{"action":"created","issue":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/3210","repository_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs","labels_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/3210/labels{/name}","comments_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/3210/comments","events_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/3210/events","html_url":"https://github.com/hpcugent/easybuild-easyconfigs/issues/3210","id":160394064,"number":3210,"title":"Minimal toolchain build failure","user":{"login":"verdurin","id":12435,"avatar_url":"https://avatars.githubusercontent.com/u/12435?v=3","gravatar_id":"","url":"https://api.github.com/users/verdurin","html_url":"https://github.com/verdurin","followers_url":"https://api.github.com/users/verdurin/followers","following_url":"https://api.github.com/users/verdurin/following{/other_user}","gists_url":"https://api.github.com/users/verdurin/gists{/gist_id}","starred_url":"https://api.github.com/users/verdurin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/verdurin/subscriptions","organizations_url":"https://api.github.com/users/verdurin/orgs","repos_url":"https://api.github.com/users/verdurin/repos","events_url":"https://api.github.com/users/verdurin/events{/privacy}","received_events_url":"https://api.github.com/users/verdurin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/milestones/30","html_url":"https://github.com/hpcugent/easybuild-easyconfigs/milestones/v2.9.0","labels_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/milestones/30/labels","id":1758894,"number":30,"title":"v2.9.0","description":"","creator":{"login":"boegel","id":620876,"avatar_url":"https://avatars.githubusercontent.com/u/620876?v=3","gravatar_id":"","url":"https://api.github.com/users/boegel","html_url":"https://github.com/boegel","followers_url":"https://api.github.com/users/boegel/followers","following_url":"https://api.github.com/users/boegel/following{/other_user}","gists_url":"https://api.github.com/users/boegel/gists{/gist_id}","starred_url":"https://api.github.com/users/boegel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/boegel/subscriptions","organizations_url":"https://api.github.com/users/boegel/orgs","repos_url":"https://api.github.com/users/boegel/repos","events_url":"https://api.github.com/users/boegel/events{/privacy}","received_events_url":"https://api.github.com/users/boegel/received_events","type":"User","site_admin":false},"open_issues":57,"closed_issues":127,"state":"open","created_at":"2016-05-10T20:40:52Z","updated_at":"2016-06-15T12:48:04Z","due_on":"2016-06-30T22:00:00Z","closed_at":null},"comments":6,"created_at":"2016-06-15T10:56:25Z","updated_at":"2016-06-15T13:03:56Z","closed_at":null,"body":"I've made the following two easyconfigs for local use (which with some cleanup will be submitted upstream):\r\n\r\n```\r\n# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild\r\n# Author: Adam Huffman\r\n# The Francis Crick Institute\r\neasyblock = 'PythonPackage'\r\n\r\nname = 'cnvkit'\r\nversion = '0.7.3'\r\nversionsuffix = '-Python-%(pyver)s'\r\n\r\nhomepage = 'http://cnvkit.readthedocs.org/'\r\ndescription = \"\"\"Copy number variant detection from targeted DNA sequencing\"\"\"\r\n\r\ntoolchain = {'name': 'foss', 'version': '2015b'}\r\n\r\nsources = ['v%(version)s.tar.gz']\r\nsource_urls = ['https://github.com/etal/cnvkit/archive']\r\n\r\ndependencies = [\r\n    ('Python', '2.7.10'),\r\n    ('Biopython', '1.66', versionsuffix),\r\n    ('%(name)s-bundle', '%(version)s', versionsuffix),\r\n    ('R-bundle-%(name)s', '0.1', '-R-3.2.3'),\r\n]\r\n\r\nsanity_check_paths = {\r\n    'files': ['bin/cnvkit.py', 'bin/reference2targets.py', 'bin/vcf_sample_filter.py',\r\n              'lib/python%(pyshortver)s/site-packages/CNVkit-%(version)s-py%(pyshortver)s.egg'],\r\n    'dirs': []\r\n}\r\n\r\noptions = {'modulename': 'cnvlib'}\r\n\r\nsanity_check_commands = [ 'cd test; make' ]\r\n\r\nmoduleclass = 'bio'\r\n```\r\n\r\nwhich relies on:\r\n\r\n```\r\n# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild\r\n# Author: Adam Huffman\r\n# The Francis Crick Institute\r\neasyblock = 'Bundle'\r\n\r\nname = 'cnvkit-bundle'\r\nversion = '0.7.3'\r\nversionsuffix = '-Python-%(pyver)s'\r\n\r\nhomepage = 'http://cnvkit.readthedocs.org/en/latest/index.html'\r\ndescription = \"\"\"CNVkit is a Python library and command-line software toolkit to infer and\r\n visualize copy number from targeted DNA sequencing data. It is designed for use with hybrid\r\n capture, including both whole-exome and custom target panels, and short-read sequencing\r\n platforms such as Illumina and Ion Torrent. This is a bundle to provide dependencies for cnvkit\r\n that aren't available in the standard EasyBuild Python.\"\"\"\r\n\r\ntoolchain = {'name': 'foss', 'version': '2015b'}\r\n\r\n# this is a bundle of Python packages\r\nexts_defaultclass = 'PythonPackage'\r\n\r\ndependencies = [\r\n    ('Python', '2.7.10'),\r\n]\r\n\r\nexts_list = [\r\n    ('reportlab', '3.3.0', {\r\n        'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'],\r\n    }),\r\n    ('PyVCF', '0.6.8', {\r\n        'modulename': 'vcf',\r\n        'source_urls': ['https://pypi.python.org/packages/source/P/PyVCF'],\r\n    }),\r\n    ('pysam', '0.9.0', {\r\n        'source_urls': ['https://pypi.python.org/packages/source/p/pysam'],\r\n    }),\r\n]\r\n\r\n# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module\r\nfull_sanity_check = True\r\n\r\nsanity_check_paths = {\r\n    'files': [],\r\n    'dirs': ['lib/python%(pyshortver)s/site-packages'],\r\n}\r\n\r\nmodextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}\r\n\r\nmoduleclass = 'bio'\r\n```\r\n\r\nThese two work on one of my test servers.\r\n\r\nHowever, I'm trying to install them on a fresh cloud instance with minimal-toolchains enabled, and the build fails:\r\n\r\n```\r\n[adam@lung-login ~]$ eb ~/src/github/easybuild-easyconfigs-devel/cnvkit-0.7.3-foss-2015b-Python-2.7.10.eb -dr\r\n== temporary log file in case of crash /tmp/eb-3Kzofr/easybuild-QsCCIE.log\r\nERROR: Failed to process easyconfig /home/adam/src/github/easybuild-easyconfigs-devel/cnvkit-0.7.3-foss-2015b-Python-2.7.10.eb: No easyconfig for {'external_module_metadata': {}, 'full_mod_name': None, 'build_only': False, 'versionsuffix': '-Python-%(pyver)s', 'external_module': False, 'dummy': False, 'toolchain': None, 'name': 'Biopython', 'short_mod_name': None, 'version': '1.66', 'hidden': False} that matches toolchain hierarchy generated by {'version': '2015b', 'name': 'foss'}\r\n```\r\n\r\nHere is the `Biopython` easyconfig that it should be using:\r\n\r\n```\r\n##\r\n# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild\r\n#\r\n# Copyright:: Copyright 2012-2013 The Cyprus Institute\r\n# Authors::   Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>\r\n# License::   MIT/GPL\r\n#\r\n##\r\neasyblock = \"PythonPackage\"\r\n\r\nname = 'Biopython'\r\nversion = '1.66'\r\nversionsuffix = '-Python-%(pyver)s'\r\n\r\nhomepage = 'http://www.biopython.org'\r\ndescription = \"\"\"Biopython is a set of freely available tools for biological computation written\r\nin Python by an international team of developers. It is a distributed collaborative effort to\r\ndevelop Python libraries and applications which address the needs of current and future work in\r\nbioinformatics. \"\"\"\r\n\r\ntoolchain = {'name': 'foss', 'version': '2015b'}\r\n\r\nsource_urls = ['http://biopython.org/DIST']\r\nsources = ['%(namelower)s-%(version)s.tar.gz']\r\n\r\ndependencies = [\r\n    ('Python', '2.7.10'),\r\n]\r\n\r\nsanity_check_paths = {\r\n    'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'],\r\n    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',\r\n             'lib/python%(pyshortver)s/site-packages/BioSQL']\r\n}\r\n\r\noptions = {'modulename': 'Bio'}\r\n\r\nmoduleclass = 'bio'\r\n```"},"comment":{"url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/comments/226180435","html_url":"https://github.com/hpcugent/easybuild-easyconfigs/issues/3210#issuecomment-226180435","issue_url":"https://api.github.com/repos/hpcugent/easybuild-easyconfigs/issues/3210","id":226180435,"user":{"login":"boegel","id":620876,"avatar_url":"https://avatars.githubusercontent.com/u/620876?v=3","gravatar_id":"","url":"https://api.github.com/users/boegel","html_url":"https://github.com/boegel","followers_url":"https://api.github.com/users/boegel/followers","following_url":"https://api.github.com/users/boegel/following{/other_user}","gists_url":"https://api.github.com/users/boegel/gists{/gist_id}","starred_url":"https://api.github.com/users/boegel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/boegel/subscriptions","organizations_url":"https://api.github.com/users/boegel/orgs","repos_url":"https://api.github.com/users/boegel/repos","events_url":"https://api.github.com/users/boegel/events{/privacy}","received_events_url":"https://api.github.com/users/boegel/received_events","type":"User","site_admin":false},"created_at":"2016-06-15T13:03:56Z","updated_at":"2016-06-15T13:03:56Z","body":"@verdurin you need to make sure that the robot can pick up any additional easyconfig files that are needed to resolve all dependencies, which doesn't seem to be the case here?"}}
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