Hello Bjoern, I believe this issue was corrected in changeset 10412:29ab5a6d75a7, which was committed to the stable branch and is running on both tool sheds. At least I am unable to reproduce the behavior you describe using 3 similar repositories in my local tool shed. Please let me know if you still encounter this issue.
Thanks, Greg Von Kuster On Aug 13, 2013, at 12:49 PM, Bjoern Gruening <bjoern.gruen...@gmail.com> wrote: > Hi Dave, > > for us I think everything is fixed. But we had a bad bug in the 'single > revision' implementation of the new 'Tool dependency definition' type. > > We had something like that: > > A (tool dependency definition) <- B (tool) <- C (workflow) > > We changed A (that was numpy) and thought it would be ok to install the > workflow afterwards. Because, if A has only one revision associated than > it should be working. But B had a reference to the old revision of A (in > the XML file) which causes an error. Or the TS wanted to install two > different versions of A. Our fix was to upload B again and than C, to > renew the revision tags. That was more a hack than a solution :) > > I do not know if that still occurs with the latest version of galaxy, we > tested it with the old stable version. > > Thanks, > Bjoern > > > >> Peter, Björn, >> >> The August Galaxy release is out, and the template_command is now in the >> stable repository and branch. Regarding matplotlib and numpy, I >> currently only see matplotlib depending on the 74c21f9bdc39 revision of >> numpy. Is this still an issue, or has it been resolved? >> >> --Dave B. >> >> On 8/12/13 11:36:00.000, Bjoern Gruening wrote: >>> On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: >>>> On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening >>>> <bjoern.gruen...@gmail.com> wrote: >>>>> On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: >>>>>> Maybe I should retitle this thread... >>>>>> >>>>>> On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock <p.j.a.c...@googlemail.com> >>>>>> wrote: >>>>>>> >>>>>>> Thank you - installing the NumPy package now works for me, >>>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 >>>>>>> >>>>>>> I'm moving on to something odd with matplotlib instead... >>>>>>> >>>>>>> Peter >>>>>> >>>>>> There are currently two revisions to the main Tool Shed >>>>>> package for numpy, >>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 >>>>>> >>>>>> Rev 0: c75482be1d3a - needs not-yet-released features >>>>>> Rev 1: 74c21f9bdc39 - simplified >>>>>> >>>>>> I'm trying to install a package dependent on this via >>>>>> matplotlib - but installing the matplotlib package fails: >>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 >>>>>> >>>>>> This is something odd, why does it think it needs to install >>>>>> the rev 0 c75482be1d3a version of package_numpy_1_7? >>>>>> See screenshot, except here: >>>>>> >>>>>> Repository dependencies - installation of these additional >>>>>> repositories is required >>>>>> Name Revision Owner Installation status >>>>>> package_freetype_2_4 8761091302c4 iuc Installed >>>>>> package_numpy_1_7 74c21f9bdc39 iuc Installed >>>>>> package_numpy_1_7 c75482be1d3a iuc Uninstalled >>>>>> >>>>>> Yes, the matplotlib tool_dependencies.xml does list the >>>>>> original revision: >>>>>> >>>>>> <package name="numpy" version="1.7.1"> >>>>>> <repository changeset_revision="c75482be1d3a" >>>>>> name="package_numpy_1_7" owner="iuc" >>>>>> prior_installation_required="True" >>>>>> toolshed="http://toolshed.g2.bx.psu.edu"; /> >>>>>> </package> >>>>>> <package name="freetype" version="2.4.11"> >>>>>> <repository changeset_revision="8761091302c4" >>>>>> name="package_freetype_2_4" owner="iuc" >>>>>> prior_installation_required="True" >>>>>> toolshed="http://toolshed.g2.bx.psu.edu"; /> >>>>>> </package> >>>>>> >>>>>> But I thought as a "Tool dependency definition" only the >>>>>> tip revision is ever used? >>>>> >>>>> That is also what I understood, regardless of the revision there is only >>>>> one install able revision. But I guess the TS is generating the path to >>>>> numpy from the <package> tag and that points to an old non existing >>>>> version. >>>> >>>> Hmm. Something for Greg to look at then. >>>> >>>>>> After attempting to install this, the status is "Installed, missing >>>>>> repository dependencies" and this oddity about wanting two >>>>>> revisions of NumPy persists. >>>>>> >>>>>> The actual failure appears to be in compiling matplotlib itself... >>>>>> I don't think it is finding the NumPy installation. >>>>>> >>>>>> Is it possible to view the INSTALLATION.log from within the >>>>>> Galaxy Admin web interface? >>>>> >>>>> Yes you should see all installed files/folder and the INSTALLATION.log >>>>> in your web browser. >>>> >>>> Can you give me a little more information on how to see >>>> this from within Galaxy? >>>> >>>> 1. Open my Galaxy instance and log in, >>>> 2. Click on "Admin" from top menu >>>> 3. Click on "Manage installed tool shed repositories" on left >>>> 4. Select repository of interest >>> >>> 5. Click, "Manage tool dependencies" >>> 6. Choose one of the dependencies >>> >>> There should be a tree like structure to navigate to your >>> INSTALLATION.log file besides your env.sh file. >>> >>>> At this point the repository drop down menus I see are >>>> "Get updates" and "Delete or inactivate". I must be looking >>>> in the wrong place? >>>> >>>>> >>>>> I can reproduce it here and it fails because of numpy. >>>> >>>> OK, that's good - it sounds like the rival revision problem >>>> is what is going wrong. >>>> >>>>> >>>>> One fix to get it working is to upload again biopython. >>>> >>>> Good plan - as discussed here: >>>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html >>> >>> Done. >>> >>>> Thank you, >>>> >>>> Peter >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
