Mercurial > repos > petr-novak > repeatexplorer2_testing
changeset 14:ba67036e6b3c draft
Uploaded
| author | petr-novak |
|---|---|
| date | Mon, 16 Oct 2023 09:22:12 +0000 |
| parents | 1eefa5b3e8b9 |
| children | 15185fe48bf8 |
| files | repex_full_clustering.xml |
| diffstat | 1 files changed, 8 insertions(+), 24 deletions(-) [+] |
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--- a/repex_full_clustering.xml Thu Jul 27 08:53:14 2023 +0000 +++ b/repex_full_clustering.xml Mon Oct 16 09:22:12 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.1" > +<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" > <stdio> <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> @@ -12,6 +12,8 @@ </requirements> <command> export PYTHONHASHSEED=0; + export TAREAN_CPU=\$GALAXY_SLOTS; + export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB; seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon #if $advanced_options.advanced: @@ -129,29 +131,11 @@ <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/> </when> </conditional> - - <conditional name="queue_definition"> - <param name="queue_select" type="select" label="Select queue"> - <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> - <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> - <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> - </param> - <when value="basic_fast_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" /> - </when> - - <when value="long_slow_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> - </when> - <when value="extra_long_slow_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> - </when> - </conditional> - - + <param name="queue_select" type="select" label="Select queue"> + <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> + <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> + <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> + </param> </inputs> <outputs>