Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 17:bfd72b90dbb2 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1ddb87e95baeea2a4ee9b95930da6e0927fb7ff7-dirty
author mvdbeek
date Fri, 28 Jul 2017 13:19:00 -0400
parents 9663fa8b9c0b
children 46e42201f2e6
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16:817db6799e96 17:bfd72b90dbb2
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
4 <requirement type="package" version="2.3.93">igv</requirement> 4 <requirement type="package" version="2.3.93">igv</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 ln -s '$genome_source.genome' genome.fa && 7 #if $genome_source.genome_source == 'history':
8 ln -s '$genome_source.genome' genome.fa &&
9 #else:
10 ln -s '$genome_source.genome.fields.path' genome.fa &&
11 #end if
8 samtools faidx genome.fa && 12 samtools faidx genome.fa &&
9 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' && 13 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
10 #for $i, $inputsection in enumerate($inputfiles): 14 #for $i, $inputsection in enumerate($inputfiles):
11 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension) 15 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
12 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' && 16 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&