{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/55866346","id":55866346,"diff_hunk":"@@ -16,9 +16,7 @@\n                         <repository name=\"package_atlas_3_10\" owner=\"iuc\">\n                             <package name=\"atlas\" version=\"3.10.2\" />\n                         </repository>\n-                        <package sha256sum=\"0075bbe07e30b659ae4415446f45812dc1b96121a493a4a1f8b1ba77b75b1e1c\">\n-                            https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz\n-                        </package>\n+                        <package sha256sum=\"9753003ab7c489968eb260e5460556fd7d533a8e11a9d5326e0995bd1aa21318\">https://depot.galaxyproject.org/software/9753003ab7c489968eb260e5460556fd7d533a8e11a9d5326e0995bd1aa21318</package>","path":"packages/package_python_2_7_numpy_1_9/tool_dependencies.xml","position":7,"original_position":7,"commit_id":"89f831a93a13f0b5f9db7e2aa71d796eee025e6b","original_commit_id":"89f831a93a13f0b5f9db7e2aa71d796eee025e6b","user":{"login":"nsoranzo","id":4924623,"avatar_url":"https://avatars.githubusercontent.com/u/4924623?v=3","gravatar_id":"","url":"https://api.github.com/users/nsoranzo","html_url":"https://github.com/nsoranzo","followers_url":"https://api.github.com/users/nsoranzo/followers","following_url":"https://api.github.com/users/nsoranzo/following{/other_user}","gists_url":"https://api.github.com/users/nsoranzo/gists{/gist_id}","starred_url":"https://api.github.com/users/nsoranzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsoranzo/subscriptions","organizations_url":"https://api.github.com/users/nsoranzo/orgs","repos_url":"https://api.github.com/users/nsoranzo/repos","events_url":"https://api.github.com/users/nsoranzo/events{/privacy}","received_events_url":"https://api.github.com/users/nsoranzo/received_events","type":"User","site_admin":false},"body":"@mvdbeek I think `<package>` is the correct tag because it is inside a `setup_python_environment` action. But you are right about the URL.","created_at":"2016-03-11T18:17:43Z","updated_at":"2016-03-11T18:17:43Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/547#discussion_r55866346","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/55866346"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/547#discussion_r55866346"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547","id":56332932,"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","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547","number":547,"state":"open","locked":false,"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},"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.","created_at":"2016-01-18T11:48:38Z","updated_at":"2016-03-11T18:17:43Z","closed_at":null,"merged_at":null,"merge_commit_sha":"dc8ed63233cc3aaec3e57844e6d3adfbb954cd7c","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/547/comments","review_comment_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/547/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/89f831a93a13f0b5f9db7e2aa71d796eee025e6b","head":{"label":"pjbriggs:fix-package_python_2_7_numpy_1_9-with-atlas","ref":"fix-package_python_2_7_numpy_1_9-with-atlas","sha":"89f831a93a13f0b5f9db7e2aa71d796eee025e6b","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},"repo":{"id":36803148,"name":"tools-iuc","full_name":"pjbriggs/tools-iuc","owner":{"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},"private":false,"html_url":"https://github.com/pjbriggs/tools-iuc","description":"Tool 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