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Update packages #745

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Update packages #745

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956d884
update minimap wrapper
SilasK Dec 17, 2024
0862a23
limit mamba =1 #742
SilasK Dec 17, 2024
ac4c5ce
use mamba as it is default with snakemak =17
SilasK Dec 17, 2024
7d9616c
up to date fastx - not teste with genecatalog
SilasK Dec 17, 2024
2331806
up to data sambamba
SilasK Dec 17, 2024
7c5ecf4
Revert "update minimap wrapper"
SilasK Dec 17, 2024
889f39d
WIP update packages
SilasK Jan 3, 2025
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2 changes: 1 addition & 1 deletion atlas/atlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,7 @@ def run_download(db_dir, jobs, snakemake_args):
cmd = (
"snakemake --snakefile {snakefile} download "
"--jobs {jobs} --rerun-incomplete "
"--conda-frontend mamba --scheduler greedy "
"--scheduler greedy "
"--nolock --use-conda --conda-prefix {conda_prefix} "
" --show-failed-logs "
"--config database_dir='{db_dir}' {add_args} "
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2 changes: 1 addition & 1 deletion atlasenv.yml
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Expand Up @@ -4,7 +4,7 @@ channels:
- defaults
dependencies:
- python >=3.8, < 3.12
- mamba
- mamba=1 # https://github.com/metagenome-atlas/atlas/issues/742
- bbmap >= 39.01, <40
- snakemake-minimal >= 7.18.1, <7.26
- pygments
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9 changes: 9 additions & 0 deletions test/test_docker.sh
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@@ -0,0 +1,9 @@
#! /bin/bash

pip install -e .

atlas --help

cd test

./test_local.sh #--conda-frontend conda
2 changes: 1 addition & 1 deletion workflow/envs/fasta.yaml
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Expand Up @@ -3,7 +3,7 @@ channels:
- bioconda
- defaults
dependencies:
- pyfastx=0.9
- pyfastx=2.1
- pandas=1.2
- pyarrow
- biopython
2 changes: 1 addition & 1 deletion workflow/envs/required_packages.yaml
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Expand Up @@ -9,4 +9,4 @@ dependencies:
- bzip2 >=1.0
- pandas >=1.2, <2
- samtools >=1.13, <2
- sambamba <1
- sambamba
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