Mercurial > repos > iuc > shovill
changeset 5:8d1af5db538d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
| author | iuc |
|---|---|
| date | Sun, 28 Jun 2020 04:16:16 -0400 |
| parents | d9f6a00b6db7 |
| children | 83ead2be47b2 |
| files | shovill.xml |
| diffstat | 1 files changed, 8 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/shovill.xml Sun Aug 25 05:14:31 2019 -0400 +++ b/shovill.xml Sun Jun 28 04:16:16 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0"> +<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1"> <description>Faster SPAdes assembly of Illumina reads</description> <macros> <token name="@TOOL_VERSION@">1.0.4</token> @@ -19,6 +19,13 @@ ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && #end if + + ## Sets the memory used by Shovill according to the following conditions + ## (1) If SHOVILL_RAM is already set, use this value + ## (2) Otherwise, set based on GALAXY_MEMORY_MB + ## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset + GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) && + SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} && shovill --outdir 'out'