Mercurial > repos > iuc > trinity
changeset 29:d5e8807a407d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
| author | iuc |
|---|---|
| date | Thu, 04 Nov 2021 21:36:57 +0000 |
| parents | 48636f857c4b |
| children | 3772d9a10f27 |
| files | trinity.xml |
| diffstat | 1 files changed, 14 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/trinity.xml Fri Sep 10 22:46:16 2021 +0000 +++ b/trinity.xml Thu Nov 04 21:36:57 2021 +0000 @@ -1,10 +1,13 @@ -<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1"> +<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy2"> <description>de novo assembly of RNA-Seq data</description> <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="8.32">coreutils</requirement> + <requirement type="package" version="3.2.3">rsync</requirement> + </expand> <command detect_errors="aggressive"><![CDATA[ if [ -z "\$GALAXY_MEMORY_MB" ] ; then GALAXY_MEMORY_GB=1 ; @@ -14,7 +17,9 @@ if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then workdir=`pwd` ; - cd "\$TRINITY_SCRATCH_DIR" ; + scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); + emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); + cd "\$scratchfolder" ; fi ; #if $additional_params.guided.is_guided == "yes": @@ -146,9 +151,15 @@ && + ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync + ## for ensuring better performances. + ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then mkdir -p "\$workdir/trinity_out_dir"; cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; + cd "\$TRINITY_SCRATCH_DIR"; + rsync -a --delete "\$emptyfolder/" "\$scratchfolder/"; + rmdir "\$emptyfolder" "\$scratchfolder/"; cd "\$workdir"; fi ;