Does Galaxy Record Tool Versions?

Question: Does Galaxy Record Tool Versions?

7.8 years ago by

Yury Bukhman • 140 wrote:

Hi, in order to reproduce an analysis, it's good to know not only what tools were used, but also their versions. Is there a way to figure that out from a Galaxy history? I would like to be able to answer questions like "what version of bowtie have I run in an analysis performed 6 months ago?" Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu

alignment bowtie • 852 views

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modified 7.8 years ago by Kanwei Li • 270 • written 7.8 years ago by Yury Bukhman • 140

7.8 years ago by

Kanwei Li • 270

Kanwei Li • 270 wrote:

Hi Yury, Yes, the "jobs" table keeps track of the tool version run. I am implementing a new "view details" feature (already on trunk) and I will add the tool version to the information displayed. Thanks, Kanwei

ADD COMMENT • link written 7.8 years ago by Kanwei Li • 270

Hmm, actually the version is the version of the tool wrapper. Unless the wrapper version reflects the actual tool version, we're not keeping track of the tool version as we're simply running the command. Perhaps history annotation is the solution here. -Kanwei

ADD REPLY • link written 7.8 years ago by Kanwei Li • 270

Using history annotation will only work well if it could be automatically populated with tool versions. Leaving it up to the user to insert them manually won't work because people would forget to do this, especially if they are working under time pressures. In my ideal world, the tool version would be recorded automatically as an attribute for each step in the history. I don't know if there's an easy way to implement that, though. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu

ADD REPLY • link written 7.8 years ago by Yury Bukhman • 140

Hash: SHA1 Hi Kanwei, I'm very much interested in this feature, i.e "to keep track of tool versions that ran automatically". What do you mean by "history annotation" ? Is it some custom editable field by the user or are you planning to set this automatically when the Job runs ? I would like it to be the latter, I cannot see either of them clearly on your commits though (need to know galaxy internals better I guess) :-S Cheers! Roman Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1C4TUACgkQEqU4jwj4DLW+owCfYslGaw4V491bymS0R9Zu6qPd s/4AnROwKBqgigTfTK21MbTguXwTZq7k =kgBd

ADD REPLY • link written 7.8 years ago by Roman Valls • 130

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