commit/galaxy-central: fubar: moved pysam import needed for picard validate from picard_wrapper - not available on test yet :( - galaxy-commits

7 May 2011

1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/f7ad12a7354b/
changeset:   r5512:f7ad12a7354b
user:        fubar
date:        2011-05-07 20:22:06
summary:     moved pysam import needed for picard validate from picard_wrapper - not available on test yet :(
affected #:  1 file (14 bytes)

--- a/tools/picard/picard_wrapper.py	Sat May 07 13:58:35 2011 -0400
+++ b/tools/picard/picard_wrapper.py	Sat May 07 14:22:06 2011 -0400
@@ -8,7 +8,7 @@
 see http://www.gnu.org/copyleft/lesser.html
 """
-import optparse, os, sys, subprocess, tempfile, shutil, time, pysam
+import optparse, os, sys, subprocess, tempfile, shutil, time
galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
@@ -682,6 +682,7 @@
         pic.runPic(opts.jar,cl)
elif pic.picname == "ValidateSamFile":
+        import pysam
         doTranspose = False
         sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
         stf = open(pic.log_filename,'w')
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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