[galaxy-user] does Galaxy record tool versions?
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: ybukh...@glbrc.wisc.edu ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] does Galaxy record tool versions?
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 On Thu, Jan 27, 2011 at 5:57 PM, Yury Bukhman 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: ybukh...@glbrc.wisc.edu > > ___ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] does Galaxy record tool versions?
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 On Thu, Jan 27, 2011 at 6:17 PM, Kanwei Li 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 > > On Thu, Jan 27, 2011 at 5:57 PM, Yury Bukhman 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: ybukh...@glbrc.wisc.edu >> >> ___ >> galaxy-user mailing list >> galaxy-user@lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user >> > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] does Galaxy record tool versions?
-BEGIN PGP SIGNED MESSAGE- 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 On 2011-01-28 00:20, Kanwei Li wrote: > 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 > > On Thu, Jan 27, 2011 at 6:17 PM, Kanwei Li 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 >> >> On Thu, Jan 27, 2011 at 5:57 PM, Yury Bukhman >> 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: ybukh...@glbrc.wisc.edu >>> >>> ___ >>> galaxy-user mailing list >>> galaxy-user@lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> > > ___ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1C4TUACgkQEqU4jwj4DLW+owCfYslGaw4V491bymS0R9Zu6qPd s/4AnROwKBqgigTfTK21MbTguXwTZq7k =kgBd -END PGP SIGNATURE- ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] does Galaxy record tool versions?
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 On 01/27/11, Kanwei Li wrote: > 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 > > On Thu, Jan 27, 2011 at 6:17 PM, Kanwei Li 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 > > > > On Thu, Jan 27, 2011 at 5:57 PM, Yury Bukhman > > 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: ybukh...@glbrc.wisc.edu > >> > >> ___ > >> galaxy-user mailing list > >> galaxy-user@lists.bx.psu.edu > >> http://lists.bx.psu.edu/listinfo/galaxy-user > >> > > -- 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: ybukh...@glbrc.wisc.edu ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
