# HG changeset patch
# User mvdbeek
# Date 1499098206 14400
# Node ID 64eb1ffd78728bc07788d51e5ca0dc22b091f424
# Parent  afb3f4c224d40cbc0e09ce2d46c59d075550b60d
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty

diff -r afb3f4c224d4 -r 64eb1ffd7872 igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Mon Jul 03 11:42:19 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 12:10:06 2017 -0400
@@ -17,7 +17,7 @@
         cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
         ## gives the cluster a bit of time to actually create the symlinks ... ughs
         sleep 10s &&
-        python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
+        python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
         cp '$igv_session' '$igv_session_out' &&
         zip screenshots.zip *.png &&
         cp screenshots.zip '$screenshots_out'
@@ -67,11 +67,13 @@
         ]]></configfile>
         <configfile name="load_session">
 load igv_session.xml
-preference SAM.SHOW_SOFT_CLIPPED str($show_softclippped)
         </configfile>
         <configfile name="exit_session">
 exit
         </configfile>
+        <configfile name="igv_preferences">
+SAM.SHOW_SOFT_CLIPPED=str($show_softclippped)
+        </configfile>
     </configfiles>
     <inputs>
         <repeat name="inputfiles" min="1" title="Add tracks">
diff -r afb3f4c224d4 -r 64eb1ffd7872 xvfb_igv.py
--- a/xvfb_igv.py	Mon Jul 03 11:42:19 2017 -0400
+++ b/xvfb_igv.py	Mon Jul 03 12:10:06 2017 -0400
@@ -5,13 +5,13 @@
 import xvfbwrapper
 
 
-def take_screenshots(igv_script, screensize):
+def take_screenshots(igv_script, preferences_file, screensize):
     width, height = screensize.split(',')
     with xvfbwrapper.Xvfb(width=width, height=height) as xvfb:
-        exit_code = subprocess.call(['igv', '--batch', igv_script], env=os.environ.copy())
+        exit_code = subprocess.call(['igv', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy())
     sys.exit(exit_code)
 
 
 if __name__ == '__main__':
-    take_screenshots(sys.argv[1], sys.argv[2])
+    take_screenshots(sys.argv[1], sys.argv[2], sys.argv[3])