Mercurial > repos > mvdbeek > igv_take_screenshots

diff igv_make_screenshots.xml @ 1:8b80357d8ab1 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, 26 Jun 2017 10:17:15 -0400
parents d828cf6bff42
children 18e36ab5e669
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jun 26 10:00:06 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jun 26 10:17:15 2017 -0400
@@ -10,10 +10,12 @@
                 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
             #end if
         #end for
+        ln -fs $igv_session igv_session.xml &&
         cat '$load_session' > load_session.txt &&
         echo snapshotDirectory "\$PWD" >> load_session.txt &&
-        cat load_session.txt '$script_file' '$exit_session' > '$igv_session_out' &&
-        python $__tool_directory__/xvfb_igv.py '$igv_session_out' $width,$height &&
+        cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
+        python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
+        cp '$igv_session' '$igv_session_out' &&
         zip '$screenshots_out' *.png
     ]]></command>
     <configfiles>
@@ -59,7 +61,7 @@
 </Session>
         ]]></configfile>
         <configfile name="load_session">
-load $igv_session
+load igv_session.xml
         </configfile>
         <configfile name="exit_session">
 exit