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Merge branch 'master' into update_prod_tpv
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cat-bro authored Nov 13, 2023
2 parents 369cabf + 2240ed4 commit 737160d
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Showing 63 changed files with 1,762 additions and 1,096 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/check_tpv_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion files/galaxy/config/local_tool_conf_dev.xml
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,6 @@
</section>
<section id="interactivetools" name="Interactive Tools">
<tool file="/mnt/galaxy/local_tools/glt_tom/tools/interactivetool_lfqanalyst/interactivetool_lfqanalyst.xml" />
<tool file="/mnt/galaxy/local_tools/zeppelin/interactivetool_zeppelin.xml" />
<tool file="/mnt/galaxy/local_tools/ena_upload/interactivetool_ena_upload.xml" />
</section>
</toolbox>
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -129,38 +129,3 @@ tools:
- if: 0.05 <= input_size
cores: 8
mem: 30.7

users:
[email protected]:
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
[email protected]:
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
accept:
- pulsar
- offline
require:
- pulsar-paw
[email protected]:
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
accept:
- pulsar
- offline
require:
- pulsar-QLD
[email protected]:
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
require:
- pulsar
- pulsar-nci-test
Original file line number Diff line number Diff line change
@@ -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)
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -110,15 +110,16 @@ 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
persistence_directory: /mnt/tmp/files/persisted_data
scheduling:
accept:
- pulsar-QLD
- pulsar-blast
require:
- pulsar

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Original file line number Diff line number Diff line change
@@ -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
[email protected]:
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
[email protected]:
inherits: test_user
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
accept:
- pulsar
- offline
require:
- pulsar-paw
[email protected]:
inherits: test_user
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
accept:
- pulsar
- offline
require:
- pulsar-QLD
[email protected]:
inherits: test_user
rules:
- if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
scheduling:
require:
- pulsar
- pulsar-nci-test
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,6 @@ destinations:
require:
- pulsar-paw
- pulsar
- offline # on loan to etca
pulsar-mel3:
inherits: _pulsar_destination
runner: pulsar-mel3_runner
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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