Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 4:a4877f60773a draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
author mvdbeek
date Mon, 03 Jul 2017 08:51:28 -0400
parents f44435b6ad19
children 20cc4cc902f4
files igv_make_screenshots.xml
diffstat 1 files changed, 1 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jul 03 08:46:22 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 08:51:28 2017 -0400
@@ -5,8 +5,7 @@
     <command detect_errors="exit_code"><![CDATA[
         #for $inputsection in $inputfiles
             #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
-            #set $abspath=os.path.abspath($path)
-            sed -i.bak -e 's|$path|$abspath|g' '$igv_session' &&
+            sed -i.bak -e 's|$path|$PWD/$path|g' '$igv_session' &&
             ln -fs $inputsection.input $path &&
             #if $inputsection.input.is_of_type('bam')
                 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&