{"action":"closed","issue":{"url":"https://api.github.com/repos/abishara/athena_meta/issues/9","repository_url":"https://api.github.com/repos/abishara/athena_meta","labels_url":"https://api.github.com/repos/abishara/athena_meta/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/abishara/athena_meta/issues/9/comments","events_url":"https://api.github.com/repos/abishara/athena_meta/issues/9/events","html_url":"https://github.com/abishara/athena_meta/issues/9","id":325901743,"number":9,"title":"pip install error","user":{"login":"vphan13","id":24552157,"avatar_url":"https://avatars0.githubusercontent.com/u/24552157?v=4","gravatar_id":"","url":"https://api.github.com/users/vphan13","html_url":"https://github.com/vphan13","followers_url":"https://api.github.com/users/vphan13/followers","following_url":"https://api.github.com/users/vphan13/following{/other_user}","gists_url":"https://api.github.com/users/vphan13/gists{/gist_id}","starred_url":"https://api.github.com/users/vphan13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vphan13/subscriptions","organizations_url":"https://api.github.com/users/vphan13/orgs","repos_url":"https://api.github.com/users/vphan13/repos","events_url":"https://api.github.com/users/vphan13/events{/privacy}","received_events_url":"https://api.github.com/users/vphan13/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-23T22:49:58Z","updated_at":"2018-05-24T19:17:20Z","closed_at":"2018-05-24T19:17:20Z","author_association":"NONE","body":"OS = CentOS release 6.2 (Final)\r\n`[root@server1 athena_meta-main]# echo $PATH\r\n/usr/local/packages/bwa-0.7.15/bin:/usr/local/packages/idba-1.1.3a1/bin:/usr/local/packages/samtools-1.3.1/bin:/usr/local/packages/htslib-1.3.2/bin:/usr/local/packages/flye-2.3.4/bin:/usr/local/packages/python-2.7.15/bin:$PATH`\r\n\r\nAll python prerequisites have been installed \r\n\r\n`[root@server1 athena_meta-main]# pip --no-cache-dir install -r requirements.txt\r\nRequirement already satisfied: bx-python==0.7.3 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (0.7.3)\r\nRequirement already satisfied: ipython-cluster-helper==0.5.2 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from -r requirements.txt (line 2)) (0.5.2)\r\nRequirement already satisfied: numpy==1.11.0 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (1.11.0)\r\nRequirement already satisfied: pysam==0.9.1 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (0.9.1)\r\nRequirement already satisfied: setuptools>=18.5 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (39.0.1)\r\nRequirement already satisfied: pyzmq>=2.1.11 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (17.0.0)\r\nRequirement already satisfied: ipython<5.0.0,>=4.0.0 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.2.1)\r\nRequirement already satisfied: ipyparallel>=4.0.0 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (6.1.1)\r\nRequirement already satisfied: netifaces>=0.10.3 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.10.7)\r\nRequirement already satisfied: decorator in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.3.0)\r\nRequirement already satisfied: pickleshare in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.7.4)\r\nRequirement already satisfied: backports.shutil-get-terminal-size; python_version == \"2.7\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (1.0.0)\r\nRequirement already satisfied: simplegeneric>0.8 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.8.1)\r\nRequirement already satisfied: pexpect; sys_platform != \"win32\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.5.0)\r\nRequirement already satisfied: traitlets in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.3.2)\r\nRequirement already satisfied: tornado>=4 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (5.0.2)\r\nRequirement already satisfied: python-dateutil>=2.1 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (2.7.3)\r\nRequirement already satisfied: jupyter-client in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (5.2.3)\r\nRequirement already satisfied: ipykernel in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.8.2)\r\nRequirement already satisfied: ipython-genutils in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.2.0)\r\nRequirement already satisfied: futures; python_version == \"2.7\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (3.2.0)\r\nRequirement already satisfied: pathlib2; python_version in \"2.6 2.7 3.2 3.3\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from pickleshare->ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (2.3.2)\r\nRequirement already satisfied: ptyprocess>=0.5 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from pexpect; sys_platform != \"win32\"->ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.5.2)\r\nRequirement already satisfied: six in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from traitlets->ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (1.11.0)\r\nRequirement already satisfied: enum34; python_version == \"2.7\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from traitlets->ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (1.1.6)\r\nRequirement already satisfied: singledispatch in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from tornado>=4->ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (3.4.0.3)\r\nRequirement already satisfied: backports_abc>=0.4 in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from tornado>=4->ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (0.5)\r\nRequirement already satisfied: jupyter-core in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from jupyter-client->ipyparallel>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (4.4.0)\r\nRequirement already satisfied: scandir; python_version < \"3.5\" in /usr/local/packages/python-2.7.15/lib/python2.7/site-packages (from pathlib2; python_version in \"2.6 2.7 3.2 3.3\"->pickleshare->ipython<5.0.0,>=4.0.0->ipython-cluster-helper==0.5.2->-r requirements.txt (line 2)) (1.7)`\r\n\r\n\r\n\r\nWhen attempting athena_meta install via pip\r\n\r\n` pip -r install -vvv .`\r\n\r\n\r\n`Traceback (most recent call last):\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/site-packages/pip/_internal/utils/outdated.py\", line 140, in pip_version_check\r\n    state.save(pypi_version, current_time)\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/site-packages/pip/_internal/utils/outdated.py\", line 73, in save\r\n    state = json.load(statefile)\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/json/__init__.py\", line 291, in load\r\n    **kw)\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/json/__init__.py\", line 339, in loads\r\n    return _default_decoder.decode(s)\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/json/decoder.py\", line 364, in decode\r\n    obj, end = self.raw_decode(s, idx=_w(s, 0).end())\r\n  File \"/usr/local/packages/python-2.7.15/lib/python2.7/json/decoder.py\", line 382, in raw_decode\r\n    raise ValueError(\"No JSON object could be decoded\")\r\nValueError: No JSON object could be decoded`\r\n"}}
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