6
@@ -1073,6 +1125,14 @@ tools:
if: 0.0002 <= input_size < 0.01
cores: 2
mem: 7.6
+ toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/.*:
+ cores: 3
+ mem: 11.5
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/.*:
+ cores: 2
+ mem: 10
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/.*:
cores: 1
mem: 3.8
@@ -1094,15 +1154,27 @@ tools:
mem: 3.8
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/.*:
cores: 5
mem: 19.1
+ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/.*:
cores: 30
mem: 480.5
scheduling:
accept:
- pulsar
+ toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
cores: 3
mem: 11.5
@@ -1140,13 +1212,18 @@ tools:
params:
singularity_enabled: true
scheduling:
- prefer:
- - pulsar
require:
- - gtdbtk_database
+ - gtdbtk_database
+ prefer:
+ - pulsar
+ toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/.*:
cores: 16
mem: 61.4
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -1179,12 +1256,6 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/.*:
cores: 32
mem: 122.8
- # scheduling:
- # accept:
- # - pulsar
- # reject:
- # - pulsar-mel2
- # - pulsar-QLD
rules:
- id: humann_small_input_rule
if: input_size < 0.01
@@ -1257,6 +1328,9 @@ tools:
accept:
- pulsar
- pulsar-quick
+ toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/.*:
cores: 3
mem: 11.5
@@ -1275,6 +1349,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/.*:
cores: 5
mem: 19.1
+ params:
+ singularity_enabled: true
rules:
- id: kallisto_quant_small_input_rule
if: input_size < 0.1
@@ -1314,12 +1390,23 @@ tools:
execute: |
from galaxy.jobs.mapper import JobNotReadyException
raise JobNotReadyException()
+ toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*:
cores: 7
mem: 26.8
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/links/links/.*:
+ cores: 4
+ mem: 15.3
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/.*:
cores: 5
mem: 19.1
@@ -1344,6 +1431,8 @@ tools:
accept:
- pulsar
- pulsar-quick
+ toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/.*:
+ mem: 12
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/.*:
scheduling:
accept:
@@ -1398,6 +1487,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/.*:
cores: 16
mem: 61.4
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -1418,6 +1509,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/.*:
cores: 60
mem: 961
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -1460,7 +1553,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/mothur.*:
params:
docker_enabled: true
- docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
+ docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env
+ TERM=vt100
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/.*:
cores: 7
mem: 26.8
@@ -1672,6 +1766,12 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/.*:
cores: 3
mem: 11.5
+ toolshed.g2.bx.psu.edu/repos/iuc/mummer.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/.*:
+ cores: 2
+ mem: 10
toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/.*:
cores: 5
mem: 19.1
@@ -1686,6 +1786,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/.*:
cores: 3
mem: 11.5
+ toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/.*:
params:
singularity_enabled: true
@@ -1704,54 +1807,54 @@ tools:
if: 0.015 <= input_size < 1
cores: 5
mem: 19.1
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/phyml/phyml/.*:
+ cores: 120
+ mem: 1922
+ scheduling:
+ accept:
+ - pulsar
+ - pulsar-training-large
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_add_descriptions/picrust2_add_descriptions/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_compare_biom/picrust_compare_biom/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_hsp/picrust2_hsp/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_format_tree_and_trait_table/picrust_format_tree_and_trait_table/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_metagenome_pipeline/picrust2_metagenome_pipeline/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pathway_pipeline/picrust2_pathway_pipeline/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_normalize_by_copy_number/picrust_normalize_by_copy_number/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pipeline/picrust2_pipeline/.*:
+ cores: 7
+ mem: 26.8
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_place_seqs/picrust2_place_seqs/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_add_descriptions/picrust2_add_descriptions/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust2_shuffle_predictions/picrust2_shuffle_predictions/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_hsp/picrust2_hsp/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_metagenome_pipeline/picrust2_metagenome_pipeline/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_compare_biom/picrust_compare_biom/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pathway_pipeline/picrust2_pathway_pipeline/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_format_tree_and_trait_table/picrust_format_tree_and_trait_table/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pipeline/picrust2_pipeline/.*:
- cores: 4
- mem: 15.3
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_place_seqs/picrust2_place_seqs/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_normalize_by_copy_number/picrust_normalize_by_copy_number/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/picrust2_shuffle_predictions/picrust2_shuffle_predictions/.*:
+ toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/.*:
params:
singularity_enabled: true
- toolshed.g2.bx.psu.edu/repos/iuc/phyml/phyml/.*:
- cores: 120
- mem: 1922
- scheduling:
- accept:
- - pulsar
- - pulsar-training-large
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/.*:
cores: 16
mem: 61.4
@@ -1833,6 +1936,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/.*:
cores: 9
mem: 34.5
+ params:
+ singularity_enabled: true
rules:
- id: qualimap_bamqc_small_input_rule
if: input_size < 0.2
@@ -1842,14 +1947,20 @@ tools:
if: 0.2 <= input_size < 30
cores: 5
mem: 19.1
+ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_rnaseq/qualimap_rnaseq/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*:
cores: 16
mem: 61.4
rules:
- id: quast_small_input_rule
if: input_size < 1
- cores: 1
- mem: 3.8
+ cores: 2
+ mem: 10
toolshed.g2.bx.psu.edu/repos/iuc/raven/raven/.*:
cores: 20
mem: 200
@@ -1906,6 +2017,8 @@ tools:
cores: 9
mem: 34.5
toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/.*:
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -1984,6 +2097,18 @@ tools:
if: 0.05 <= input_size < 0.5
cores: 5
mem: 19.1
+ toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/.*:
+ params:
+ singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/.*:
cores: 20
mem: 200
@@ -2060,18 +2185,114 @@ tools:
cores: 3
mem: 11.5
toolshed.g2.bx.psu.edu/repos/iuc/spades_biosyntheticspades/spades_biosyntheticspades/.*:
- inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
+ cores: 20
+ mem: 500
+ params:
+ singularity_enabled: true
+ scheduling:
+ accept:
+ - pulsar
+ - pulsar-training-large
+ rules:
+ - id: spades_biosyntheticspades_small_input_rule
+ if: input_size < 0.005
+ cores: 2
+ mem: 7.6
+ - id: spades_biosyntheticspades_medium_input_rule
+ if: 0.005 <= input_size < 2
+ cores: 8
+ mem: 30.7
+ - id: spades_biosyntheticspades_fail_rule
+ if: input_size >= 60
+ fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_coronaspades/spades_coronaspades/.*:
+ cores: 20
+ mem: 500
scheduling:
accept:
- pulsar-paw
- inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
+ - pulsar
+ - pulsar-training-large
+ rules:
+ - if: |
+ minimum_singularity_version = '3.15.4+galaxy0'
+ helpers.tool_version_gte(tool, minimum_singularity_version)
+ params:
+ singularity_enabled: true
+ - id: spades_coronaspades_small_input_rule
+ if: input_size < 0.005
+ cores: 2
+ mem: 7.6
+ - id: spades_coronaspades_medium_input_rule
+ if: 0.005 <= input_size < 2
+ cores: 8
+ mem: 30.7
+ - id: spades_coronaspades_fail_rule
+ if: input_size >= 60
+ fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaplasmidspades/spades_metaplasmidspades/.*:
- inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
+ cores: 20
+ mem: 500
+ params:
+ singularity_enabled: true
+ scheduling:
+ accept:
+ - pulsar
+ - pulsar-training-large
+ rules:
+ - id: spades_metaplasmidspades_small_input_rule
+ if: input_size < 0.005
+ cores: 2
+ mem: 7.6
+ - id: spades_metaplasmidspades_medium_input_rule
+ if: 0.005 <= input_size < 2
+ cores: 8
+ mem: 30.7
+ - id: spades_metaplasmidspades_fail_rule
+ if: input_size >= 60
+ fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/.*:
- inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
+ cores: 20
+ mem: 500
+ params:
+ singularity_enabled: true
+ scheduling:
+ accept:
+ - pulsar
+ - pulsar-training-large
+ rules:
+ - id: spades_metaviralspades_small_input_rule
+ if: input_size < 0.005
+ cores: 2
+ mem: 7.6
+ - id: spades_metaviralspades_medium_input_rule
+ if: 0.005 <= input_size < 2
+ cores: 8
+ mem: 30.7
+ - id: spades_metaviralspades_fail_rule
+ if: input_size >= 60
+ fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/.*:
- inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
+ cores: 20
+ mem: 500
+ params:
+ singularity_enabled: true
+ scheduling:
+ accept:
+ - pulsar
+ - pulsar-training-large
+ rules:
+ - id: spades_plasmidspades_small_input_rule
+ if: input_size < 0.005
+ cores: 2
+ mem: 7.6
+ - id: spades_plasmidspades_medium_input_rule
+ if: 0.005 <= input_size < 2
+ cores: 8
+ mem: 30.7
+ - id: spades_plasmidspades_fail_rule
+ if: input_size >= 60
+ fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_rnaviralspades/spades_rnaviralspades/.*:
cores: 10
mem: 250
@@ -2080,6 +2301,11 @@ tools:
- pulsar
- pulsar-training-large
rules:
+ - if: |
+ minimum_singularity_version = '3.15.4+galaxy1'
+ helpers.tool_version_gte(tool, minimum_singularity_version)
+ params:
+ singularity_enabled: true
- id: spades_rnaviralspades_small_input_rule
if: input_size < 0.005
cores: 2
@@ -2129,18 +2355,10 @@ tools:
mem: 61.4
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_ustacks/stacks2_ustacks/.*:
cores: 16
- mem: 61.4
+ mem: 100
scheduling:
accept:
- pulsar
- - pulsar-quick
- rules:
- - id: rule_stacks2_ustacks_limit_concurrency
- if: |
- helpers.concurrent_job_count_for_tool(app, tool, user) >= 3 # concurrent jobs per user
- execute: |
- from galaxy.jobs.mapper import JobNotReadyException
- raise JobNotReadyException()
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/.*:
cores: 5
mem: 19.1
@@ -2308,7 +2526,7 @@ tools:
cores: 1
mem: 3.8
- id: unicycler_medium_input_rule
- if: 0.05 <= input_size < 2
+ if: 0.05 <= input_size < 0.3
cores: 8
mem: 30.7
toolshed.g2.bx.psu.edu/repos/iuc/vcf2maf/vcf2maf/.*:
@@ -2376,6 +2594,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/.*:
cores: 16
mem: 61.4
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -2395,6 +2615,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*:
cores: 20
mem: 500
+ params:
+ singularity_enabled: true
scheduling:
accept:
- pulsar
@@ -2408,12 +2630,14 @@ tools:
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- - id: spades_fail_rule # TODO: Ask IM whether we still need the spades fail rule
- if: input_size >= 20
+ - id: spades_fail_rule
+ if: input_size >= 60
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/.*:
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/.*:
+ mem: 12
toolshed.g2.bx.psu.edu/repos/pjbriggs/macs21/macs2_1_peakcalling/.*:
cores: 9
mem: 34.5
@@ -2421,8 +2645,8 @@ tools:
cores: 3
mem: 11.5
env:
- _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+ _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
scheduling:
accept:
- pulsar
@@ -2447,6 +2671,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/recetox/.*:
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/.*:
cores: 8
mem: 30.7
@@ -2466,18 +2693,6 @@ tools:
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/.*:
cores: 8
mem: 30.7
- toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/.*:
- cores: 7
- mem: 26.8
- rules:
- - id: krona-text_small_input_rule
- if: input_size < 0.02
- cores: 1
- mem: 3.8
- - id: krona-text_medium_input_rule
- if: 0.02 <= input_size < 2
- cores: 5
- mem: 19.1
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/.*:
cores: 4
mem: 15.3
@@ -2498,6 +2713,9 @@ tools:
mem: 3.8
params:
singularity_enabled: true
+ toolshed.g2.bx.psu.edu/repos/wolma/mimodd.*:
+ params:
+ singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align/.*:
cores: 5
mem: 19.1
@@ -2506,9 +2724,6 @@ tools:
if: input_size < 0.01
cores: 1
mem: 3.8
- toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/.*:
- cores: 3
- mem: 11.5
.*bowtie2_index_builder_data_manager.*:
cores: 16
mem: 61.4
@@ -2601,6 +2816,26 @@ tools:
require:
- pulsar
- pulsar-azure-gpu
+ cellranger:
+ cores: 6
+ mem: 20
+ params:
+ singularity_enabled: true
+ rules:
+ - if: |
+ not user or not 'cellranger' in [role.name for role in user.all_roles() if not role.deleted]
+ fail: Your account has not been given access to cellranger. Contact help@genome.edu.au
+ if you think this is in error.
+ fgenesh:
+ cores: 24
+ mem: 12
+ params:
+ singularity_enabled: true
+ rules:
+ - if: |
+ not user or not 'Fgenesh' in [role.name for role in user.all_roles() if not role.deleted]
+ fail: Your account has not been given access to fgenesh. Contact help@genome.edu.au
+ if you think this is in error.
gtdbtk_classify_wf_test:
cores: 16
mem: 60
@@ -2644,33 +2879,7 @@ tools:
cores: 1
mem: 3.8
wig_to_bigWig:
- cores: 5
mem: 19.1
- cellranger:
- cores: 6
- mem: 20
- params:
- singularity_enabled: true
- rules:
- - if: |
- not user or not 'cellranger' in [role.name for role in user.all_roles() if not role.deleted]
- fail: Your account has not been given access to cellranger. Contact help@genome.edu.au if you think this is in error.
- fgenesh:
- cores: 24
- mem: 12
- params:
- singularity_enabled: true
- rules:
- - if: |
- not user or not 'Fgenesh' in [role.name for role in user.all_roles() if not role.deleted]
- fail: Your account has not been given access to fgenesh. Contact help@genome.edu.au if you think this is in error.
-
- toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
- mem: 4
- cores: 6
- params:
- singularity_container_id_override: docker://teambraker/braker3:v.1.0.4
- singularity_enabled: true
scheduling:
- require:
- - pulsar
+ accept:
+ - training-exempt # these jobs are exempt from training rules that would reduce allocated memory
diff --git a/files/keys/internal_hop_key.pub b/files/keys/internal_hop_key.pub
new file mode 100644
index 000000000..98812490b
--- /dev/null
+++ b/files/keys/internal_hop_key.pub
@@ -0,0 +1 @@
+ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC+HmTcHhYpvhy0J+h5/XUrWJ/S6/94Ju48B9NF+4cqdcIGtUFFK8mM5bDPGc36a7+NkH0JL+DoG1X7hbjX13B2kQTVVB5tvSIzsSpx79zTwxMSSQJIcZ0Z99GXclzt81KLQ0zCYnN8X42+Cq4mU9jaXUnnmFlcmjTP2XmB311VGqv3ujCdYjaoyqB9C8kP2/dtuMHXCDZ9urg9pGlkb/3354tehahbFgA9XazCe8sMGApXloa9xMHdiCkTZ0YXSI9bvyEQIuWmgZL5ZNjlF41hnYk/b+u/22xFlvetot5OMYOONuQN6UMlVwua2lakmO7Q8zWRLunGIBxfmuJceheT internal_hop_key
diff --git a/galaxy-backup_playbook.yml b/galaxy-backup_playbook.yml
index 1252c045c..5a335a58c 100644
--- a/galaxy-backup_playbook.yml
+++ b/galaxy-backup_playbook.yml
@@ -6,6 +6,7 @@
- group_vars/VAULT
- host_vars/galaxy-backup.yml
- secret_group_vars/stats_server_vault
+ - secret_group_vars/ubuntu_maintenance_key
pre_tasks:
- name: Attach volume to instance
include_role:
@@ -16,7 +17,7 @@
roles:
- common
- geerlingguy.pip
- # - slg.db-backup # Do not include this role until galaxy production is in Sydney
+ - slg.db-backup
- dj-wasabi.telegraf
post_tasks:
- name: Ensure desired version of ansible is installed
diff --git a/galaxy-db_playbook.yml b/galaxy-db_playbook.yml
index 5961263e7..7cf3c4663 100644
--- a/galaxy-db_playbook.yml
+++ b/galaxy-db_playbook.yml
@@ -7,6 +7,7 @@
- group_vars/dbservers.yml
- host_vars/galaxy-db.usegalaxy.org.au.yml
- secret_group_vars/stats_server_vault
+ - secret_group_vars/ubuntu_maintenance_key
pre_tasks:
- name: Attach volume to instance
include_role:
diff --git a/galaxy-misc-nfs_playbook.yml b/galaxy-misc-nfs_playbook.yml
index bef1ecd49..0258cd261 100644
--- a/galaxy-misc-nfs_playbook.yml
+++ b/galaxy-misc-nfs_playbook.yml
@@ -6,6 +6,7 @@
- group_vars/VAULT
- group_vars/nfs_servers.yml
- host_vars/galaxy-misc-nfs.usegalaxy.org.au.yml
+ - secret_group_vars/ubuntu_maintenance_key
- secret_group_vars/stats_server_vault
pre_tasks:
- name: Create nfs directories
diff --git a/galaxy-queue_playbook.yml b/galaxy-queue_playbook.yml
index 00be7bff4..78f01f2af 100644
--- a/galaxy-queue_playbook.yml
+++ b/galaxy-queue_playbook.yml
@@ -9,6 +9,7 @@
- group_vars/galaxy_etca_slurm.yml
- secret_group_vars/stats_server_vault
- secret_group_vars/etca_vault.yml
+ - secret_group_vars/ubuntu_maintenance_key
roles:
- common
- insspb.hostname
diff --git a/galaxy-user-nfs_playbook.yml b/galaxy-user-nfs_playbook.yml
index 25313e55f..ba99c1112 100644
--- a/galaxy-user-nfs_playbook.yml
+++ b/galaxy-user-nfs_playbook.yml
@@ -7,10 +7,11 @@
- group_vars/nfs_servers.yml
- host_vars/galaxy-user-nfs.usegalaxy.org.au.yml
- secret_group_vars/stats_server_vault
+ - secret_group_vars/ubuntu_maintenance_key
pre_tasks:
- - name: Attach volumes to instance
- include_role:
- name: attached-volumes
+ # - name: Attach volumes to instance # handle user nfs mounting manually
+ # include_role:
+ # name: attached-volumes
- name: Ensure galaxy nfs user data directories exist
file:
path: "{{ item }}"
diff --git a/galaxy-workers_playbook.yml b/galaxy-workers_playbook.yml
index 95e77dee7..4f6c16dbc 100644
--- a/galaxy-workers_playbook.yml
+++ b/galaxy-workers_playbook.yml
@@ -6,6 +6,7 @@
- group_vars/VAULT
- group_vars/galaxy_etca_slurm.yml
- group_vars/galaxy_workers.yml
+ - secret_group_vars/ubuntu_maintenance_key # TODO: when branches are merged, rename this file to internal_keys
- secret_group_vars/stats_server_vault
pre_tasks:
- name: Attach volume to instance
diff --git a/galaxy_playbook.yml b/galaxy_playbook.yml
index 765903df2..1de09aa7f 100644
--- a/galaxy_playbook.yml
+++ b/galaxy_playbook.yml
@@ -33,9 +33,11 @@
- mounts
- geerlingguy.pip
- galaxyproject.galaxy
- - role: galaxyproject.miniconda
- become: true
- become_user: galaxy
+ # - role: galaxyproject.miniconda # this role is needed for a fresh installation, but for subsequent playbook runs can take far too much time. TODO: fix this somehow
+ # become: true
+ # become_user: galaxy
+ - usegalaxy_eu.galaxy_subdomains
+ - webhooks
- nginx-upload-module
- galaxyproject.nginx
- galaxyproject.tusd
@@ -48,9 +50,10 @@
- geerlingguy.nfs
- galaxyproject.gxadmin
- pg-post-tasks
- # - remote-pulsar-cron # commented out until galaxy etca is production galaxy
+ - postfix-mail-relay
+ - remote-pulsar-cron
# - delete-tmp-jwds-cron # commented out until galaxy etca is production galaxy, also needs to be enabled
- # - slg.galaxy_stats # commented out until galaxy etca is production galaxy
+ - slg.galaxy_stats
- galaxy-pg-cleanup
- galaxyproject.tiaas2
post_tasks:
diff --git a/galaxy_update_configs_playbook.yml b/galaxy_update_configs_playbook.yml
new file mode 100644
index 000000000..c205afe4c
--- /dev/null
+++ b/galaxy_update_configs_playbook.yml
@@ -0,0 +1,59 @@
+- hosts: galaxy-handlers
+ become: true
+ vars_files:
+ - group_vars/all.yml
+ - group_vars/galaxy_etca.yml
+ - group_vars/VAULT
+ - group_vars/galaxyservers.yml
+ - group_vars/galaxy_etca_slurm.yml
+ - host_vars/galaxy.usegalaxy.org.au.yml
+ - host_vars/galaxy-handlers.usegalaxy.org.au.yml
+ - secret_group_vars/stats_server_vault
+ handlers:
+ - include: handlers/galaxy_handlers.yml
+ tasks:
+ - name: copy job_conf file
+ template:
+ src: "{{ galaxy_config_template_src_dir }}/config/galaxy_job_conf.yml.j2"
+ dest: "{{ galaxy_config_dir }}/job_conf.yml"
+ notify: restart handlers
+ # TODO: better linting of job conf, then it is probably entirely acceptable to let the jenkins_bot trigger a graceful restart of handlers
+ when: not ansible_user == 'jenkins_bot' # do not let the automatic process update the job conf
+ # Previous process would update object store, toolbox filters. TODO: Find another place to do this
+ # - name: template object store conf file
+ # template:
+ # src: "{{ galaxy_config_template_src_dir }}/config/galaxy_object_store_conf.xml.j2"
+ # dest: "{{ galaxy_config_dir }}/object_store_conf.xml"
+ # notify: restart galaxy
+ # when: not ansible_user == 'jenkins_bot' # do not let the automatic process object store or restart galaxy
+ # - name: template toolbox filters
+ # template:
+ # src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2"
+ # dest: "{{ galaxy_server_dir }}/lib/galaxy/tools/toolbox/filters/ga_filters.py"
+ # notify: restart galaxy
+ # when: not ansible_user == 'jenkins_bot' # do not let the automatic process restart galaxy
+ - name: Copy local tool conf file
+ copy:
+ src: "{{ galaxy_config_file_src_dir }}/config/{{ item }}"
+ dest: "{{ galaxy_config_dir }}/{{ item }}"
+ with_items:
+ - local_tool_conf.xml
+ when: not ansible_user == 'jenkins_bot'
+ - name: Install dynamic job rules (static) # dynamic job rules tasks copied from https://github.com/galaxyproject/ansible-galaxy/blob/main/tasks/static_setup.yml
+ copy:
+ src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
+ dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item }}"
+ mode: 0644
+ with_items: "{{ galaxy_dynamic_job_rules }}"
+ when: not item.endswith(".j2")
+ notify: restart handlers
+ - name: Install dynamic job rules (template)
+ template:
+ src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
+ dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | regex_replace(regex) }}"
+ mode: 0644
+ vars:
+ regex: '\.j2$'
+ with_items: "{{ galaxy_dynamic_job_rules }}"
+ when: item.endswith(".j2")
+ notify: restart handlers
diff --git a/galaxy_update_slurm_playbook.yml b/galaxy_update_slurm_playbook.yml
index a056d7cd2..2c56d86cd 100644
--- a/galaxy_update_slurm_playbook.yml
+++ b/galaxy_update_slurm_playbook.yml
@@ -1,4 +1,4 @@
-- hosts: galaxy, galaxy-queue, galaxy_workers
+- hosts: galaxy, galaxy-handlers, galaxy-queue, galaxy_workers
become: true
vars_files:
- group_vars/all.yml
diff --git a/group_vars/VAULT b/group_vars/VAULT
index d33d5fddb..bae822b44 100644
--- a/group_vars/VAULT
+++ b/group_vars/VAULT
@@ -1,430 +1,441 @@
$ANSIBLE_VAULT;1.1;AES256
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diff --git a/group_vars/all.yml b/group_vars/all.yml
index 3aa891ae2..08560b01e 100644
--- a/group_vars/all.yml
+++ b/group_vars/all.yml
@@ -156,6 +156,8 @@ common_packages:
- jq
- glances
- fail2ban
+ - software-properties-common
+ - pigz
#Set pip to be pip3 by default - see roles/geerlingguy.pip/defaults/main.yml
pip_package: python3-pip
@@ -226,6 +228,10 @@ internal_ssh_keys:
private_key_content: "{{ vault_ubuntu_maintenance_key }}"
public_key_src: files/keys/ubuntu_maintenance_key.pub
user: ubuntu
+ internal_hop_key:
+ private_key_content: "{{ vault_internal_hop_key }}"
+ public_key_src: files/keys/internal_hop_key.pub
+ user: ubuntu
# Golang
golang_version: '1.15.6' # default for role version 2.6.3
diff --git a/group_vars/galaxy_etca.yml b/group_vars/galaxy_etca.yml
index 92f5f7252..e07bc0f12 100644
--- a/group_vars/galaxy_etca.yml
+++ b/group_vars/galaxy_etca.yml
@@ -6,6 +6,8 @@ use_internal_ips: true
influx_url: stats.usegalaxy.org.au
grafana_server_url: "https://{{ influx_url }}:8086"
+install_python_311: True
+
# Monitoring
telegraf_agent_output:
- type: influxdb
@@ -23,59 +25,63 @@ galaxy_db_tiaasadmin_password: "{{ vault_galaxy_db_tiaasadmin_password }}"
galaxy_db_tiaas_password: "{{ vault_galaxy_db_tiaas_password }}"
galaxy_server_and_worker_shared_mounts: # Everything mounted on galaxy, galaxy_handlers and workers
+ # galaxy-misc-nfs
- path: /mnt/tools
src: "{{ hostvars['galaxy-misc-nfs']['internal_ip'] }}:/mnt/tools"
fstype: nfs
state: mounted
- - path: /mnt/user-data-test # TEMPORARY
- src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/volB/user-data-test"
- fstype: nfs
- state: mounted
- opts: 'actimeo=2,defaults'
- path: /mnt/custom-indices
src: "{{ hostvars['galaxy-misc-nfs']['internal_ip'] }}:/mnt/custom-indices"
fstype: nfs
state: mounted
-# - path: /mnt/user-data
-# src: "pawsey-user-nfs.usegalaxy.org.au:/mnt/user-data"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-2
-# src: "pawsey-user-nfs.usegalaxy.org.au:/user-data-2"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-3
-# src: "pawsey-user-nfs.usegalaxy.org.au:/user-data-3"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-4
-# src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/user-data4"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-5
-# src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/user-data5"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-6
-# src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/user-data6"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/user-data-7
-# src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/user-data7"
-# fstype: nfs
-# state: mounted
+ # galaxy-job-nfs
- path: /mnt/tmp
src: "{{ hostvars['galaxy-job-nfs']['internal_ip'] }}:/mnt/tmp"
fstype: nfs
state: mounted
-# - path: /mnt/files
-# src: "galaxy-aust-exports.genome.edu.au:/Q0028_files"
-# fstype: nfs
-# state: mounted
-# - path: /mnt/files2
-# src: "galaxy-aust-exports.genome.edu.au:/mnt/files2"
-# fstype: nfs
-# state: mounted
+ opts: 'actimeo=0,defaults'
+ # galaxy-user-nfs
+ - path: /mnt/user-data-volA # 150T volume
+ src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/volA"
+ fstype: nfs
+ opts: 'actimeo=0,defaults'
+ state: mounted
+ - path: /mnt/user-data-volB # 50T volume
+ src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/volB"
+ fstype: nfs
+ opts: 'actimeo=0,defaults'
+ state: mounted
+ - path: /mnt/user-data-volC # 42T volume
+ src: "{{ hostvars['galaxy-user-nfs']['internal_ip'] }}:/mnt/volC"
+ fstype: nfs
+ opts: 'actimeo=0,defaults'
+ state: mounted
+ # pawsey data volumes
+ - path: /mnt/user-data
+ src: "pawsey-user-nfs.usegalaxy.org.au:/mnt/user-data"
+ fstype: nfs
+ state: mounted
+ - path: /mnt/user-data-2
+ src: "pawsey-user-nfs.usegalaxy.org.au:/user-data-2"
+ fstype: nfs
+ state: mounted
+ - path: /mnt/user-data-3
+ src: "pawsey-user-nfs.usegalaxy.org.au:/user-data-3"
+ fstype: nfs
+ state: mounted
+ - path: /mnt/user-data-4
+ src: "pawsey-user-nfs.usegalaxy.org.au:/user-data-4"
+ fstype: nfs
+ state: mounted
+ # QLD data volumes
+ - path: /mnt/files
+ src: "galaxy-aust-exports.genome.edu.au:/Q0028_files"
+ fstype: nfs
+ state: mounted
+ - path: /mnt/files2
+ src: "galaxy-aust-exports.genome.edu.au:/mnt/files2"
+ fstype: nfs
+ state: mounted
galaxy_worker_mounts:
- path: /mnt/galaxy
diff --git a/group_vars/galaxy_etca_slurm.yml b/group_vars/galaxy_etca_slurm.yml
index 5a5ea297e..365100783 100644
--- a/group_vars/galaxy_etca_slurm.yml
+++ b/group_vars/galaxy_etca_slurm.yml
@@ -12,51 +12,61 @@ slurm_nodes:
NodeAddr: "{{ hostvars['galaxy-w1']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w2
NodeAddr: "{{ hostvars['galaxy-w2']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w3
NodeAddr: "{{ hostvars['galaxy-w3']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w4
NodeAddr: "{{ hostvars['galaxy-w4']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w5
NodeAddr: "{{ hostvars['galaxy-w5']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w6
NodeAddr: "{{ hostvars['galaxy-w6']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w7
NodeAddr: "{{ hostvars['galaxy-w7']['internal_ip'] }}"
CPUs: 16
RealMemory: 64000
+ Weight: 10
State: UNKNOWN
- name: galaxy-w8
NodeAddr: "{{ hostvars['galaxy-w8']['internal_ip'] }}"
CPUs: 32
RealMemory: 128000
+ Weight: 100
State: UNKNOWN
- name: galaxy-w9
NodeAddr: "{{ hostvars['galaxy-w9']['internal_ip'] }}"
CPUs: 32
RealMemory: 128000
+ Weight: 100
State: UNKNOWN
- name: galaxy-w10
NodeAddr: "{{ hostvars['galaxy-w10']['internal_ip'] }}"
CPUs: 32
RealMemory: 128000
+ Weight: 100
State: UNKNOWN
- name: galaxy-queue
NodeAddr: "{{ hostvars['galaxy-queue']['internal_ip'] }}"
@@ -69,11 +79,11 @@ slurm_nodes:
RealMemory: 64000
State: UNKNOWN
##& Include galaxy-handlers in slurm config for 2-VM galaxy server. Comment out when using a single VM for galaxy server
- # - name: galaxy-handlers
- # NodeAddr: "{{ hostvars['galaxy-handlers']['internal_ip'] }}"
- # CPUs: 16
- # RealMemory: 64000
- # State: UNKNOWN
+ - name: galaxy-handlers
+ NodeAddr: "{{ hostvars['galaxy-handlers']['internal_ip'] }}"
+ CPUs: 16
+ RealMemory: 64000
+ State: UNKNOWN
slurm_partitions:
diff --git a/group_vars/galaxy_workers.yml b/group_vars/galaxy_workers.yml
index 12288b933..749b091f4 100644
--- a/group_vars/galaxy_workers.yml
+++ b/group_vars/galaxy_workers.yml
@@ -28,3 +28,9 @@ docker_users:
- "{{ galaxy_user.name }}"
docker_daemon_options: # TODO: Uncomment as soon as there is a volume
data-root: /mnt/docker-data
+
+# internal ssh keys
+extra_keys:
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml
index bc2e77b81..da759fbef 100644
--- a/group_vars/galaxyservers.yml
+++ b/group_vars/galaxyservers.yml
@@ -86,6 +86,8 @@ nginx_upload_module_url: https://swift.rc.nectar.org.au/v1/AUTH_377/galaxy_infra
# miniconda
miniconda_prefix: "{{ galaxy_conda_prefix }}"
+num_gunicorn_processes: 1
+
# singularity cache of galaxy user (this defaults to /home/galaxy/.singularity). Not to be confused with cache directory for built sif files in galaxy_config.galaxy.container_resolvers_conf
galaxy_user_singularity_cachedir: /mnt/singularity_data
galaxy_user_singularity_tmpdir: "{{ galaxy_user_singularity_cachedir }}/tmp"
@@ -122,6 +124,8 @@ galaxy_config_dir: "{{ galaxy_root }}/config"
galaxy_conda_prefix: "{{ galaxy_tools_indices_dir }}/tool_dependencies/_conda"
galaxy_conda_exec: mamba
+galaxy_toolbox_filters_dir: "{{ galaxy_server_dir }}/lib/galaxy/tools/toolbox/filters"
+
galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
tpv_version: "2.3.2"
@@ -156,7 +160,6 @@ group_galaxy_config:
use_interactive: false
expose_dataset_path: true
enable_unique_workflow_defaults: true
- database_engine_option_server_side_cursors: true
track_jobs_in_database: true
use_heartbeat: true
allow_user_dataset_purge: true
@@ -204,6 +207,7 @@ group_galaxy_config:
themes_config_file: "{{ galaxy_config_dir }}/themes_conf.yml"
library_import_dir: "{{ galaxy_tmp_dir }}/library_import_dir"
cluster_files_directory: "{{ galaxy_tmp_dir }}/pbs"
+ short_term_storage_dir: "{{ galaxy_tmp_dir }}/short_term_web_storage"
templates_dir: "{{ galaxy_config_dir }}"
diff --git a/group_vars/pulsarservers.yml b/group_vars/pulsarservers.yml
index 71bedcea2..f73921647 100644
--- a/group_vars/pulsarservers.yml
+++ b/group_vars/pulsarservers.yml
@@ -68,6 +68,7 @@ pulsar_optional_dependencies:
- pycurl
- drmaa
- kombu>=5.2.0
+ - sentry-sdk
install_drmaa: true
pulsar_drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so.1
@@ -107,6 +108,7 @@ pulsar_yaml_config:
amqp_publish_retry_interval_start: 10
amqp_publish_retry_interval_step: 10
amqp_publish_retry_interval_max: 60
+ sentry_dsn: "{{ vault_sentry_url_pulsar_production if ansible_hostname in groups['production_pulsars'] else omit }}"
pulsar_conda_prefix: "{{ pulsar_dependencies_dir }}/_conda"
miniconda_prefix: "{{ pulsar_conda_prefix }}"
diff --git a/host_vars/aarnet.usegalaxy.org.au.yml b/host_vars/aarnet.usegalaxy.org.au.yml
index ac4e06381..60d2b4896 100644
--- a/host_vars/aarnet.usegalaxy.org.au.yml
+++ b/host_vars/aarnet.usegalaxy.org.au.yml
@@ -140,7 +140,7 @@ host_galaxy_config_templates:
- src: "{{ galaxy_config_template_src_dir }}/config/aarnet_job_conf.yml.j2"
dest: "{{ galaxy_config_dir }}/job_conf.yml"
- src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2" ## File cannot be created at dest on first run of playbook
- dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/ga_filters.py"
+ dest: "{{ galaxy_toolbox_filters_dir }}/ga_filters.py"
host_galaxy_config: # renamed from __galaxy_config
gravity:
diff --git a/host_vars/dev.gvl.org.au.yml b/host_vars/dev.gvl.org.au.yml
index f73bf9b02..04b5606b7 100644
--- a/host_vars/dev.gvl.org.au.yml
+++ b/host_vars/dev.gvl.org.au.yml
@@ -81,7 +81,7 @@ host_galaxy_config_templates:
- src: "{{ galaxy_config_template_src_dir }}/config/dev_job_conf.yml.j2"
dest: "{{ galaxy_config_dir}}/job_conf.yml"
- src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2"
- dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/ga_filters.py"
+ dest: "{{ galaxy_toolbox_filters_dir }}/ga_filters.py"
- src: "{{ galaxy_config_file_src_dir }}/config/web-gravity.yml"
dest: /opt/galaxy/web-gravity.yml
diff --git a/host_vars/galaxy-backup.yml b/host_vars/galaxy-backup.yml
index 17bbe7f3c..303963718 100644
--- a/host_vars/galaxy-backup.yml
+++ b/host_vars/galaxy-backup.yml
@@ -1,40 +1,51 @@
---
# volume stuff
-# attached_volumes: # TODO: Probably the same. check this. Uncomment when this VM has a volume
-# - device: /dev/vdb
-# path: /mnt
-# fstype: ext4
-# partition: 1
+attached_volumes:
+ - device: /dev/vdb
+ path: /mnt
+ fstype: ext4
+ partition: 1
#paths
script_path: /home/ubuntu/galaxy_backup
backup_path: /mnt/galaxy-backups
-# Comment out galaxy db backup variables until galaxy Sydney is production galaxy
-# #swift for backups
-# use_swift: true
-
-# swift_backup_container: 'usegalaxy-au-db'
-# swift_cred_file: "{{ script_path }}/GenomicsVL-openrc.sh" # IMPORTANT: this file needs to be added by a user with credentials
-# venv_location: "{{ script_path }}/venv"
-
-# #slack integration
-# use_slack: true
-# slack_galaxy_log_webhook: "{{ vault_slack_galaxy_log_webhook }}"
-
-# #The name of the database to backup
-# psql_db: 'galaxy'
-
-# #Database connection vars
-# db_user: galaxy
-# db_password: "{{ vault_galaxy_db_user_password }}"
-# db_server: "{{ hostvars['galaxy-db']['internal_ip'] }}"
-# db_port: 5432
-
-# # Retention time variables
-# monthly_backup_day: 1 #Monthly backups will run on this day of the month
-# weekly_backup_day: 6 #Weekly backups will run on this day of the week
-# retention_day: 6 #Keep daily backups for this many days (6 days)
-# retention_week: 21 #Keep weekly backups for this many days (21 days = 3 weeks)
-# retention_month: 92 #Keep monthly backups for this many days (92 days ~ 3 months)
\ No newline at end of file
+#swift for backups
+use_swift: true
+
+swift_backup_container: 'usegalaxy-au-db'
+swift_cred_file: "{{ script_path }}/GenomicsVL-openrc.sh" # IMPORTANT: this file needs to be added by a user with credentials
+venv_location: "{{ script_path }}/venv"
+
+#slack integration
+use_slack: true
+slack_galaxy_log_webhook: "{{ vault_slack_galaxy_log_webhook }}"
+
+#The name of the database to backup
+psql_db: 'galaxy'
+
+#Database connection vars
+db_user: galaxy
+db_password: "{{ vault_galaxy_db_user_password }}"
+db_server: "{{ hostvars['galaxy-db']['internal_ip'] }}"
+db_port: 5432
+
+# Retention time variables
+monthly_backup_day: 1 #Monthly backups will run on this day of the month
+weekly_backup_day: 6 #Weekly backups will run on this day of the week
+retention_day: 6 #Keep daily backups for this many days (6 days)
+retention_week: 21 #Keep weekly backups for this many days (21 days = 3 weeks)
+retention_month: 61 #Keep monthly backups for this many days (61 days ~ 2 months)
+
+extra_keys:
+ - id: internal_hop_key
+ type: private
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
+
+# ssh config, only for ubuntu
+ssh_config_id_file: "/home/{{ ssh_config_user }}/.ssh/internal_hop_key"
+ssh_config_user: ubuntu
+ssh_config_hosts: "{{ groups['galaxy_group'] }}"
diff --git a/host_vars/galaxy-db.usegalaxy.org.au.yml b/host_vars/galaxy-db.usegalaxy.org.au.yml
index 950adac53..9c088ef58 100644
--- a/host_vars/galaxy-db.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-db.usegalaxy.org.au.yml
@@ -17,7 +17,7 @@ postgresql_conf:
# CPUs num: 8
# Connections num: 100
# Data Storage: san
- - max_connections: 200
+ - max_connections: 300
- listen_addresses: "'*'" # Allow remote connections
- data_directory: "'/data/production'"
- shared_buffers: 8GB
@@ -46,3 +46,8 @@ postgresql_pg_hba_conf:
- host all all "{{ hostvars['galaxy']['internal_ip'] }}/32" md5
- host all all "{{ hostvars['galaxy-handlers']['internal_ip'] }}/32" md5
- host all all "{{ hostvars['galaxy-backup']['internal_ip'] }}/32" md5
+
+extra_keys:
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }}"
diff --git a/host_vars/galaxy-handlers.usegalaxy.org.au.yml b/host_vars/galaxy-handlers.usegalaxy.org.au.yml
index d072b8799..9af7a3d60 100644
--- a/host_vars/galaxy-handlers.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-handlers.usegalaxy.org.au.yml
@@ -72,3 +72,14 @@ flower_galaxy_conf: "{{ galaxy_config_file }}"
# #flower_broker_api: "https://flower:{{ rabbitmq_password_flower }}@{{ rabbitmq_url }}/api/"
flower_broker_url: "pyamqp://flower:{{ vault_rabbitmq_password_galaxy_prod }}@{{ hostvars['galaxy-queue']['internal_ip'] }}:5671//galaxy/galaxy_queues?ssl=1"
+
+extra_keys:
+ - id: internal_hop_key
+ type: private
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }}"
+
+# override docker-data location
+docker_daemon_options:
+ data-root: /pvol/docker-data
diff --git a/host_vars/galaxy-job-nfs.usegalaxy.org.au.yml b/host_vars/galaxy-job-nfs.usegalaxy.org.au.yml
index 24ff7bed8..b2b461c62 100644
--- a/host_vars/galaxy-job-nfs.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-job-nfs.usegalaxy.org.au.yml
@@ -13,3 +13,6 @@ extra_keys:
- id: ubuntu_maintenance_key
type: public
from: "{{ hostvars['galaxy']['internal_ip'] }}"
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
diff --git a/host_vars/galaxy-misc-nfs.usegalaxy.org.au.yml b/host_vars/galaxy-misc-nfs.usegalaxy.org.au.yml
index d0e92e83c..9a56226b9 100644
--- a/host_vars/galaxy-misc-nfs.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-misc-nfs.usegalaxy.org.au.yml
@@ -25,3 +25,9 @@ nfs_exports:
- "{{ nfs_app_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
- "{{ nfs_tools_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
- "{{ nfs_custom_indices_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
+
+# internal ssh keys
+extra_keys:
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
diff --git a/host_vars/galaxy-queue.usegalaxy.org.au.yml b/host_vars/galaxy-queue.usegalaxy.org.au.yml
index b79ba8606..d963c2277 100644
--- a/host_vars/galaxy-queue.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-queue.usegalaxy.org.au.yml
@@ -215,4 +215,16 @@ pip_install_packages:
nginx_check_conf: False
redis_requirepass: "{{ vault_redis_requirepass }}"
-redis_bind_interface: 0.0.0.0
\ No newline at end of file
+redis_bind_interface: 0.0.0.0
+
+extra_keys:
+ - id: internal_hop_key
+ type: private
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
+
+# ssh config, only for ubuntu
+ssh_config_id_file: "/home/{{ ssh_config_user }}/.ssh/internal_hop_key"
+ssh_config_user: ubuntu
+ssh_config_hosts: "{{ groups['galaxy_group'] }}"
diff --git a/host_vars/galaxy-user-nfs.usegalaxy.org.au.yml b/host_vars/galaxy-user-nfs.usegalaxy.org.au.yml
index 3f229dc7e..be9f83634 100644
--- a/host_vars/galaxy-user-nfs.usegalaxy.org.au.yml
+++ b/host_vars/galaxy-user-nfs.usegalaxy.org.au.yml
@@ -1,32 +1,44 @@
-nfs_user_data_test_dir: /mnt/volB/user-data-test
+volA_path: /mnt/volA
+volB_path: /mnt/volB
+volC_path: /mnt/volC
+
+nfs_user_data_5_dir: "{{ volA_path }}/user-data-5"
+nfs_user_data_7_dir: "{{ volA_path }}/user-data-7"
+nfs_data08_dir: "{{ volA_path }}/data08"
+
+nfs_user_data_6_dir: "{{ volB_path }}/user-data-6"
+nfs_data09_dir: "{{ volB_path }}/data09"
+nfs_user_data10_dir: "{{ volC_path }}/data10"
attached_volumes:
- device: /dev/vdb
- path: /mnt/volA
- fstype: ext4
partition: 1
+ path: "{{ volA_path }}" # contains user-data-5, user-data-7, data08
+ fstype: ext4
- device: /dev/vdc
partition: 1
- path: /mnt/volB
+ path: "{{ volB_path }}" # contains user-data-6, data09
+ fstype: ext4
+ - device: /dev/vdd
+ partition: 1
+ path: "{{ volC_path }}" # contains data10
fstype: ext4
nfs_dirs:
- - "{{ nfs_user_data_test_dir }}"
-
-# nfs_user_data_dir: /mnt/user-data
-# nfs_user_data_2_dir: /mnt/user-data2
-# nfs_user_data_3_dir: /mnt/user-data3
-# nfs_user_data_4_dir: /mnt/user-data4
-# nfs_user_data_5_dir: /mnt/user-data5
-# nfs_user_data_6_dir: /user-data6
-# nfs_user_data_7_dir: /mnt/user-data7
+ - "{{ nfs_user_data_5_dir }}"
+ - "{{ nfs_user_data_7_dir }}"
+ - "{{ nfs_data08_dir }}"
+ - "{{ nfs_user_data_6_dir }}"
+ - "{{ nfs_data09_dir }}"
+ - "{{ nfs_user_data10_dir }}"
nfs_exports:
- - "{{ nfs_user_data_test_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_2_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_3_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_4_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_5_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_6_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
-# - "{{ nfs_user_data_7_dir }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
+ - "{{ volA_path }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
+ - "{{ volB_path }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
+ - "{{ volC_path }} {{ hostvars['galaxy'].internal_ip.split('.')[:-1] | join('.') }}.0/24(rw,async,no_root_squash,no_subtree_check)"
+
+# internal ssh keys
+extra_keys:
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy']['internal_ip'] }},{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }}"
diff --git a/host_vars/galaxy.usegalaxy.org.au.yml b/host_vars/galaxy.usegalaxy.org.au.yml
index 929ef6d49..b3d63c8fa 100644
--- a/host_vars/galaxy.usegalaxy.org.au.yml
+++ b/host_vars/galaxy.usegalaxy.org.au.yml
@@ -3,8 +3,8 @@
galaxy_config_file: /opt/galaxy/galaxy.yml
# legacy_file_mounts_available: set to true if /mnt/files, /mnt/files2 should be in the object store
-legacy_file_mounts_available: False # assume true unless set to false
-pawsey_file_mounts_available: False # assume true unless set to false
+legacy_file_mounts_available: True # assume true unless set to false
+pawsey_file_mounts_available: True # assume true unless set to false
# variables for attaching mounted volume to application server
attached_volumes: # TODO: check this
@@ -15,10 +15,11 @@ attached_volumes: # TODO: check this
certbot_domains:
- "{{ hostname }}" # galaxy.usegalaxy.org.au
-# - "usegalaxy.org.au"
-# - "www.usegalaxy.org.au"
-# - "*.interactivetoolentrypoint.interactivetool.usegalaxy.org.au"
- - "*.interactivetoolentrypoint.interactivetool.galaxy.usegalaxy.org.au"
+ - "usegalaxy.org.au"
+ - "www.usegalaxy.org.au"
+ - "*.interactivetoolentrypoint.interactivetool.usegalaxy.org.au"
+ - "genome.usegalaxy.org.au"
+ - "proteomics.usegalaxy.org.au"
certbot_dns_provider: cloudflare
certbot_dns_credentials:
api_token: "{{ vault_dns_cloudflare_api_token }}"
@@ -28,31 +29,26 @@ nginx_ssl_servers:
- galaxy
- galaxy-gie-proxy ## we still do this?
+num_gunicorn_processes: 2
+
# gie proxy hostname
-interactive_tools_server_name: "galaxy.usegalaxy.org.au"
+interactive_tools_server_name: "usegalaxy.org.au"
galaxy_repo: https://github.com/galaxyproject/galaxy.git
-galaxy_commit_id: release_23.0
+galaxy_commit_id: release_23.1
# TODO: check list concatenation with versions of ansible > 2.12
shared_mounts: "{{ galaxy_server_and_worker_shared_mounts + galaxy_web_server_mounts }}" # sourced from galaxy_etca.yml
# ansible-galaxy
-# galaxy_dynamic_job_rules_src_dir: files/galaxy/dynamic_job_rules/production
-# galaxy_dynamic_job_rules_dir: "{{ galaxy_root }}/dynamic_job_rules"
-# galaxy_dynamic_job_rules:
-# - total_perspective_vortex/tools.yml
-# - total_perspective_vortex/destinations.yml.j2
-# - total_perspective_vortex/users.yml
-# - total_perspective_vortex/roles.yml
-# - total_perspective_vortex/default_tool.yml.j2
-# - readme.txt
-
-galaxy_dynamic_job_rules_src_dir: files/galaxy/dynamic_job_rules/load-testing
+galaxy_dynamic_job_rules_src_dir: files/galaxy/dynamic_job_rules/production
galaxy_dynamic_job_rules_dir: "{{ galaxy_root }}/dynamic_job_rules"
galaxy_dynamic_job_rules:
- - total_perspective_vortex/testing_tpv_config.yml
- - total_perspective_vortex/testing_tpv_destinations.yml.j2
+ - total_perspective_vortex/tools.yml
+ - total_perspective_vortex/destinations.yml.j2
+ - total_perspective_vortex/users.yml
+ - total_perspective_vortex/roles.yml
+ - total_perspective_vortex/default_tool.yml.j2
- readme.txt
galaxy_systemd_mode: gravity
@@ -64,25 +60,33 @@ galaxy_custom_indices_dir: /mnt/custom-indices
galaxy_tmp_dir: /mnt/tmp
galaxy_tus_upload_store: "{{ galaxy_tmp_dir }}/tus"
-galaxy_infrastructure_url: https://galaxy.usegalaxy.org.au
+galaxy_infrastructure_url: https://usegalaxy.org.au
-galaxy_file_path: /mnt/user-data-test
-nginx_upload_store_base_dir: "{{ galaxy_file_path }}/upload_store"
+upload_store_volume_dir: /mnt/user-data-volA
+nginx_upload_store_base_dir: "{{ upload_store_volume_dir }}/upload_store"
nginx_upload_store_dir: "{{ nginx_upload_store_base_dir }}/uploads"
nginx_upload_job_files_store_dir: "{{ nginx_upload_store_base_dir }}/job_files"
nginx_upload_store_set_cleanup_cron_job: true
+# galaxy_virtualenv_python: python3.11 # deferred until release 23.2 probably
+
host_galaxy_config_files:
- src: "{{ galaxy_config_file_src_dir }}/config/trs_servers_conf.yml"
dest: "{{ galaxy_config_dir }}/trs_servers_conf.yml"
+ - src: "{{ galaxy_config_file_src_dir }}/config/tool_data_table_conf.xml" # TODO: etca will need this too
+ dest: "{{ galaxy_config_dir }}/tool_data_table_conf.xml"
+ - src: "{{ galaxy_config_file_src_dir }}/config/activation-email.html"
+ dest: "{{ galaxy_config_dir }}/mail/activation-email.html"
+ - src: "{{ galaxy_config_file_src_dir }}/config/activation-email.txt"
+ dest: "{{ galaxy_config_dir }}/mail/activation-email.txt"
host_galaxy_config_templates:
- - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_object_store_conf.xml.j2" # TODO: create me
+ - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_object_store_conf.xml.j2"
dest: "{{ galaxy_config_dir }}/object_store_conf.xml"
- - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_job_conf.yml.j2" # TODO: create me
+ - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_job_conf.yml.j2"
dest: "{{ galaxy_config_dir }}/job_conf.yml"
-# - src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2" ## File cannot be created at dest on first run of playbook
-# dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/ga_filters.py"
+ - src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2" ## File cannot be created at dest on first run of playbook
+ dest: "{{ galaxy_toolbox_filters_dir }}/ga_filters.py"
host_galaxy_config_gravity:
@@ -92,18 +96,30 @@ host_galaxy_config_gravity:
app_server: gunicorn
virtualenv: "{{ galaxy_venv_dir }}"
gunicorn:
- # listening options
- bind: "unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock"
- # performance options
- workers: 4
- # Other options that will be passed to gunicorn
- extra_args: '--forwarded-allow-ips="*"'
- preload: true
- environment:
- VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
- DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
- SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
- SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
+ - bind: unix:{{ galaxy_mutable_config_dir }}/gunicorn1.sock
+ workers: 2
+ # Other options that will be passed to gunicorn
+ extra_args: '--forwarded-allow-ips="*"'
+ timeout: 600
+ restart_timeout: 600
+ preload: true
+ environment:
+ VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
+ DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
+ SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
+ SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
+ - bind: unix:{{ galaxy_mutable_config_dir }}/gunicorn2.sock
+ workers: 2
+ # Other options that will be passed to gunicorn
+ extra_args: '--forwarded-allow-ips="*"'
+ timeout: 600
+ restart_timeout: 600
+ preload: true
+ environment:
+ VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
+ DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
+ SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
+ SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
tusd:
enable: true
tusd_path: /usr/local/sbin/tusd
@@ -121,39 +137,39 @@ host_galaxy_config_gravity:
bind: "unix:{{ galaxy_mutable_config_dir }}/reports.sock"
config_file: "{{ galaxy_config_dir }}/reports.yml"
##& handlers and celery are on galaxy-handlers VM with 2-VM galaxy server. Uncomment these entries when using a single VM
- celery:
- concurrency: 2
- loglevel: DEBUG
- handlers:
- handler:
- environment:
- DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
- SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
- SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
- processes: 5
- pools:
- - job-handlers
- - workflow-schedulers
+ # celery:
+ # concurrency: 2
+ # loglevel: DEBUG
+ # handlers:
+ # handler:
+ # environment:
+ # DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
+ # SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
+ # SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
+ # processes: 5
+ # pools:
+ # - job-handlers
+ # - workflow-schedulers
host_galaxy_config: # renamed from __galaxy_config
gravity: "{{ host_galaxy_config_gravity }}"
galaxy:
##& amqp_internal_connection for 2-VM galaxy server. Comment this out when out when using a single VM
- # amqp_internal_connection: "pyamqp://galaxy_queues:{{ vault_rabbitmq_password_galaxy_prod }}@{{ hostvars['galaxy-queue']['internal_ip'] }}:5671//galaxy/galaxy_queues?ssl=1"
+ amqp_internal_connection: "pyamqp://galaxy_queues:{{ vault_rabbitmq_password_galaxy_prod }}@{{ hostvars['galaxy-queue']['internal_ip'] }}:5671//galaxy/galaxy_queues?ssl=1"
admin_users: "{{ machine_users | selectattr('email', 'defined') | selectattr('roles', 'contains', 'galaxy_admin') | map(attribute='email') | join(',') }},{{ bpa_email }}"
- brand: "E T C A"
+ brand: "Australia"
database_connection: "postgresql://galaxy:{{ galaxy_db_user_password }}@{{ hostvars['galaxy-db']['internal_ip'] }}:5432/galaxy"
- id_secret: "{{ vault_aarnet_id_secret }}" # TODO: this need to stay the same wherever production galaxy is runninig, but the name of the vault variable is misleading
- file_path: "{{ galaxy_file_path }}"
+ id_secret: "{{ vault_aarnet_id_secret }}" # TODO: this need to stay the same wherever production galaxy is running, but the name of the vault variable is misleading
object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml"
smtp_server: localhost
- # ga_code: "{{ vault_prod_ga_code }}" ## swich off ga_code while testing. TODO: uncomment this when we go live
+ ga_code: "{{ vault_prod_ga_code }}" ## swich off ga_code while testing. TODO: uncomment this when we go live
interactivetools_enable: true
interactivetools_map: "{{ gie_proxy_sessions_path }}"
- # enable_oidc: true # TODO: Can we switch this on before galaxy-etca is production galaxy or should we wait until moving day?
- # oidc_config_file: "{{ galaxy_config_dir }}/oidc_config.xml"
- # oidc_backends_config_file: "{{ galaxy_config_dir }}/oidc_backends_config.xml"
+ enable_oidc: true
+ oidc_config_file: "{{ galaxy_config_dir }}/oidc_config.xml"
+ oidc_backends_config_file: "{{ galaxy_config_dir }}/oidc_backends_config.xml"
+ tool_data_table_config_path: "{{ galaxy_config_dir }}/tool_data_table_conf.xml,{{ galaxy_mutable_config_dir }}/shed_tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml"
# nginx upload module
nginx_upload_store: "{{ nginx_upload_store_dir }}"
nginx_upload_path: "/_upload"
@@ -170,23 +186,25 @@ host_galaxy_config: # renamed from __galaxy_config
tus_upload_store: "{{ galaxy_tus_upload_store }}"
# Allow cross-subdomain cookie sharing:
- # cookie_domain: usegalaxy.org.au # TODO: switch from null to usegalaxy.org.au when etca is production site
- cookie_domain: null
-
- ##& comment out celery_conf and enable_celery_tasks when using single VM
- # celery_conf:
- # result_backend: "redis://:{{ vault_redis_requirepass }}@{{ hostvars['galaxy-queue']['internal_ip'] }}:6379/0"
- # # result_backend: "{{ redis_connection_string }}"
- # task_routes:
- # galaxy.fetch_data: disabled
- # # galaxy.fetch_data: galaxy.external
- # galaxy.set_job_metadata: galaxy.external
-
- # # Offload long-running tasks to a Celery task queue. Activate this
- # # only if you have setup a Celery worker for Galaxy. For details, see
- # # https://docs.galaxyproject.org/en/master/admin/production.html
- # enable_celery_tasks: true
+ cookie_domain: usegalaxy.org.au
+
+ user_activation_on: true
+ activation_email:
+ #sentry_dsn: "{{ vault_sentry_url_galaxy_production }}" # commented out, waiting for change in 23.1 to reduce severity of startup logs
+
+ celery_conf:
+ result_backend: "redis://:{{ vault_redis_requirepass }}@{{ hostvars['galaxy-queue']['internal_ip'] }}:6379/0"
+ # result_backend: "{{ redis_connection_string }}"
+ task_routes:
+ galaxy.fetch_data: disabled
+ # galaxy.fetch_data: galaxy.external
+ galaxy.set_job_metadata: galaxy.external
+
+ # Offload long-running tasks to a Celery task queue. Activate this
+ # only if you have setup a Celery worker for Galaxy. For details, see
+ # https://docs.galaxyproject.org/en/master/admin/production.html
+ enable_celery_tasks: true
# cvmfs
cvmfs_cache_base: /mnt/var/lib/cvmfs
@@ -213,8 +231,14 @@ add_monthly_stats: true
add_utilisation_info: true
add_queue_info: true
+# host-specific settings for postfix
+postfix_host_domain: "usegalaxy.org.au"
+postfix_hostname: "galaxy"
+smtp_login: "{{ vault_smtp_login_prod }}"
+smtp_password: "{{ vault_smtp_password_prod }}"
+
#Vars for TIaaS
-tiaas_galaxy_db_host: "galaxy-db.usegalaxy.org.au"
+tiaas_galaxy_db_host: "{{ hostvars['galaxy-db']['internal_ip'] }}"
tiaas_galaxy_db_port: "5432"
tiaas_galaxy_db_user: "tiaas"
tiaas_galaxy_db_pass: "{{ galaxy_db_tiaas_password }}"
@@ -222,7 +246,7 @@ tiaas_info:
owner: "Galaxy Australia"
owner_email: help@genome.edu.au
owner_site: "https://site.usegalaxy.org.au"
- domain: galaxy.usegalaxy.org.au # TODO: update when galaxy-etca is production galaxy
+ domain: usegalaxy.org.au
tiaas_other_config: |
EMAIL_HOST="localhost"
EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
@@ -346,6 +370,11 @@ rpc_pulsar_machines:
extra_keys:
- id: ubuntu_maintenance_key
type: private
+ - id: internal_hop_key
+ type: private
+ - id: internal_hop_key
+ type: public
+ from: "{{ hostvars['galaxy-backup']['internal_ip'] }},{{ hostvars['galaxy-handlers']['internal_ip'] }},{{ hostvars['galaxy-queue']['internal_ip'] }}"
# # grt-sender role # TODO: what of GRT??
# grt_sender_dir: /mnt/var/galactic_radio_telescope
@@ -511,19 +540,16 @@ slurm_singularity_volumes_list_restricted:
- $job_directory:rw
- $galaxy_root:ro
- $tool_directory:ro
- - /mnt/user-data-test # TEMPORARY
-# - /mnt/user-data-7:ro
-# - /mnt/user-data-6:ro
-# - /mnt/user-data-5:ro
-# - /mnt/user-data-4:ro
-# - /mnt/user-data:ro
+ - /mnt/user-data-volA:ro
+ - /mnt/user-data-volB:ro
+ - /mnt/user-data-volC:ro
- /mnt/custom-indices:ro
- /cvmfs/data.galaxyproject.org:ro
- /tmp:rw
legacy_singularity_volumes_list: "{{ ['/mnt/files:ro', '/mnt/files2:ro'] if legacy_file_mounts_available|d(True) else [] }}"
-pawsey_singularity_volumes_list: "{{ ['/mnt/user-data-2:ro', '/mnt/user-data-3:ro'] if pawsey_file_mounts_available|d(True) else [] }}"
+pawsey_singularity_volumes_list: "{{ ['/mnt/user-data:ro', '/mnt/user-data-2:ro', '/mnt/user-data-3:ro', '/mnt/user-data-4:ro'] if pawsey_file_mounts_available|d(True) else [] }}"
slurm_singularity_volumes_list: "{{ slurm_singularity_volumes_list_restricted + legacy_singularity_volumes_list + pawsey_singularity_volumes_list }}"
@@ -555,4 +581,59 @@ dt_connection_string: "postgres://reader:{{ galaxy_db_reader_password }}@{{ host
# NFS stuff (for exporting so galaxy-handlers can mount)
nfs_exports:
- - "{{ galaxy_root }} *(rw,async,no_root_squash,no_subtree_check)"
\ No newline at end of file
+ - "{{ galaxy_root }} *(rw,async,no_root_squash,no_subtree_check)"
+
+# Subdomains
+galaxy_subsite_base_domain: "usegalaxy.org.au"
+galaxy_subsite_default_welcome: "https://site.usegalaxy.org.au"
+galaxy_subsite_dir: /mnt/galaxy/subsites
+galaxy_subsites:
+ - name: genome
+ brand: Genome Lab
+ iframe: "https://site.usegalaxy.org.au/landing/genome"
+ wallpaper: false # If wallpaper is true, then files/subsites/{name}.png will be copied to /static/dist/{name}.png, and can be used exactly like that in the CSS.
+ tool_sections: []
+ custom_css: |
+ #masthead .navbar-nav>li.active {
+ background: #2c3067 !important;
+ }
+ #masthead {
+ background: #3a3e87 !important;
+ }
+ #masthead a.navbar-brand::after {
+ content: "Australia - Genome Lab";
+ }
+ #masthead .navbar-text {
+ display: none;
+ }
+ - name: proteomics
+ hidden: true
+ brand: Proteomics lab
+ iframe: "https://site.usegalaxy.org.au/landing/proteomics"
+ wallpaper: false # If wallpaper is true, then files/subsites/{name}.png will be copied to /static/dist/{name}.png, and can be used exactly like that in the CSS.
+ tool_sections: []
+ custom_css: |
+ #masthead .navbar-nav>li.active {
+ background: #402668 !important;
+ }
+ #masthead {
+ background: #542a95 !important;
+ }
+ #masthead a.navbar-brand::after {
+ content: "Australia - Proteomics Lab";
+ }
+ #masthead .navbar-text {
+ display: none;
+ }
+
+webhook_plugins:
+ - subdomain_switcher
+ # These ones aren't in the playbook as they are included in the galaxy repo:
+ - demo
+ - gtn
+ - news
+
+# ssh config, only for ubuntu
+ssh_config_id_file: "/home/{{ ssh_config_user }}/.ssh/internal_hop_key"
+ssh_config_user: ubuntu
+ssh_config_hosts: "{{ groups['galaxy_group'] }}"
diff --git a/host_vars/pawsey-user-nfs.usegalaxy.org.au.yml b/host_vars/pawsey-user-nfs.usegalaxy.org.au.yml
index 2f909a5e1..43284a91f 100644
--- a/host_vars/pawsey-user-nfs.usegalaxy.org.au.yml
+++ b/host_vars/pawsey-user-nfs.usegalaxy.org.au.yml
@@ -20,7 +20,7 @@ galaxy_user_data_3_dir: /user-data-3
galaxy_user_data_4_dir: /user-data-4
nfs_exports:
- - "{{ galaxy_user_data_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
- - "{{ galaxy_user_data_2_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
- - "{{ galaxy_user_data_3_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
- - "{{ galaxy_user_data_4_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
+ - "{{ galaxy_user_data_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.153/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.157/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.152/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
+ - "{{ galaxy_user_data_2_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.153/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.157/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.152/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
+ - "{{ galaxy_user_data_3_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.153/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.157/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.152/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
+ - "{{ galaxy_user_data_4_dir }} 192.168.0.0/24(rw,async,no_root_squash,no_subtree_check) 138.44.80.40/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.80.112/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.153/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.157/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check) 138.44.7.152/32(rw,async,all_squash,anonuid=10010,anongid=10010,no_subtree_check)"
diff --git a/host_vars/pulsar-QLD/pulsar-QLD-job-nfs.genome.edu.au.yml b/host_vars/pulsar-QLD/pulsar-QLD-job-nfs.genome.edu.au.yml
index 99a9b3fff..dabcc6344 100644
--- a/host_vars/pulsar-QLD/pulsar-QLD-job-nfs.genome.edu.au.yml
+++ b/host_vars/pulsar-QLD/pulsar-QLD-job-nfs.genome.edu.au.yml
@@ -9,8 +9,3 @@ galaxy_job_dir: /mnt/tmp
nfs_exports:
#- "{{ pulsar_custom_indices_dir }} *(rw,async,no_root_squash,no_subtree_check)"
- "{{ galaxy_job_dir }} 203.101.224.0/19(rw,async,no_root_squash,no_subtree_check)"
-
-extra_keys:
- - id: ubuntu_maintenance_key
- type: public
- from: "{{ hostvars['pawsey']['ansible_ssh_host'] }}"
diff --git a/host_vars/pulsar-QLD/pulsar-QLD.genome.edu.au.yml b/host_vars/pulsar-QLD/pulsar-QLD.genome.edu.au.yml
index deadd9e7a..43f80ecd6 100644
--- a/host_vars/pulsar-QLD/pulsar-QLD.genome.edu.au.yml
+++ b/host_vars/pulsar-QLD/pulsar-QLD.genome.edu.au.yml
@@ -49,4 +49,5 @@ pulsar_conda_exec: "mamba" # Use mamba as replacement for conda
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
+
diff --git a/host_vars/pulsar-high-mem1/pulsar-high-mem1.yml b/host_vars/pulsar-high-mem1/pulsar-high-mem1.yml
index bf0416971..59b0fdcae 100644
--- a/host_vars/pulsar-high-mem1/pulsar-high-mem1.yml
+++ b/host_vars/pulsar-high-mem1/pulsar-high-mem1.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_hm1_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_hm1"
pulsar_rabbit_vhost: "/pulsar/galaxy_hm1"
@@ -70,7 +70,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-high-mem2/pulsar-high-mem2.yml b/host_vars/pulsar-high-mem2/pulsar-high-mem2.yml
index 74d6245c5..6230bcd7e 100644
--- a/host_vars/pulsar-high-mem2/pulsar-high-mem2.yml
+++ b/host_vars/pulsar-high-mem2/pulsar-high-mem2.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_hm2_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_hm2"
pulsar_rabbit_vhost: "/pulsar/galaxy_hm2"
@@ -69,7 +69,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-mel2/pulsar-mel2.genome.edu.au.yml b/host_vars/pulsar-mel2/pulsar-mel2.genome.edu.au.yml
index e23f4a5fc..5ef6a214e 100644
--- a/host_vars/pulsar-mel2/pulsar-mel2.genome.edu.au.yml
+++ b/host_vars/pulsar-mel2/pulsar-mel2.genome.edu.au.yml
@@ -29,7 +29,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_mel2_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_mel2"
pulsar_rabbit_vhost: "/pulsar/galaxy_mel2"
@@ -38,7 +38,7 @@ pulsar_conda_exec: "mamba" # Use mamba as replacement for conda
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-mel3/pulsar-mel3.genome.edu.au.yml b/host_vars/pulsar-mel3/pulsar-mel3.genome.edu.au.yml
index 6d7f82454..fd9990772 100644
--- a/host_vars/pulsar-mel3/pulsar-mel3.genome.edu.au.yml
+++ b/host_vars/pulsar-mel3/pulsar-mel3.genome.edu.au.yml
@@ -20,7 +20,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_mel3_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_mel3"
pulsar_rabbit_vhost: "/pulsar/galaxy_mel3"
@@ -38,7 +38,7 @@ attached_volumes:
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-nci-training/pulsar-nci-training.usegalaxy.org.au.yml b/host_vars/pulsar-nci-training/pulsar-nci-training.usegalaxy.org.au.yml
index 1a31e8485..ad6b7df43 100644
--- a/host_vars/pulsar-nci-training/pulsar-nci-training.usegalaxy.org.au.yml
+++ b/host_vars/pulsar-nci-training/pulsar-nci-training.usegalaxy.org.au.yml
@@ -20,14 +20,15 @@ add_hosts_workers: yes
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_nci_training_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_nci_training"
pulsar_rabbit_vhost: "/pulsar/galaxy_nci_training"
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
+
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-paw/pulsar-paw.genome.edu.au.yml b/host_vars/pulsar-paw/pulsar-paw.genome.edu.au.yml
index 3e8c30700..99e347bbb 100644
--- a/host_vars/pulsar-paw/pulsar-paw.genome.edu.au.yml
+++ b/host_vars/pulsar-paw/pulsar-paw.genome.edu.au.yml
@@ -27,7 +27,7 @@ attached_volumes:
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/pulsar-qld-blast.yml b/host_vars/pulsar-qld-blast.yml
index 5ab2fcf0a..5d2abb815 100644
--- a/host_vars/pulsar-qld-blast.yml
+++ b/host_vars/pulsar-qld-blast.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_qld_blast_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_qld_blast"
pulsar_rabbit_vhost: "/pulsar/galaxy_qld_blast"
@@ -68,7 +68,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/qld-pulsar-himem-0.yml b/host_vars/qld-pulsar-himem-0.yml
index f68292f8a..f4f83c5c8 100644
--- a/host_vars/qld-pulsar-himem-0.yml
+++ b/host_vars/qld-pulsar-himem-0.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_qld_hm0_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_qld_hm0"
pulsar_rabbit_vhost: "/pulsar/galaxy_qld_hm0"
@@ -74,7 +74,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/qld-pulsar-himem-1.yml b/host_vars/qld-pulsar-himem-1.yml
index 45d689158..7cc2a4eba 100644
--- a/host_vars/qld-pulsar-himem-1.yml
+++ b/host_vars/qld-pulsar-himem-1.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_qld_hm1_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_qld_hm1"
pulsar_rabbit_vhost: "/pulsar/galaxy_qld_hm1"
@@ -74,7 +74,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/qld-pulsar-himem-2.yml b/host_vars/qld-pulsar-himem-2.yml
index 7d98a3e86..8615ecf75 100644
--- a/host_vars/qld-pulsar-himem-2.yml
+++ b/host_vars/qld-pulsar-himem-2.yml
@@ -13,7 +13,7 @@ ssl_email: "help@genome.edu.au"
#host specific pulsar settings
rabbitmq_password_galaxy_au: "{{ vault_rabbitmq_password_galaxy_qld_hm2_prod }}"
-pulsar_queue_url: "aarnet-queue.usegalaxy.org.au"
+pulsar_queue_url: "galaxy-queue.usegalaxy.org.au"
pulsar_rabbit_username: "galaxy_qld_hm2"
pulsar_rabbit_vhost: "/pulsar/galaxy_qld_hm2"
@@ -74,7 +74,7 @@ slurm_munge_key: files/keys/munge.key
extra_keys:
- id: ubuntu_maintenance_key
type: public
- from: "{{ hostvars['aarnet']['ansible_ssh_host'] }}"
+ from: "{{ hostvars['galaxy']['ansible_ssh_host'] }},{{ hostvars['galaxy-handlers']['ansible_ssh_host'] }},{{ hostvars['galaxy-backup']['ansible_ssh_host'] }}"
# docker
docker_daemon_options:
diff --git a/host_vars/staging.gvl.org.au.yml b/host_vars/staging.gvl.org.au.yml
index 7d250ca1c..d08c71783 100644
--- a/host_vars/staging.gvl.org.au.yml
+++ b/host_vars/staging.gvl.org.au.yml
@@ -65,7 +65,7 @@ host_galaxy_config_templates:
- src: "{{ galaxy_config_template_src_dir }}/config/staging_job_conf.yml.j2"
dest: "{{ galaxy_config_dir}}/job_conf.yml"
- src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2"
- dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/ga_filters.py"
+ dest: "{{ galaxy_toolbox_filters_dir }}/ga_filters.py"
host_galaxy_config_files:
- src: "{{ galaxy_config_file_src_dir }}/config/oidc_config.xml"
diff --git a/hosts b/hosts
index 827ae507b..b7f8ce694 100644
--- a/hosts
+++ b/hosts
@@ -172,6 +172,18 @@ pulsar-nci-training-w9 ansible_ssh_host=10.0.2.254 internal_ip=10.0.2.254
pulsar-nci-training-w10 ansible_ssh_host=10.0.1.110 internal_ip=10.0.1.110
pulsar-nci-training-w11 ansible_ssh_host=10.0.2.82 internal_ip=10.0.2.82
+[production_pulsars:children]
+pulsar_mel3_head
+pulsar_mel2_head
+pulsar_paw_head
+pulsar_QLD_head
+pulsar_qld_himems
+pulsar_high_mem2
+pulsar_high_mem1
+pulsar_qld_blast
+pulsar_nci_training_head
+pulsar_azure_0_head
+
[nvme]
qld-nvme ansible_ssh_host=203.101.231.166
diff --git a/jenkins/config_backup/config_backup_playbook.yml b/jenkins/config_backup/config_backup_playbook.yml
index 819779fbb..940d687d4 100644
--- a/jenkins/config_backup/config_backup_playbook.yml
+++ b/jenkins/config_backup/config_backup_playbook.yml
@@ -1,5 +1,5 @@
- hosts:
- - aarnet
+ - galaxy
- staging
- dev
become: true
@@ -26,7 +26,8 @@
dest: "{{ backup_dir }}/{{ ansible_hostname }}/config/"
with_items:
- build_sites.yml
- - galaxy.yml
+ # - galaxy.yml # TODO: galaxy.yml is now at /opt/galaxy/galaxy.yml on both galaxy and galaxy-handlers and these are different files.
+ # ansible saving backups of these in /mnt/galaxy/config when changes are made - these will have to do for now.
- job_conf.yml
- object_store_conf.xml
- nagios_tool_conf.xml
diff --git a/jenkins/update_labels/update_tool_labels.sh b/jenkins/update_labels/update_tool_labels.sh
index 11a32905e..f634860ed 100644
--- a/jenkins/update_labels/update_tool_labels.sh
+++ b/jenkins/update_labels/update_tool_labels.sh
@@ -5,6 +5,6 @@ source jenkins/utils.sh
activate_virtualenv
echo "secret" > .vault_pass.txt # ansible needs .vault_pass.txt to exist
-ansible-playbook -i hosts jenkins/update_labels/update_tool_labels_playbook.yml --extra-vars "ansible_user=jenkins_bot update_labels_hostname=staging_galaxy_server"
+ansible-playbook -i hosts jenkins/update_labels/update_tool_labels_playbook.yml --extra-vars "ansible_user=jenkins_bot update_labels_hostname=staging"
-ansible-playbook -i hosts jenkins/update_labels/update_tool_labels_playbook.yml --extra-vars "ansible_user=jenkins_bot update_labels_hostname=aarnet_galaxy_server"
\ No newline at end of file
+ansible-playbook -i hosts jenkins/update_labels/update_tool_labels_playbook.yml --extra-vars "ansible_user=jenkins_bot update_labels_hostname=galaxy"
\ No newline at end of file
diff --git a/jenkins/update_tool_destinations.sh b/jenkins/update_tool_destinations.sh
index 4b57b146b..89eb9e453 100644
--- a/jenkins/update_tool_destinations.sh
+++ b/jenkins/update_tool_destinations.sh
@@ -31,7 +31,7 @@ echo "helloworld" > .vault_pass.txt # ansible needs .vault_pass.txt to exist
if [ "$PROD_TPV_UPDATED" ]; then
echo -e "\nUpdating tool destinations file on Galaxy production instance\n"
- ansible-playbook -i hosts aarnet_update_configs_playbook.yml --extra-vars "ansible_user=jenkins_bot" --vault-password-file "$VAULT_PASS"
+ ansible-playbook -i hosts galaxy_update_configs_playbook.yml --extra-vars "ansible_user=jenkins_bot" --vault-password-file "$VAULT_PASS"
fi
if [ "$DEV_RELEVANT_FILES_UPDATED" ]; then
diff --git a/one-offs/migrate-tools/templates/tool_migration_rsync_script.sh.j2 b/one-offs/migrate-tools/templates/tool_migration_rsync_script.sh.j2
index a186eb27e..307714499 100644
--- a/one-offs/migrate-tools/templates/tool_migration_rsync_script.sh.j2
+++ b/one-offs/migrate-tools/templates/tool_migration_rsync_script.sh.j2
@@ -42,5 +42,5 @@ rsync -e "ssh -i {{ ssh_key }} -o StrictHostKeyChecking=no" -av \
{% if migrate_custom_indices %}
rsync -e "ssh -i {{ ssh_key }} -o StrictHostKeyChecking=no" -av \
galaxy@{{ source_galaxy_ip }}:{{ source_custom_indices_dir }} \
- {{ dest_custom_indices_dir }}
-{% endif %}
\ No newline at end of file
+ {{ dest_custom_indices_dir | dirname }}
+{% endif %}
diff --git a/roles/common/tasks/main.yml b/roles/common/tasks/main.yml
index b8a0e14af..f19d75d10 100644
--- a/roles/common/tasks/main.yml
+++ b/roles/common/tasks/main.yml
@@ -9,7 +9,6 @@
ansible.builtin.apt_key:
url: https://repos.influxdata.com/influxdata-archive_compat.key
state: present
- when: ansible_distribution_major_version is version('22', '<')
- name: Update the apt repos and base OS
apt:
@@ -38,6 +37,20 @@
vars:
hosts_filename: "/etc/hosts"
+- name: Install python 3.11
+ block:
+ - name: Add ppa
+ apt_repository:
+ repo: ppa:deadsnakes/ppa
+ state: present
+ - name: Install python 3.11
+ apt:
+ name:
+ - python3.11
+ - python3.11-venv
+ state: present
+ when: install_python_311|d(False)
+
- name: Add Galaxy group to relevant machines
become: yes
become_user: root
@@ -77,6 +90,10 @@
loop_control:
loop_var: extra_key
+- name: Add ssh config
+ import_tasks: ssh_config.yml
+ when: ssh_config_hosts is defined
+
- name: Make sure cloud configured hostname control is not present
file:
path: /etc/cloud/cloud.cfg.d/07_hostnamefix.cfg
diff --git a/roles/common/tasks/ssh_config.yml b/roles/common/tasks/ssh_config.yml
new file mode 100644
index 000000000..da7389cf9
--- /dev/null
+++ b/roles/common/tasks/ssh_config.yml
@@ -0,0 +1,12 @@
+- name: Add entries to ssh config
+ blockinfile:
+ marker: "# {mark} ANSIBLE MANAGED BLOCK (common role: add ssh config entries)"
+ dest: "/home/{{ ssh_config_user }}/.ssh/config"
+ create: true
+ block: |
+ {% for item in ssh_config_hosts %}
+ Host {{ item }}
+ HostName {{ item }}
+ User {{ ssh_config_user }}
+ IdentityFile {{ ssh_config_id_file }}
+ {% endfor %}
\ No newline at end of file
diff --git a/roles/install-tpv/tasks/main.yml b/roles/install-tpv/tasks/main.yml
index 5c1b21f78..cea5d1d5f 100644
--- a/roles/install-tpv/tasks/main.yml
+++ b/roles/install-tpv/tasks/main.yml
@@ -3,10 +3,12 @@
pip:
name: "total-perspective-vortex=={{ tpv_version }}"
virtualenv: "{{ galaxy_venv_dir }}"
+ virtualenv_python: "{{ galaxy_virtualenv_python | default(omit) }}"
when: tpv_version is defined
- name: Install Total Perspective Vortex (from git commit)
pip:
name: "git+{{ tpv_repo }}{% if tpv_commit_id|d('') %}@{{ tpv_commit_id }}{% endif %}"
virtualenv: "{{ galaxy_venv_dir }}"
+ virtualenv_python: "{{ galaxy_virtualenv_python | default(omit) }}"
state: forcereinstall
when: tpv_version is not defined and tpv_repo is defined
\ No newline at end of file
diff --git a/secret_group_vars/ubuntu_maintenance_key b/secret_group_vars/ubuntu_maintenance_key
index 1aef0914a..06976344b 100644
--- a/secret_group_vars/ubuntu_maintenance_key
+++ b/secret_group_vars/ubuntu_maintenance_key
@@ -1,182 +1,279 @@
$ANSIBLE_VAULT;1.1;AES256
-34646232633761396232623538313065613037323535313639336538643031393065373234386265
-6236646365623530653133623438383766666538303738330a376638383034613537656637323037
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-66376439646161346161363639656564653039643336396662333465623432336464376437323032
-33333631353039356330383236313536356538356361643532666135333137343265663766666362
-33383830386633383064356637303364326635636263306666303731346532346638303136343937
-33636236636133366162396538363431653864633161336430383734646661633136666133346138
-34373530313630363632653764363830383966613762663762326534633233343035383737336362
-62326433393430643831353633653738656266356235636630333564396264643932636165396663
-39666163646331376665626333333131353362383563333339633632643465316364366634643865
-31363534333864643435316639616435666363393032653131653630376535306534333134643963
-34633434383737383463303438353863343964313365656235376132313531353861376536373231
-64366564663162623735663165656464316136316437373364363935383330646630336562616562
-36336232366135393832313639303132663365366433386538636437306663303263616364316561
-64393039303164376438626435316638613631626436653835346365353331393536303538303038
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-66613566396662353338663763326664323637376266636637656635666534616434323434353933
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diff --git a/templates/galaxy/config/galaxy_job_conf.yml.j2 b/templates/galaxy/config/galaxy_job_conf.yml.j2
index 3ea2ac1ba..6931fea4f 100644
--- a/templates/galaxy/config/galaxy_job_conf.yml.j2
+++ b/templates/galaxy/config/galaxy_job_conf.yml.j2
@@ -23,7 +23,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_mel2:{{ vault_rabbitmq_password_galaxy_mel2_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_mel2?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-paw_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -33,7 +33,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_paw:{{ vault_rabbitmq_password_galaxy_paw_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_paw?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-mel3_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -43,7 +43,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_mel3:{{ vault_rabbitmq_password_galaxy_mel3_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_mel3?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-high-mem1_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -53,7 +53,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_hm1:{{ vault_rabbitmq_password_galaxy_hm1_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_hm1?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-high-mem2_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -63,7 +63,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_hm2:{{ vault_rabbitmq_password_galaxy_hm2_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_hm2?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-qld-high-mem0_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -73,7 +73,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_qld_hm0:{{ vault_rabbitmq_password_galaxy_qld_hm0_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_qld_hm0?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-qld-high-mem1_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -83,7 +83,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_qld_hm1:{{ vault_rabbitmq_password_galaxy_qld_hm1_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_qld_hm1?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-qld-high-mem2_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -93,7 +93,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_qld_hm2:{{ vault_rabbitmq_password_galaxy_qld_hm2_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_qld_hm2?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-nci-training_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -103,7 +103,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_nci_training:{{ vault_rabbitmq_password_galaxy_nci_training_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_nci_training?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-qld-blast_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -113,7 +113,7 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_qld_blast:{{ vault_rabbitmq_password_galaxy_qld_blast_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_qld_blast?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar-QLD_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
@@ -123,12 +123,12 @@ runners:
amqp_publish_retry: true
amqp_publish_retry_max_retries: 60
amqp_url: "pyamqp://galaxy_QLD:{{ vault_rabbitmq_password_galaxy_QLD_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_QLD?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
pulsar_azure_0_runner:
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
amqp_url: "pyamqp://galaxy_azure_0:{{ vault_rabbitmq_password_galaxy_azure_0_prod }}@galaxy-queue.usegalaxy.org.au:5671//pulsar/galaxy_azure_0?ssl=1"
- galaxy_url: "{{ galaxy_infrastructure_url }}"
+ galaxy_url: https://galaxy.usegalaxy.org.au
manager: _default_
amqp_acknowledge: True
amqp_ack_republish_time: 1200
@@ -149,14 +149,18 @@ execution:
function: map_tool_to_destination
rules_module: tpv.rules
tpv_config_files:
- # shared db commented out until rules are updated to accommodate it (rank function, high-mem tag)
- # - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml
- # - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/default_tool.yml"
- # - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/tools.yml"
- # - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/users.yml"
- # - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/roles.yml"
- # - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/destinations.yml"
- - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/testing_tpv_config.yml"
- - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/testing_tpv_destinations.yml"
-limits: {} # TODO - put job conf limits back here once one load testing is finished (saved in trello card)
+ - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml
+ - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/default_tool.yml"
+ - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/tools.yml"
+ - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/users.yml"
+ - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/roles.yml"
+ - "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/destinations.yml"
+{% if job_conf_limits %}
+{% for env in job_conf_limits.environments|d({}) %}
+ {{ env }}:
+ tags: {{ job_conf_limits.environments[env].tags }}
+{% endfor %}
+limits:
+{{ job_conf_limits.limits | to_nice_yaml }}
+{% endif %}
diff --git a/templates/galaxy/config/galaxy_object_store_conf.xml.j2 b/templates/galaxy/config/galaxy_object_store_conf.xml.j2
index e0ec8a7c1..9056a8d76 100644
--- a/templates/galaxy/config/galaxy_object_store_conf.xml.j2
+++ b/templates/galaxy/config/galaxy_object_store_conf.xml.j2
@@ -1,9 +1,46 @@
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+{% if pawsey_file_mounts_available|d(True) %}
+
+
+
+
+
+
+
+
+
+
+
+
+{% endif %}
+{% if legacy_file_mounts_available|d(True) %}
+
+
+
+
+
+
+{% endif %}
diff --git a/templates/galaxy/toolbox/filters/test_ga_filters.py b/templates/galaxy/toolbox/filters/test_ga_filters.py
index 27bd7ba19..9010f6843 100644
--- a/templates/galaxy/toolbox/filters/test_ga_filters.py
+++ b/templates/galaxy/toolbox/filters/test_ga_filters.py
@@ -24,6 +24,10 @@ def restrict_alphafold(context, tool):
'id': 'maxquant_test',
'role': 'maxquant_test',
},
+ {
+ 'id': 'cellranger',
+ 'role': 'cellranger',
+ },
]
def hide_test_tools(context, tool):
@@ -84,7 +88,7 @@ def restrict_alphafold(context, tool):
assert restrict_alphafold(context1, tool2) == True # any tool other than alphafold is visible
-roleA = Role('maxquant_test', False)
+roleA = Role('cellranger', False)
userA = User(lambda: [roleA], 'amy@email.org')
userB = User(lambda: [], 'amy@email.org')
@@ -98,7 +102,7 @@ def restrict_alphafold(context, tool):
contextB = context(transB)
contextC = context(transC)
-toolA = Tool('maxquant_test', ['test'])
+toolA = Tool('cellranger', ['test'])
toolB = Tool('something_else', ['test'])
assert hide_test_tools(contextA, toolA) == True
diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2
index 0658373bc..7e2fd34b3 100644
--- a/templates/nginx/galaxy.j2
+++ b/templates/nginx/galaxy.j2
@@ -1,3 +1,10 @@
+{% if num_gunicorn_processes == 2 %}
+upstream galaxy {
+ server unix://{{ galaxy_mutable_config_dir }}/gunicorn1.sock;
+ server unix://{{ galaxy_mutable_config_dir }}/gunicorn2.sock;
+}
+{% endif %}
+
server {
# Listen on port 443
listen *:443 ssl default_server;
@@ -12,32 +19,9 @@ server {
uwsgi_buffer_size 16k;
uwsgi_busy_buffers_size 24k;
-{% if galaxy_commit_id == "release_22.01" %}
-
- # The most important location block, by default all requests are sent to uWSGI
- location / {
- # This is the backend to send the requests to.
- uwsgi_pass 127.0.0.1:8080;
- uwsgi_param UWSGI_SCHEME $scheme;
- include uwsgi_params;
-
- add_header X-Clacks-Overhead 'GNU James Taylor (@jxtx) Simon Gladman (@slugger70)';
- }
-
- location ~ ^/api/dataset_collections/([^/]+)/download/?$ {
- proxy_buffering off;
- uwsgi_pass 127.0.0.1:8080;
- uwsgi_param UWSGI_SCHEME $scheme;
- include uwsgi_params;
- }
-
-{% endif %}
-
-{% if galaxy_commit_id != "release_22.01" %}
-
# The most important location block, by default all requests are sent to Gunicorn
location / {
- proxy_pass http://unix://{{ galaxy_mutable_config_dir }}/gunicorn.sock;
+ proxy_pass {% if num_gunicorn_processes == 2 %}http://galaxy{% else %}http://unix://{{ galaxy_mutable_config_dir }}/gunicorn.sock{% endif %};
proxy_redirect off;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
@@ -49,15 +33,13 @@ server {
location ~ ^/api/dataset_collections/([^/]+)/download/?$ {
proxy_buffering off;
- proxy_pass http://unix://{{ galaxy_mutable_config_dir }}/gunicorn.sock;
+ proxy_pass {% if num_gunicorn_processes == 2 %}http://galaxy{% else %}http://unix://{{ galaxy_mutable_config_dir }}/gunicorn.sock{% endif %};
proxy_set_header Host $http_host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $scheme;
proxy_set_header Upgrade $http_upgrade;
}
-{% endif %}
-
# Static files can be more efficiently served by Nginx. Why send the
# request to uWSGI which should be spending its time doing more useful
# things like serving Galaxy!