Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
Hi, also fixed, yes! Good start in a day, to write positive mails :) Bjoern 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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
Hi Peter, I believe this behavior is resolved with change set 10412:29ab5a6d75a7, which was committed to the stable branch and is running on both tool sheds. You'll need to update your Galaxy instance to get the fix. Pleaser let me know if I have misunderstood the steps necessary to reproduce the behavior you're discussing here. Thanks! Greg Von Kuster On Aug 12, 2013, at 10:55 AM, Peter Cock p.j.a.c...@googlemail.com 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: On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Ok reverted it! Its now to a normal bash definition and I removed the atlas and lapack definitions. So it should build but it has performance regressions. If the new galaxy stable is out, I will upload the new version. Hope it builds now for you. Bjoern 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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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? 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? Should I just email that too? Peter Screen Shot 2013-08-12 at 15.42.31.png___ 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Tue, Aug 13, 2013 at 2:01 PM, Dave Bouvier d...@bx.psu.edu wrote: 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. Thanks Dave, In the short term simplifying the NumPy package then (in a cascade) updating other packages dependent on that new latest revision was enough to get the packages I was testing to install on the July stable release. Updating to the new August stable release should hopefully fix some/all of the issues we were struggling with - if there are any still outstanding we will let you know. The sooner the Tool Shed starts testing package installation the better though - for example this would have caught the template_command problem much quicker (using a new unreleased feature on the main Tool Shed): https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Cheers, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote: Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version TypeStatus Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? Yes. e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a One way to catch this kind of error would be if the nightly Tool Shed tests included attempting to install package repositories (e.g. the new Tool dependency definition) explicitly. Oh that would be so nice! +1 for me. And by the way, notifications about new orphan tool dependencies also do not happen. I think that would be very useful for a few developers that are waiting for numpy, blast+ and so on. (I think I've suggested this before - but it is worth reiterating) Thanks, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote: Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version TypeStatus Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a Yes. Is there an easy fix where you could upload an older version of the installation script before you started using the new template_command action? One way to catch this kind of error would be if the nightly Tool Shed tests included attempting to install package repositories (e.g. the new Tool dependency definition) explicitly. (I think I've suggested this before - but it is worth reiterating) Oh that would be so nice! +1 for me. And by the way, notifications about new orphan tool dependencies also do not happen. I think that would be very useful for a few developers that are waiting for numpy, blast+ and so on. Logged on Trello, please subscribe and vote: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote: Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version TypeStatus Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a Yes. Is there an easy fix where you could upload an older version of the installation script before you started using the new template_command action? Sorry, I do not understand the question. To you mean if I could revert the changes and go back to old bash scripts for the time being? In theory it should be possible. But the aim of my cheetah template patch was to make it easier to write such if else conditions. And create a save fallback to non-atlas users. The next stable release should be out that week, or? One way to catch this kind of error would be if the nightly Tool Shed tests included attempting to install package repositories (e.g. the new Tool dependency definition) explicitly. (I think I've suggested this before - but it is worth reiterating) Oh that would be so nice! +1 for me. And by the way, notifications about new orphan tool dependencies also do not happen. I think that would be very useful for a few developers that are waiting for numpy, blast+ and so on. Logged on Trello, please subscribe and vote: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Done! 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote: Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version TypeStatus Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a Yes. Is there an easy fix where you could upload an older version of the installation script before you started using the new template_command action? Sorry, I do not understand the question. To you mean if I could revert the changes and go back to old bash scripts for the time being? Yes, that is what I meant. In theory it should be possible. But the aim of my cheetah template patch was to make it easier to write such if else conditions. And create a save fallback to non-atlas users. The next stable release should be out that week, or? I expect that in the meantime this bug will hit other people as well (and until the Tool Shed testing is improved I'm a little worried there could be other 'broken' packages) :( If you had a working (minimal non-Altas non-lapack) numpy tool_dependencies.xml pre-dating the template_command action it would seem sensible to upload it now to fix the numpy package on the main Tool Shed. I would have thought one of the old revisions from the numpy package on the Test Tool Shed would work? Thanks, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote: Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user:Dannon Baker dannonba...@me.com date:Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version TypeStatus Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a Yes. Is there an easy fix where you could upload an older version of the installation script before you started using the new template_command action? Sorry, I do not understand the question. To you mean if I could revert the changes and go back to old bash scripts for the time being? Yes, that is what I meant. In theory it should be possible. But the aim of my cheetah template patch was to make it easier to write such if else conditions. And create a save fallback to non-atlas users. The next stable release should be out that week, or? I expect that in the meantime this bug will hit other people as well (and until the Tool Shed testing is improved I'm a little worried there could be other 'broken' packages) :( If you had a working (minimal non-Altas non-lapack) numpy tool_dependencies.xml pre-dating the template_command action it would seem sensible to upload it now to fix the numpy package on the main Tool Shed. I would have thought one of the old revisions from the numpy package on the Test Tool Shed would work? Yes they do. But if you could not deactivate cpu throttling it will crash and all other dependent packages will not be installed. The numpy package on main under the IUC account was uploaded yesterday. I do not think any other package is using it, or? Maybe I should update the repository description to reflect that the newest version is needed? Thanks, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote: I expect that in the meantime this bug will hit other people as well (and until the Tool Shed testing is improved I'm a little worried there could be other 'broken' packages) :( If you had a working (minimal non-Altas non-lapack) numpy tool_dependencies.xml pre-dating the template_command action it would seem sensible to upload it now to fix the numpy package on the main Tool Shed. I would have thought one of the old revisions from the numpy package on the Test Tool Shed would work? Yes they do. But if you could not deactivate cpu throttling it will crash and all other dependent packages will not be installed. Ah. But at least it would work on some machines, whereas right now it will fail on all galaxy-dist installations (until the next stable release happens). The numpy package on main under the IUC account was uploaded yesterday. I do not think any other package is using it, or? Too late :( These repositories on the Main Tool Shed use the numpy package directly: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 These all use it via the Biopython package: http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss These will all use it via the Biopython package when next updated: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id There are probably more - Greg can perhaps do a search for declared dependencies directly even if this isn't an option via the Tool Shed website. For these Biopython examples, they don't actually need NumPy - so we could perhaps temporarily update the Biopython package on the main Tool Shed to install without NumPy... Maybe I should update the repository description to reflect that the newest version is needed? Updating the description might help - but it doesn't need the newest version, it needs the not-yet-released stable version of Galaxy :( 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, 2013-08-12 at 14:30 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote: I expect that in the meantime this bug will hit other people as well (and until the Tool Shed testing is improved I'm a little worried there could be other 'broken' packages) :( If you had a working (minimal non-Altas non-lapack) numpy tool_dependencies.xml pre-dating the template_command action it would seem sensible to upload it now to fix the numpy package on the main Tool Shed. I would have thought one of the old revisions from the numpy package on the Test Tool Shed would work? Yes they do. But if you could not deactivate cpu throttling it will crash and all other dependent packages will not be installed. Ah. But at least it would work on some machines, whereas right now it will fail on all galaxy-dist installations (until the next stable release happens). The numpy package on main under the IUC account was uploaded yesterday. I do not think any other package is using it, or? Too late :( These repositories on the Main Tool Shed use the numpy package directly: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 These all use it via the Biopython package: http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss These will all use it via the Biopython package when next updated: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id There are probably more - Greg can perhaps do a search for declared dependencies directly even if this isn't an option via the Tool Shed website. For these Biopython examples, they don't actually need NumPy - so we could perhaps temporarily update the Biopython package on the main Tool Shed to install without NumPy... Maybe I should update the repository description to reflect that the newest version is needed? Updating the description might help - but it doesn't need the newest version, it needs the not-yet-released stable version of Galaxy :( Ahhh, right the revisions are gone. So the latest is always the one that are used. Oh oh ... I will screen through my github history and try to revert the numpy package until next stable is out. Oh that was a bad move from me. Sorry, Bjoern 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, Aug 12, 2013 at 2:49 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Ahhh, right the revisions are gone. So the latest is always the one that are used. Oh oh ... I will screen through my github history and try to revert the numpy package until next stable is out. My guess is that the Main Tool Shed only ever had one numpy revision: http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 (rev 0) Likewise the IUC account on the Main Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 (rev 0) Your original Test Tool Shed entry has lots of revisions: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_numpy_1_7 (rev 22) That should match up with the GitHub revisions, https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_numpy_1_7/tool_dependencies.xml Oh that was a bad move from me. Sorry, Bjoern Easily done - don't feel bad, I've made mistakes uploading to the Tool Shed too :( The good news is this has underlined the need for the Tool Shed to do more testing: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Regards, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
Ok reverted it! Its now to a normal bash definition and I removed the atlas and lapack definitions. So it should build but it has performance regressions. If the new galaxy stable is out, I will upload the new version. Hope it builds now for you. Bjoern bjoern.gruen...@gmail.com wrote: Ahhh, right the revisions are gone. So the latest is always the one that are used. Oh oh ... I will screen through my github history and try to revert the numpy package until next stable is out. My guess is that the Main Tool Shed only ever had one numpy revision: http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 (rev 0) Likewise the IUC account on the Main Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 (rev 0) Your original Test Tool Shed entry has lots of revisions: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_numpy_1_7 (rev 22) That should match up with the GitHub revisions, https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_numpy_1_7/tool_dependencies.xml Oh that was a bad move from me. Sorry, Bjoern Easily done - don't feel bad, I've made mistakes uploading to the Tool Shed too :( The good news is this has underlined the need for the Tool Shed to do more testing: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Regards, 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Ok reverted it! Its now to a normal bash definition and I removed the atlas and lapack definitions. So it should build but it has performance regressions. If the new galaxy stable is out, I will upload the new version. Hope it builds now for you. Bjoern 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 ___ 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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: On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Ok reverted it! Its now to a normal bash definition and I removed the atlas and lapack definitions. So it should build but it has performance regressions. If the new galaxy stable is out, I will upload the new version. Hope it builds now for you. Bjoern 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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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. 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. I can reproduce it here and it fails because of numpy. One fix to get it working is to upload again biopython. Should I just email that too? 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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 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 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
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 RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc 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/
