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comparison trinity.xml @ 29:d5e8807a407d draft

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"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
comparison
equal deleted inserted replaced
28:48636f857c4b 29:d5e8807a407d
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy2">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <expand macro="bio_tools"/> 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements">
8 <requirement type="package" version="8.32">coreutils</requirement>
9 <requirement type="package" version="3.2.3">rsync</requirement>
10 </expand>
8 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
9 if [ -z "\$GALAXY_MEMORY_MB" ] ; then 12 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
10 GALAXY_MEMORY_GB=1 ; 13 GALAXY_MEMORY_GB=1 ;
11 else 14 else
12 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ; 15 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
13 fi ; 16 fi ;
14 17
15 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then 18 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
16 workdir=`pwd` ; 19 workdir=`pwd` ;
17 cd "\$TRINITY_SCRATCH_DIR" ; 20 scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
21 emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
22 cd "\$scratchfolder" ;
18 fi ; 23 fi ;
19 24
20 #if $additional_params.guided.is_guided == "yes": 25 #if $additional_params.guided.is_guided == "yes":
21 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && 26 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
22 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && 27 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
144 149
145 ## > $trinity_log 2>&1 150 ## > $trinity_log 2>&1
146 151
147 && 152 &&
148 153
154 ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync
155 ## for ensuring better performances.
156 ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html
149 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then 157 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
150 mkdir -p "\$workdir/trinity_out_dir"; 158 mkdir -p "\$workdir/trinity_out_dir";
151 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; 159 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
160 cd "\$TRINITY_SCRATCH_DIR";
161 rsync -a --delete "\$emptyfolder/" "\$scratchfolder/";
162 rmdir "\$emptyfolder" "\$scratchfolder/";
152 cd "\$workdir"; 163 cd "\$workdir";
153 fi ; 164 fi ;
154 165
155 ]]></command> 166 ]]></command>
156 <inputs> 167 <inputs>