Mercurial > repos > mvdbeek > docker_scriptrunner
changeset 10:ed7cf3f35799 draft
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit d8d8e8e063698813c9eb646e0df7d93118fd0520
| author | mvdbeek |
|---|---|
| date | Sat, 09 Jul 2016 07:12:40 -0400 |
| parents | 77dca93454b7 |
| children | 8571d1c719ee |
| files | dockerfiles/r-bioperl-python/Dockerfile scriptrunner.py |
| diffstat | 2 files changed, 4 insertions(+), 7 deletions(-) [+] |
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--- 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
--- 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]]