Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? Thanks for the fast fix! Bjoern Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hi Greg, seems to work fine! Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Just a thought ... is it really the next or the top (valid)? Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Ah ok, yes that makes sense. Also if it is not installable, it probably should not be possible to upload it, or? Thanks for the clarification. Bjoern Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, On Aug 21, 2013, at 1:27 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, seems to work fine! Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Just a thought ... is it really the next or the top (valid)? In the case of repositories of type tool_dependency_definition, if the repository is associated with an installable revision, it will always be the tip. So in these cases, next will be tip or None, in which case an error has been encountered and should be handled as usual. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Ah ok, yes that makes sense. Also if it is not installable, it probably should not be possible to upload it, or? It has always been possible to upload changeset revisions with invalid contents. The tool shed will simply attempt to communicate the reason the contents are invalid. I'm not sure this case should be handled differently. Thanks for the clarification. Bjoern Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, I just wanted to let you know I've determined the cause of this issue and should have a fix for it committed by tomorrow (US Easter Time). I'll let you know as soon as the fix is committed. Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
[galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Peter, I've duplicated the installation error on the scipy tool dependency, and will be looking into the cause. Thanks for the report. --Dave B. On 8/15/13 09:01:17.000, Bjoern Gruening wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. 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
