Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 29:dd61761307ca draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
author mvdbeek
date Fri, 15 Jun 2018 13:33:51 -0400
parents d6541171175c
children 9d6b4d2ca187
comparison
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28:d6541171175c 29:dd61761307ca
26 samtools faidx genome.fa && 26 samtools faidx genome.fa &&
27 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' && 27 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
28 #for $i, $inputsection in enumerate($inputfiles): 28 #for $i, $inputsection in enumerate($inputfiles):
29 @PATH@ 29 @PATH@
30 ln -fs '$inputsection.input' '$path' && 30 ln -fs '$inputsection.input' '$path' &&
31 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
31 #if $inputsection.input.is_of_type('bam') 32 #if $inputsection.input.is_of_type('bam')
32 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 33 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
33 #end if 34 #end if
34 #end for 35 #end for
35 ln -fs $igv_session igv_session.xml && 36 ln -fs $igv_session igv_session.xml &&