{"action":"created","comment":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/comments/29334543","id":29334543,"diff_hunk":"@@ -0,0 +1,52 @@\n+##\n+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild\n+#\n+# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine\n+# Authors::   Robert Schmidt <roschmidt@ohri.ca>,Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste\n+# License::   MIT/GPL\n+# $Id$\n+#\n+##\n+\"\"\"\n+EasyBuild support for building BCFtools (BCF - Binary VCF - Variant Call Format), implemented as an easyblock\n+\n+@author: Robert Schmidt (Ottawa Hospital Research Institute)\n+@author: Cedric Laczny (Uni.Lu)\n+@author: Fotis Georgatos (Uni.Lu)\n+@author: Kenneth Hoste (Ghent University)\n+\"\"\"\n+import os\n+import shutil\n+import stat\n+from distutils.version import LooseVersion\n+\n+from easybuild.easyblocks.generic.configuremake import ConfigureMake\n+from easybuild.tools.filetools import adjust_permissions\n+\n+class EB_BCFtools(ConfigureMake):\n+    \"\"\"\n+    Support for building BCFtools; \n+    Specs for the formats can be found here:\n+    https://github.com/samtools/hts-specs\n+    \"\"\"\n+\n+    def __init__(self, *args, **kwargs):\n+        \"\"\"Define lists of files to install.\"\"\"\n+        super(EB_BCFtools, self).__init__(*args, **kwargs)\n+\n+\n+    def configure_step(self):\n+        \"\"\"\n+        No configure\n+        \"\"\"\n+        pass\n+\n+    def sanity_check_step(self):\n+        \"\"\"Custom sanity check for BCFtools.\"\"\"\n+\n+        custom_paths = {\n+                        'files': ['bin/%s' % x for x in [f.split('/')[-1] for f in self.bin_files]] ,","path":"easybuild/easyblocks/b/bcftools.py","position":48,"original_position":48,"commit_id":"3dcd33b32a29bda226cb7ed2a5869991271ac1ee","original_commit_id":"3dcd33b32a29bda226cb7ed2a5869991271ac1ee","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},"body":"and, it also shows why, the proposition of enforced sanitychecks within easyblocks and 1-1 correspondence of easyblocks to software components should rather be dropped as unsustainable, ie. it does not promote good reusability of python objects, where otherwise it should be possible (and clean to do so).","created_at":"2015-04-29T13:25:08Z","updated_at":"2015-04-29T13:25:08Z","html_url":"https://github.com/hpcugent/easybuild-easyblocks/pull/511#discussion_r29334543","pull_request_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/511","_links":{"self":{"href":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/comments/29334543"},"html":{"href":"https://github.com/hpcugent/easybuild-easyblocks/pull/511#discussion_r29334543"},"pull_request":{"href":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/511"}}},"pull_request":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/511","id":24710164,"html_url":"https://github.com/hpcugent/easybuild-easyblocks/pull/511","diff_url":"https://github.com/hpcugent/easybuild-easyblocks/pull/511.diff","patch_url":"https://github.com/hpcugent/easybuild-easyblocks/pull/511.patch","issue_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/issues/511","number":511,"state":"open","locked":false,"title":"adding a new bcftools block for the new SAMtools separated bcftools","user":{"login":"rjeschmi","id":266522,"avatar_url":"https://avatars.githubusercontent.com/u/266522?v=3","gravatar_id":"","url":"https://api.github.com/users/rjeschmi","html_url":"https://github.com/rjeschmi","followers_url":"https://api.github.com/users/rjeschmi/followers","following_url":"https://api.github.com/users/rjeschmi/following{/other_user}","gists_url":"https://api.github.com/users/rjeschmi/gists{/gist_id}","starred_url":"https://api.github.com/users/rjeschmi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rjeschmi/subscriptions","organizations_url":"https://api.github.com/users/rjeschmi/orgs","repos_url":"https://api.github.com/users/rjeschmi/repos","events_url":"https://api.github.com/users/rjeschmi/events{/privacy}","received_events_url":"https://api.github.com/users/rjeschmi/received_events","type":"User","site_admin":false},"body":"This is the block to install the new separate bcftools. It is a copy of the samtools block, with the filelist changed to covery the files included with bcftools.\r\n\r\nThere is a corresponding easyconfig which I'll merge.","created_at":"2014-11-19T18:36:23Z","updated_at":"2015-04-29T13:25:08Z","closed_at":null,"merged_at":null,"merge_commit_sha":"1cb3d529449ee9371233379e2f092bc844db02c4","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/511/commits","review_comments_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/511/comments","review_comment_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/pulls/comments{/number}","comments_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/issues/511/comments","statuses_url":"https://api.github.com/repos/hpcugent/easybuild-easyblocks/statuses/3dcd33b32a29bda226cb7ed2a5869991271ac1ee","head":{"label":"rjeschmi:bcftools_new","ref":"bcftools_new","sha":"3dcd33b32a29bda226cb7ed2a5869991271ac1ee","user":{"login":"rjeschmi","id":266522,"avatar_url":"https://avatars.githubusercontent.com/u/266522?v=3","gravatar_id":"","url":"https://api.github.com/users/rjeschmi","html_url":"https://github.com/rjeschmi","followers_url":"https://api.github.com/users/rjeschmi/followers","following_url":"https://api.github.com/users/rjeschmi/following{/other_user}","gists_url":"https://api.github.com/users/rjeschmi/gists{/gist_id}","starred_url":"https://api.github.com/users/rjeschmi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rjeschmi/subscriptions","organizations_url":"https://api.github.com/users/rjeschmi/orgs","repos_url":"https://api.github.com/users/rjeschmi/repos","events_url":"https://api.github.com/users/rjeschmi/events{/privacy}","received_events_url":"https://api.github.com/users/rjeschmi/received_events","type":"User","site_admin":false},"repo":{"id":26606344,"name":"easybuild-easyblocks","full_name":"rjeschmi/easybuild-easyblocks","owner":{"login":"rjeschmi","id":266522,"avatar_url":"https://avatars.githubusercontent.com/u/266522?v=3","gravatar_id":"","url":"https://api.github.com/users/rjeschmi","html_url":"https://github.com/rjeschmi","followers_url":"https://api.github.com/users/rjeschmi/followers","following_url":"https://api.github.com/users/rjeschmi/following{/other_user}","gists_url":"https://api.github.com/users/rjeschmi/gists{/gist_id}","starred_url":"https://api.github.com/users/rjeschmi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rjeschmi/subscriptions","organizations_url":"https://api.github.com/users/rjeschmi/orgs","repos_url":"https://api.github.com/users/rjeschmi/repos","events_url":"https://api.github.com/users/rjeschmi/events{/privacy}","received_events_url":"https://api.github.com/users/rjeschmi/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/rjeschmi/easybuild-easyblocks","description":"Collection 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