Hey Peter, Right now the output is stored to a file, so we can do any processing in python, or just keep the multi-line as it is. I agree version_string should be version_cmd... didn't change it since working on it at the Conference ;) On Thu, Jul 7, 2011 at 6:27 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
This new feature looks very exciting for tracking reproducibility - now in theory both the tool wrapper version (explicit in the XML) and any underlying tool version will both be recorded:
https://bitbucket.org/galaxy/galaxy-central/changeset/84b20f29dfdf
I have updated the NCBI BLAST+ wrappers to use the new feature, please merge/transplant this branch/commit:
https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_07_07 https://bitbucket.org/peterjc/galaxy-central/changeset/11f425f4e137
I hope the new tool version string will get its own field in the database soon (and be viewable via the web interface). Note that string may well be multi-line, e.g.
$ blastp -version blastp: 2.2.25+ Package: blast 2.2.25, build Apr 6 2011 13:59:28
Unless that is you go for more fragile solutions like these to ensure a single line:
$ samtools 2>&1 | grep -i "^Version" Version: 0.1.16 (r963:234)
$ bwa 2>&1 | grep -i "^Version" Version: 0.5.9-r16
Thanks,
Peter
P.S. I would say the name <version_string> is a bit confusing, I'd have picked <version_cmd> or <version_command> instead.