{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/547","id":127210633,"number":547,"title":"package_python_2_7_numpy_1_9 update to explicitly specify ATLAS libs from toolshed","user":{"login":"pjbriggs","id":840204,"avatar_url":"https://avatars.githubusercontent.com/u/840204?v=3","gravatar_id":"","url":"https://api.github.com/users/pjbriggs","html_url":"https://github.com/pjbriggs","followers_url":"https://api.github.com/users/pjbriggs/followers","following_url":"https://api.github.com/users/pjbriggs/following{/other_user}","gists_url":"https://api.github.com/users/pjbriggs/gists{/gist_id}","starred_url":"https://api.github.com/users/pjbriggs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pjbriggs/subscriptions","organizations_url":"https://api.github.com/users/pjbriggs/orgs","repos_url":"https://api.github.com/users/pjbriggs/repos","events_url":"https://api.github.com/users/pjbriggs/events{/privacy}","received_events_url":"https://api.github.com/users/pjbriggs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-01-18T11:48:38Z","updated_at":"2016-01-26T16:02:38Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547","html_url":"https://github.com/galaxyproject/tools-iuc/pull/547","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/547.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/547.patch"},"body":"This PR attempts to fix an issue with `package_python_2_7_numpy_1_9` and its dependency on `package_atlas_3_10`; essentially the former fails to use the ATLAS libraries provided by the latter when building `numpy`:\r\n\r\n* In cases where there is a pre-existing set of ATLAS libraries on the system, `numpy` may compile against these instead and cause installation failures subsequently for other packages that depend on `numpy` (for example `package_python_2_7_scipy_0_14`). This is what I'm observing on our production server when trying to update the `deepTools` tool (we are running Scientific Linux and have the `devel` package for the ATLAS libraries installed).\r\n\r\n* In cases where the system ATLAS is not picked up (or doesn't exist), the installation failures may not be observed - however the `numpy` installation logs suggest that the toolshed ATLAS libs are not picked up either.\r\n\r\nTo address this I've updated the `tool_dependencies.xml` file for `package_python_2_7_numpy_1_9` to create a `site.cfg` file that explicitly specifies the location of the toolshed ATLAS libraries (as per the instructions in `numpy`'s `INSTALL.txt`). Unfortunately this has meant that I've also had to replace the \"magic\" `<package ...>` command (which appears to download, unpack and install `numpy` in a single stage), so I don't know if there is a better/more concise way to do this.\r\n\r\nHopefully this makes sense - I'm happy to provide more details etc. Thanks for your consideration."},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/175092194","html_url":"https://github.com/galaxyproject/tools-iuc/pull/547#issuecomment-175092194","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547","id":175092194,"user":{"login":"blankenberg","id":1231190,"avatar_url":"https://avatars.githubusercontent.com/u/1231190?v=3","gravatar_id":"","url":"https://api.github.com/users/blankenberg","html_url":"https://github.com/blankenberg","followers_url":"https://api.github.com/users/blankenberg/followers","following_url":"https://api.github.com/users/blankenberg/following{/other_user}","gists_url":"https://api.github.com/users/blankenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/blankenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blankenberg/subscriptions","organizations_url":"https://api.github.com/users/blankenberg/orgs","repos_url":"https://api.github.com/users/blankenberg/repos","events_url":"https://api.github.com/users/blankenberg/events{/privacy}","received_events_url":"https://api.github.com/users/blankenberg/received_events","type":"User","site_admin":false},"created_at":"2016-01-26T16:02:38Z","updated_at":"2016-01-26T16:02:38Z","body":"@bgruening @pjbriggs \r\nhttps://depot.galaxyproject.org/software/ or https://github.com/bgruening/download_store ?"}}