# HG changeset patch
# User mvdbeek
# Date 1468062760 14400
# Node ID ed7cf3f35799e2448976aa8e056fe2cdf0b1b9de
# Parent  77dca93454b7a392ef1bc1e32384d577d33904ea
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit d8d8e8e063698813c9eb646e0df7d93118fd0520

diff -r 77dca93454b7 -r ed7cf3f35799 dockerfiles/r-bioperl-python/Dockerfile
--- a/dockerfiles/r-bioperl-python/Dockerfile	Sat Jul 09 05:07:15 2016 -0400
+++ b/dockerfiles/r-bioperl-python/Dockerfile	Sat Jul 09 07:12:40 2016 -0400
@@ -7,8 +7,7 @@
 
 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
 
-USER galaxy
-RUN bash -c ". activate default && \
-    conda install -y ncurses biopython perl-bioperl bedtools bioconductor-deseq2 bioconductor-edger numpy scipy"
 USER root
-RUN chown -R galaxy:users /home/galaxy && chmod g=rwx /home/galaxy
+RUN su - galaxy -c 'bash -c ". /home/galaxy/conda/bin/activate default && \
+    conda install -y ncurses biopython perl-bioperl bedtools bioconductor-deseq2 bioconductor-edger numpy scipy"' && \
+    chown -R galaxy:users /home/galaxy && chmod g=rwx /home/galaxy
diff -r 77dca93454b7 -r ed7cf3f35799 scriptrunner.py
--- a/scriptrunner.py	Sat Jul 09 05:07:15 2016 -0400
+++ b/scriptrunner.py	Sat Jul 09 07:12:40 2016 -0400
@@ -337,8 +337,6 @@
                 sto = open(self.tlog,'w')
                 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
                 sto.flush()
-                print("commandline is %s" % (self.cl))
-                print("environment is %s" % (os.environ))
                 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
             else:
                 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
@@ -382,7 +380,7 @@
     """
     cmd1 = ["/usr/sbin/usermod", "-d", "/var/home/galaxy", "galaxy"]
     cmd2 = ["/usr/sbin/usermod", "-u", new_uid, "galaxy"]
-    cmd3 = ["/usr/sbin/groupmod", "-g", "1450", new_gid]
+    cmd3 = ["/usr/sbin/groupmod", "-g", new_gid, "galaxy"]
     cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"]
     [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]]