{"action":"created","issue":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/1689","labels_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/1689/labels{/name}","comments_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/1689/comments","events_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/1689/events","html_url":"https://github.com/hpcugent/easybuild-easyconfigs/issues/1689","id":87688781,"number":1689,"title":"Request for Comments, as regards `common_deps`","user":{"login":"fgeorgatos","id":1531968,"avatar_url":"https://avatars.githubusercontent.com/u/1531968?v=3","gravatar_id":"","url":"https://api.github.com/users/fgeorgatos","html_url":"https://github.com/fgeorgatos","followers_url":"https://api.github.com/users/fgeorgatos/followers","following_url":"https://api.github.com/users/fgeorgatos/following{/other_user}","gists_url":"https://api.github.com/users/fgeorgatos/gists{/gist_id}","starred_url":"https://api.github.com/users/fgeorgatos/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fgeorgatos/subscriptions","organizations_url":"https://api.github.com/users/fgeorgatos/orgs","repos_url":"https://api.github.com/users/fgeorgatos/repos","events_url":"https://api.github.com/users/fgeorgatos/events{/privacy}","received_events_url":"https://api.github.com/users/fgeorgatos/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-06-12T10:49:31Z","updated_at":"2015-06-12T12:57:49Z","closed_at":null,"body":"Hellos to all,\r\n\r\nI have been bugging fellows for a while yet this should not wait any longer,\r\nwe discussed this in yesterday's EB hangout:\r\n- we need to specify (as far as feasible) a *preferred* list of common dependencies;\r\nIt does not have to be final/perfect/ideal, but there has to be some *guideline* today;\r\nif not we will pay the high price of effort duplication in the next weeks/months.\r\n\r\nThis issue intends to supersede #384, so I copy-paste from that:\r\n\r\n```\r\neasyblock = 'Bundle'\r\n\r\nname = 'common_deps'\r\nversion = '2.0'\r\n\r\nhomepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html'\r\ndescription = \"\"\"The purpose of this collection is to provide common dependencies in a bundle,\r\n so that software/modules can be mixed and matched easily for composite pipelines \r\n in Life Sciences and other fields\"\"\"\r\n\r\ntoolchain = {'name': 'goolf', 'version': '1.7.20'}\r\n\r\ndependencies = [\r\n    ('bzip2', '1.0.6'),\r\n    ('zlib', '1.2.8'),\r\n    ('libreadline', '6.3'),\r\n    ('ncurses', '5.9'),\r\n# **the ones beyond this line are also known as biodeps**\r\n    ('Boost', '1.58.0', '-Python-2.7.10'),\r\n    ('SAMtools', '0.1.19'),\r\n    ('Perl', '5.20.0', '-bare'),\r\n    ('Java', '1.7.0_80', '', True),\r\n    ('libpng', '1.6.17'),\r\n]\r\n\r\nmoduleclass = 'bundle'\r\n```\r\n\r\nThis is intentionally a conservative upgrade over `biodeps/1.6`, to minimize issues.\r\n\r\nI am a little bit inclined to serve life scientists' needs (because applications are many and painful),\r\nhowever your arguments should be shot from all directions, regardless of my priorities.\r\n\r\nRequest For Comments, as regards effects of version advancement/creep for:\r\n* `SAMtools/1.2` is known to be better than others; \r\n  however @rjeschmi reports TopHat compatibility issues, so 0.1.19 might be more prudent choice\r\n* `Perl/5.22` was released last week; \r\n  @rjeschmi reports that 5.20 has greater compatibility and should play conservative\r\n* `ncurses/6.0` pre-release is out since last week; it should be backwards compatible with `5.9` line;\r\n my guess is that we will assume \"do-not-fix-if-not-broken\" for now, although `6.0` would be nice\r\n* Boost is known to be incompatible with itself. For now we make the assumption `1.58` is OK\r\n* `Java/1.8` is supposed to be better and compatible; not all might agree, fi. look for GATK here:\r\n  http://stackoverflow.com/questions/21402136/java-1-8-versus-java-1-7-compatibility-issue\r\n\r\nIn short, the above proposition is a somewhat conservative upgrade,\r\nwith the outlook of making a more advanced common_deps release in the future.\r\n\r\nyour feedback?!\r\n"},"comment":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/comments/111483820","html_url":"https://github.com/hpcugent/easybuild-easyconfigs/issues/1689#issuecomment-111483820","issue_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/1689","id":111483820,"user":{"login":"fgeorgatos","id":1531968,"avatar_url":"https://avatars.githubusercontent.com/u/1531968?v=3","gravatar_id":"","url":"https://api.github.com/users/fgeorgatos","html_url":"https://github.com/fgeorgatos","followers_url":"https://api.github.com/users/fgeorgatos/followers","following_url":"https://api.github.com/users/fgeorgatos/following{/other_user}","gists_url":"https://api.github.com/users/fgeorgatos/gists{/gist_id}","starred_url":"https://api.github.com/users/fgeorgatos/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fgeorgatos/subscriptions","organizations_url":"https://api.github.com/users/fgeorgatos/orgs","repos_url":"https://api.github.com/users/fgeorgatos/repos","events_url":"https://api.github.com/users/fgeorgatos/events{/privacy}","received_events_url":"https://api.github.com/users/fgeorgatos/received_events","type":"User","site_admin":false},"created_at":"2015-06-12T12:57:49Z","updated_at":"2015-06-12T12:57:49Z","body":"@pescobar: OK, thanks.\r\n\r\nAs I see it, we converge as of today (ncurses/6.0 is not released yet).\r\nIn the meeting we thought of renaming biodeps to common_deps, to make it more appealing for other fields; ie. it is going to include: bzip2, zlib, libreadline, ncurses, libpng\r\n\r\nN.B. Not having a PR for `common_deps` today does not block us from now on to advance:\r\n* as long as people stick on these versions, many new PRs are going to be aligned:\r\n\r\n```\r\ndependencies = [\r\n    ('bzip2', '1.0.6'),\r\n    ('zlib', '1.2.8'),\r\n    ('libreadline', '6.3'),\r\n    ('ncurses', '5.9'),\r\n    ('libpng', '1.6.17'),\r\n]\r\n```\r\n\r\nThanks for pruning a good part of the ongoing dependency hell tree!\r\n"}}