{"action":"created","issue":{"url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/12","labels_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/12/comments","events_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/12/events","html_url":"https://github.com/GreenleafLab/NucleoATAC/issues/12","id":107110195,"number":12,"title":"Problem running NucleoAtac","user":{"login":"kesteph","id":14339828,"avatar_url":"https://avatars.githubusercontent.com/u/14339828?v=3","gravatar_id":"","url":"https://api.github.com/users/kesteph","html_url":"https://github.com/kesteph","followers_url":"https://api.github.com/users/kesteph/followers","following_url":"https://api.github.com/users/kesteph/following{/other_user}","gists_url":"https://api.github.com/users/kesteph/gists{/gist_id}","starred_url":"https://api.github.com/users/kesteph/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kesteph/subscriptions","organizations_url":"https://api.github.com/users/kesteph/orgs","repos_url":"https://api.github.com/users/kesteph/repos","events_url":"https://api.github.com/users/kesteph/events{/privacy}","received_events_url":"https://api.github.com/users/kesteph/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"AliciaSchep","id":6809790,"avatar_url":"https://avatars.githubusercontent.com/u/6809790?v=3","gravatar_id":"","url":"https://api.github.com/users/AliciaSchep","html_url":"https://github.com/AliciaSchep","followers_url":"https://api.github.com/users/AliciaSchep/followers","following_url":"https://api.github.com/users/AliciaSchep/following{/other_user}","gists_url":"https://api.github.com/users/AliciaSchep/gists{/gist_id}","starred_url":"https://api.github.com/users/AliciaSchep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AliciaSchep/subscriptions","organizations_url":"https://api.github.com/users/AliciaSchep/orgs","repos_url":"https://api.github.com/users/AliciaSchep/repos","events_url":"https://api.github.com/users/AliciaSchep/events{/privacy}","received_events_url":"https://api.github.com/users/AliciaSchep/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-09-18T01:08:22Z","updated_at":"2015-09-18T02:10:57Z","closed_at":null,"body":"Hello\r\nI'm trying to run NucleoATAC, but I receive the following error:\r\n\r\n[compute-078]$ nucleoatac run --bed KSN_C_peaks.narrowPeak.sorted.slopped.bed --bam KSN_C.bam --fasta rn5.fa --out KSN_C.NucleoATAC\r\nCommand run:  /home/jhmi/kstephen/.local/bin/nucleoatac run --bed KSN_C_peaks.narrowPeak.sorted.slopped.bed --bam KSN_C.bam --fasta mm9.fa --out KSN_C.NucleoATAC\r\nnucleoatac version 0.2.1\r\nstart run at: 2015-09-17 20:46\r\nTraceback (most recent call last):\r\n  File \"/home/jhmi/kstephen/.local/bin/nucleoatac\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('NucleoATAC==0.2.1', 'nucleoatac')\r\n  File \"/jhpce/shared/community/compiler/gcc/4.4.7/python/2.7.6/lib/python2.7/site-packages/pkg_resources.py\", line 517, in run_script\r\n    self.require(requires)[0].run_script(script_name, ns)\r\n  File \"/jhpce/shared/community/compiler/gcc/4.4.7/python/2.7.6/lib/python2.7/site-packages/pkg_resources.py\", line 1423, in run_script\r\n    exec(code, namespace, namespace)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/EGG-INFO/scripts/nucleoatac\", line 291, in <module>\r\n    main()\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/EGG-INFO/scripts/nucleoatac\", line 69, in main\r\n    from nucleoatac.run_occ import run_occ\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/nucleoatac/run_occ.py\", line 19, in <module>\r\n    from nucleoatac.Occupancy import FragmentMixDistribution, OccupancyParameters, OccChunk\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/nucleoatac/Occupancy.py\", line 12, in <module>\r\n    from pyatac.fragmentsizes import FragmentSizes\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/pyatac/fragmentsizes.py\", line 10, in <module>\r\n    from pyatac.fragments import getAllFragmentSizes, getFragmentSizesFromChunkList\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 435, in load_module\r\n    language_level=self.language_level)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 227, in load_module\r\n    exec(\"raise exc, None, tb\", {'exc': exc, 'tb': tb})\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 209, in load_module\r\n    inplace=build_inplace, language_level=language_level)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 174, in build_module\r\n    extension_mod,setup_args = get_distutils_extension(name, pyxfilename, language_level)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 94, in get_distutils_extension\r\n    extension_mod,setup_args = handle_special_build(modname, pyxfilename)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/pyximport/pyximport.py\", line 118, in handle_special_build\r\n    ext = make_ext(modname, pyxfilename)\r\n  File \"/home/jhmi/kstephen/.local/lib/python2.7/site-packages/NucleoATAC-0.2.1-py2.7.egg/pyatac/fragments.pyxbld\", line 7, in make_ext\r\n    extra_link_args=pysam.get_libraries(),\r\nImportError: Building module pyatac.fragments failed: [\"AttributeError: 'module' object has no attribute 'get_libraries'\\n\"]\r\n\r\n\r\nI'm running python 2.7.6 with spicy version 0.15.1, numpy version 1.9.2, & python  version 0.23.2 on red hat 4.4.7-4\r\n\r\nthank you\r\nKim\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/comments/141309179","html_url":"https://github.com/GreenleafLab/NucleoATAC/issues/12#issuecomment-141309179","issue_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/12","id":141309179,"user":{"login":"kesteph","id":14339828,"avatar_url":"https://avatars.githubusercontent.com/u/14339828?v=3","gravatar_id":"","url":"https://api.github.com/users/kesteph","html_url":"https://github.com/kesteph","followers_url":"https://api.github.com/users/kesteph/followers","following_url":"https://api.github.com/users/kesteph/following{/other_user}","gists_url":"https://api.github.com/users/kesteph/gists{/gist_id}","starred_url":"https://api.github.com/users/kesteph/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kesteph/subscriptions","organizations_url":"https://api.github.com/users/kesteph/orgs","repos_url":"https://api.github.com/users/kesteph/repos","events_url":"https://api.github.com/users/kesteph/events{/privacy}","received_events_url":"https://api.github.com/users/kesteph/received_events","type":"User","site_admin":false},"created_at":"2015-09-18T02:10:56Z","updated_at":"2015-09-18T02:10:56Z","body":"Pysam version 0.8.3\n\nFrom: Alicia Schep <notifications@github.com<mailto:notifications@github.com>>\nReply-To: GreenleafLab/NucleoATAC <reply@reply.github.com<mailto:reply@reply.github.com>>\nDate: Thursday, September 17, 2015 at 9:54 PM\nTo: GreenleafLab/NucleoATAC <NucleoATAC@noreply.github.com<mailto:NucleoATAC@noreply.github.com>>\nCc: Kimberly Stephens <kstephe3@jhu.edu<mailto:kstephe3@jhu.edu>>\nSubject: Re: [NucleoATAC] Problem running NucleoAtac (#12)\n\n\nWhat is version of pysam? (Error appears to be in pysam.get_libraries() that is called while building one of the files)\n\n-\nReply to this email directly or view it on GitHub<https://github.com/GreenleafLab/NucleoATAC/issues/12#issuecomment-141305511>.\n"}}