Mercurial > repos > simon-gladman > velvetoptimiser
comparison velvetoptimiser.xml @ 4:4a53b89fa703 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 36de8aa1927d0204107371ffad76bdfe921be44a"
| author | iuc |
|---|---|
| date | Wed, 13 Jan 2021 15:31:18 +0000 |
| parents | 37d88f41c810 |
| children | 82398ba86ba7 |
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| 3:37d88f41c810 | 4:4a53b89fa703 |
|---|---|
| 1 <tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6"> | 1 <tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy1"> |
| 2 <description>Automatically optimize Velvet assemblies</description> | 2 <description>Automatically optimize Velvet assemblies</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.2.10">velvet</requirement> | 4 <requirement type="package" version="1.2.10">velvet</requirement> |
| 5 <requirement type="package" version="2.2.6">perl-velvetoptimiser</requirement> | 5 <requirement type="package" version="2.2.6">perl-velvetoptimiser</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <version_command>VelvetOptimiser.pl --version</version_command> | 7 <version_command>VelvetOptimiser.pl --version</version_command> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 export OMP_NUM_THREADS=2 && | 9 ## In Galaxy we do not us mutlithreading for the velvet |
| 10 export OMP_THREAD_LIMIT=2 && | 10 ## subprocesses, but only run multiple velvet calls in |
| 11 ## parallel. Otherwise CPUs are overutilized. | |
| 12 export OMP_NUM_THREADS=1 && | |
| 13 ## export OMP_THREAD_LIMIT=1 && | |
| 11 VelvetOptimiser.pl | 14 VelvetOptimiser.pl |
| 12 -t "\${GALAXY_SLOTS:-1}" | 15 -t "\${GALAXY_SLOTS:-1}" |
| 13 -s $start_kmer | 16 -s $start_kmer |
| 14 -e $end_kmer | 17 -e $end_kmer |
| 15 -d out | 18 -d out |