Created
May 20, 2016 10:38
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Example of fresh install of pbsmrtpipe and deps in a VE and running the test suite
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| tmp $> cd test-ve/ | |
| test-ve $> virtualenv ve | |
| New python executable in /Users/mkocher/tmp/test-ve/ve/bin/python2.7 | |
| Also creating executable in /Users/mkocher/tmp/test-ve/ve/bin/python | |
| Installing setuptools, pip, wheel...done. | |
| test-ve $> git clone [email protected]:PacificBiosciences/pbsmrtpipe.git | |
| Cloning into 'pbsmrtpipe'... | |
| remote: Counting objects: 6672, done. | |
| remote: Compressing objects: 100% (93/93), done. | |
| remote: Total 6672 (delta 60), reused 0 (delta 0), pack-reused 6579 | |
| Receiving objects: 100% (6672/6672), 3.30 MiB | 874.00 KiB/s, done. | |
| Resolving deltas: 100% (5091/5091), done. | |
| Checking connectivity... done. | |
| test-ve $> source ve/bin/activate | |
| (ve) test-ve $> cd pbsmrtpipe/ | |
| (ve) pbsmrtpipe $> pip install -r PB_REQUIREMENTS.txt | |
| Collecting numpy (from -r PB_REQUIREMENTS.txt (line 1)) | |
| Using cached numpy-1.11.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl | |
| Collecting h5py (from -r PB_REQUIREMENTS.txt (line 2)) | |
| Collecting jinja2 (from -r PB_REQUIREMENTS.txt (line 3)) | |
| Using cached Jinja2-2.8-py2.py3-none-any.whl | |
| Collecting networkx (from -r PB_REQUIREMENTS.txt (line 4)) | |
| Downloading networkx-1.11-py2.py3-none-any.whl (1.3MB) | |
| 100% |████████████████████████████████| 1.3MB 981kB/s | |
| Obtaining pbcore from git+git://github.com/PacificBiosciences/pbcore.git@master#egg=pbcore (from -r PB_REQUIREMENTS.txt (line 6)) | |
| Cloning git://github.com/PacificBiosciences/pbcore.git (to master) to /Users/mkocher/tmp/test-ve/ve/src/pbcore | |
| Obtaining pbcommand from git+git://github.com/PacificBiosciences/pbcommand.git#egg=pbcommand (from -r PB_REQUIREMENTS.txt (line 7)) | |
| Cloning git://github.com/PacificBiosciences/pbcommand.git to /Users/mkocher/tmp/test-ve/ve/src/pbcommand | |
| Obtaining pbcoretools from git+git://github.com/PacificBiosciences/pbcoretools.git#egg=pbcoretools (from -r PB_REQUIREMENTS.txt (line 8)) | |
| Cloning git://github.com/PacificBiosciences/pbcoretools.git to /Users/mkocher/tmp/test-ve/ve/src/pbcoretools | |
| Collecting pyparsing==1.5.7 (from -r PB_REQUIREMENTS.txt (line 9)) | |
| Downloading pyparsing-1.5.7.zip (965kB) | |
| 100% |████████████████████████████████| 972kB 1.3MB/s | |
| Collecting pydot (from -r PB_REQUIREMENTS.txt (line 10)) | |
| Downloading pydot-1.0.29.tar.gz | |
| Collecting jsonschema (from -r PB_REQUIREMENTS.txt (line 11)) | |
| Using cached jsonschema-2.5.1-py2.py3-none-any.whl | |
| Collecting xmlbuilder (from -r PB_REQUIREMENTS.txt (line 12)) | |
| Collecting fabric>=1.9.1 (from -r PB_REQUIREMENTS.txt (line 15)) | |
| Using cached Fabric-1.11.1-py2-none-any.whl | |
| Collecting six (from h5py->-r PB_REQUIREMENTS.txt (line 2)) | |
| Using cached six-1.10.0-py2.py3-none-any.whl | |
| Collecting MarkupSafe (from jinja2->-r PB_REQUIREMENTS.txt (line 3)) | |
| Collecting decorator>=3.4.0 (from networkx->-r PB_REQUIREMENTS.txt (line 4)) | |
| Using cached decorator-4.0.9-py2.py3-none-any.whl | |
| Collecting cython (from pbcore->-r PB_REQUIREMENTS.txt (line 6)) | |
| Using cached Cython-0.24-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl | |
| Collecting pysam>=0.9.0 (from pbcore->-r PB_REQUIREMENTS.txt (line 6)) | |
| Collecting avro (from pbcommand->-r PB_REQUIREMENTS.txt (line 7)) | |
| Collecting requests (from pbcommand->-r PB_REQUIREMENTS.txt (line 7)) | |
| Using cached requests-2.10.0-py2.py3-none-any.whl | |
| Collecting iso8601 (from pbcommand->-r PB_REQUIREMENTS.txt (line 7)) | |
| Using cached iso8601-0.1.11-py2.py3-none-any.whl | |
| Collecting functools32; python_version == "2.7" (from jsonschema->-r PB_REQUIREMENTS.txt (line 11)) | |
| Collecting paramiko<2.0,>=1.10 (from fabric>=1.9.1->-r PB_REQUIREMENTS.txt (line 15)) | |
| Using cached paramiko-1.17.0-py2.py3-none-any.whl | |
| Collecting pycrypto!=2.4,>=2.1 (from paramiko<2.0,>=1.10->fabric>=1.9.1->-r PB_REQUIREMENTS.txt (line 15)) | |
| Collecting ecdsa>=0.11 (from paramiko<2.0,>=1.10->fabric>=1.9.1->-r PB_REQUIREMENTS.txt (line 15)) | |
| Using cached ecdsa-0.13-py2.py3-none-any.whl | |
| Building wheels for collected packages: pyparsing, pydot | |
| Running setup.py bdist_wheel for pyparsing ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/a5/6a/b2/2e2e0422eb4b72ead13570e09a22d6dfdf8219225b4b71bb3e | |
| Running setup.py bdist_wheel for pydot ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/50/4c/a0/58ab4e9d31d798d26bf97bb207d974380051b2586c4a10ddb1 | |
| Successfully built pyparsing pydot | |
| Installing collected packages: numpy, six, h5py, MarkupSafe, jinja2, decorator, networkx, cython, pysam, pbcore, xmlbuilder, functools32, jsonschema, avro, requests, iso8601, pbcommand, pbcoretools, pyparsing, pydot, pycrypto, ecdsa, paramiko, fabric | |
| Running setup.py develop for pbcore | |
| Running setup.py develop for pbcommand | |
| Running setup.py develop for pbcoretools | |
| Successfully installed MarkupSafe-0.23 avro-1.8.0 cython-0.24 decorator-4.0.9 ecdsa-0.13 fabric-1.11.1 functools32-3.2.3.post2 h5py-2.6.0 iso8601-0.1.11 jinja2-2.8 jsonschema-2.5.1 networkx-1.11 numpy-1.11.0 paramiko-1.17.0 pbcommand pbcore pbcoretools pycrypto-2.6.1 pydot-1.0.29 pyparsing-1.5.7 pysam-0.9.0 requests-2.10.0 six-1.10.0 xmlbuilder-1.0 | |
| (ve) pbsmrtpipe $> pip install . | |
| Processing /Users/mkocher/tmp/test-ve/pbsmrtpipe | |
| Requirement already satisfied (use --upgrade to upgrade): jinja2 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): networkx in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pbcore>=1.2.10 in /Users/mkocher/tmp/test-ve/ve/src/pbcore (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pbcommand>=0.3.24 in /Users/mkocher/tmp/test-ve/ve/src/pbcommand (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pyparsing==1.5.7 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pydot in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): jsonschema in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): xmlbuilder in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): requests in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): fabric>=1.9.1 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): MarkupSafe in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from jinja2->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from networkx->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): cython in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcore>=1.2.10->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): numpy>=1.7.1 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcore>=1.2.10->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): h5py>=2.0.1 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcore>=1.2.10->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pysam>=0.9.0 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcore>=1.2.10->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): avro in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcommand>=0.3.24->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): iso8601 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pbcommand>=0.3.24->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): functools32; python_version == "2.7" in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from jsonschema->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): paramiko<2.0,>=1.10 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from fabric>=1.9.1->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): six in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from h5py>=2.0.1->pbcore>=1.2.10->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): pycrypto!=2.4,>=2.1 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from paramiko<2.0,>=1.10->fabric>=1.9.1->pbsmrtpipe==0.40.0) | |
| Requirement already satisfied (use --upgrade to upgrade): ecdsa>=0.11 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from paramiko<2.0,>=1.10->fabric>=1.9.1->pbsmrtpipe==0.40.0) | |
| Installing collected packages: pbsmrtpipe | |
| Running setup.py install for pbsmrtpipe ... done | |
| Successfully installed pbsmrtpipe-0.40.0 | |
| (ve) pbsmrtpipe $> make test-sanity | |
| python -c "import pbsmrtpipe.loader as L; L.load_all()" | |
| nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/tests/test_pb_pipelines_sanity.py | |
| make: nosetests: No such file or directory | |
| make: *** [test-pipelines] Error 1 | |
| (ve) pbsmrtpipe $> pip install -r REQUIREMENTS_DEV.txt | |
| Collecting nose (from -r REQUIREMENTS_DEV.txt (line 1)) | |
| Using cached nose-1.3.7-py2-none-any.whl | |
| Collecting nosexcover (from -r REQUIREMENTS_DEV.txt (line 2)) | |
| Downloading nosexcover-1.0.10.tar.gz | |
| Collecting ipython (from -r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached ipython-4.2.0-py2-none-any.whl | |
| Collecting pyzmq (from -r REQUIREMENTS_DEV.txt (line 4)) | |
| Using cached pyzmq-15.2.0-cp27-none-macosx_10_6_intel.whl | |
| Collecting tornado (from -r REQUIREMENTS_DEV.txt (line 5)) | |
| Collecting pylint (from -r REQUIREMENTS_DEV.txt (line 6)) | |
| Using cached pylint-1.5.5-py2.py3-none-any.whl | |
| Collecting pep8 (from -r REQUIREMENTS_DEV.txt (line 7)) | |
| Using cached pep8-1.7.0-py2.py3-none-any.whl | |
| Collecting autopep8 (from -r REQUIREMENTS_DEV.txt (line 8)) | |
| Collecting rednose (from -r REQUIREMENTS_DEV.txt (line 9)) | |
| Downloading rednose-1.1.1.tar.gz | |
| Collecting ipdb (from -r REQUIREMENTS_DEV.txt (line 10)) | |
| Collecting ipdbplugin (from -r REQUIREMENTS_DEV.txt (line 11)) | |
| Downloading ipdbplugin-1.4.5.tar.gz | |
| Collecting sphinx (from -r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached Sphinx-1.4.1-py2.py3-none-any.whl | |
| Collecting sphinx-bootstrap-theme (from -r REQUIREMENTS_DEV.txt (line 13)) | |
| Downloading sphinx-bootstrap-theme-0.4.9.tar.gz (1.1MB) | |
| 100% |████████████████████████████████| 1.1MB 965kB/s | |
| Collecting mock (from -r REQUIREMENTS_DEV.txt (line 15)) | |
| Downloading mock-2.0.0-py2.py3-none-any.whl (56kB) | |
| 100% |████████████████████████████████| 61kB 3.4MB/s | |
| Collecting coverage>=3.4 (from nosexcover->-r REQUIREMENTS_DEV.txt (line 2)) | |
| Downloading coverage-4.0.3-cp27-none-macosx_10_10_x86_64.whl (158kB) | |
| 100% |████████████████████████████████| 163kB 6.1MB/s | |
| Collecting pickleshare (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached pickleshare-0.7.2-py2.py3-none-any.whl | |
| Collecting simplegeneric>0.8 (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Collecting gnureadline; sys_platform == "darwin" and platform_python_implementation == "CPython" (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached gnureadline-6.3.3-cp27-none-macosx_10_9_x86_64.whl | |
| Collecting backports.shutil-get-terminal-size (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached backports.shutil_get_terminal_size-1.0.0-py2.py3-none-any.whl | |
| Collecting traitlets (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached traitlets-4.2.1-py2.py3-none-any.whl | |
| Collecting pexpect; sys_platform != "win32" (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Requirement already satisfied (use --upgrade to upgrade): decorator in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Requirement already satisfied (use --upgrade to upgrade): setuptools>=18.5 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Collecting appnope; sys_platform == "darwin" (from ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached appnope-0.1.0-py2.py3-none-any.whl | |
| Collecting singledispatch (from tornado->-r REQUIREMENTS_DEV.txt (line 5)) | |
| Using cached singledispatch-3.4.0.3-py2.py3-none-any.whl | |
| Collecting certifi (from tornado->-r REQUIREMENTS_DEV.txt (line 5)) | |
| Using cached certifi-2016.2.28-py2.py3-none-any.whl | |
| Collecting backports-abc>=0.4 (from tornado->-r REQUIREMENTS_DEV.txt (line 5)) | |
| Using cached backports_abc-0.4-py2.py3-none-any.whl | |
| Collecting backports.ssl-match-hostname (from tornado->-r REQUIREMENTS_DEV.txt (line 5)) | |
| Collecting colorama (from pylint->-r REQUIREMENTS_DEV.txt (line 6)) | |
| Using cached colorama-0.3.7-py2.py3-none-any.whl | |
| Collecting astroid<1.5.0,>=1.4.5 (from pylint->-r REQUIREMENTS_DEV.txt (line 6)) | |
| Using cached astroid-1.4.5-py2.py3-none-any.whl | |
| Requirement already satisfied (use --upgrade to upgrade): six in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from pylint->-r REQUIREMENTS_DEV.txt (line 6)) | |
| Collecting python-termstyle>=0.1.7 (from rednose->-r REQUIREMENTS_DEV.txt (line 9)) | |
| Downloading python-termstyle-0.1.10.tar.gz | |
| Collecting docutils>=0.11 (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Downloading docutils-0.12.tar.gz (1.6MB) | |
| 100% |████████████████████████████████| 1.6MB 810kB/s | |
| Collecting Pygments>=2.0 (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached Pygments-2.1.3-py2.py3-none-any.whl | |
| Collecting babel!=2.0,>=1.3 (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached Babel-2.3.4-py2.py3-none-any.whl | |
| Collecting imagesize (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached imagesize-0.7.1-py2.py3-none-any.whl | |
| Requirement already satisfied (use --upgrade to upgrade): Jinja2>=2.3 in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Collecting alabaster<0.8,>=0.7 (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Downloading alabaster-0.7.8-py2.py3-none-any.whl | |
| Collecting snowballstemmer>=1.1 (from sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached snowballstemmer-1.2.1-py2.py3-none-any.whl | |
| Collecting funcsigs>=1; python_version < "3.3" (from mock->-r REQUIREMENTS_DEV.txt (line 15)) | |
| Downloading funcsigs-1.0.2-py2.py3-none-any.whl | |
| Collecting pbr>=0.11 (from mock->-r REQUIREMENTS_DEV.txt (line 15)) | |
| Downloading pbr-1.9.1-py2.py3-none-any.whl (96kB) | |
| 100% |████████████████████████████████| 102kB 7.8MB/s | |
| Collecting pathlib2; python_version in "2.6 2.7 3.2 3.3" (from pickleshare->ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached pathlib2-2.1.0-py2.py3-none-any.whl | |
| Collecting ipython-genutils (from traitlets->ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached ipython_genutils-0.1.0-py2.py3-none-any.whl | |
| Collecting ptyprocess>=0.5 (from pexpect; sys_platform != "win32"->ipython->-r REQUIREMENTS_DEV.txt (line 3)) | |
| Using cached ptyprocess-0.5.1-py2.py3-none-any.whl | |
| Collecting lazy-object-proxy (from astroid<1.5.0,>=1.4.5->pylint->-r REQUIREMENTS_DEV.txt (line 6)) | |
| Collecting wrapt (from astroid<1.5.0,>=1.4.5->pylint->-r REQUIREMENTS_DEV.txt (line 6)) | |
| Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Using cached pytz-2016.4-py2.py3-none-any.whl | |
| Requirement already satisfied (use --upgrade to upgrade): MarkupSafe in /Users/mkocher/tmp/test-ve/ve/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r REQUIREMENTS_DEV.txt (line 12)) | |
| Building wheels for collected packages: nosexcover, rednose, ipdbplugin, sphinx-bootstrap-theme, python-termstyle, docutils | |
| Running setup.py bdist_wheel for nosexcover ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/7f/0b/ca/e0b9157a5fa42051b33db99abc9243976a97cce2a671096f35 | |
| Running setup.py bdist_wheel for rednose ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/cb/d1/0a/4097180851284b5fa4a882f1836e02823f192a3c996f9577d0 | |
| Running setup.py bdist_wheel for ipdbplugin ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/36/4b/04/296a8d14cd3641bb80bf90ab7daa138c1b06b0cd4c9e701bd2 | |
| Running setup.py bdist_wheel for sphinx-bootstrap-theme ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/3c/91/df/ccd9118f6a6eaacb37d35989c3ced5a039b91452beaf7b4030 | |
| Running setup.py bdist_wheel for python-termstyle ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/1c/e4/f2/9debde18c5d514f1746df68c36a255c2e1d0c21172dc0c8e7d | |
| Running setup.py bdist_wheel for docutils ... done | |
| Stored in directory: /Users/mkocher/Library/Caches/pip/wheels/db/de/bd/b99b1e12d321fbc950766c58894c6576b1a73ae3131b29a151 | |
| Successfully built nosexcover rednose ipdbplugin sphinx-bootstrap-theme python-termstyle docutils | |
| Installing collected packages: nose, coverage, nosexcover, pathlib2, pickleshare, simplegeneric, gnureadline, backports.shutil-get-terminal-size, ipython-genutils, traitlets, ptyprocess, pexpect, appnope, ipython, pyzmq, singledispatch, certifi, backports-abc, backports.ssl-match-hostname, tornado, colorama, lazy-object-proxy, wrapt, astroid, pylint, pep8, autopep8, python-termstyle, rednose, ipdb, ipdbplugin, docutils, Pygments, pytz, babel, imagesize, alabaster, snowballstemmer, sphinx, sphinx-bootstrap-theme, funcsigs, pbr, mock | |
| Successfully installed Pygments-2.1.3 alabaster-0.7.8 appnope-0.1.0 astroid-1.4.5 autopep8-1.2.2 babel-2.3.4 backports-abc-0.4 backports.shutil-get-terminal-size-1.0.0 backports.ssl-match-hostname-3.5.0.1 certifi-2016.2.28 colorama-0.3.7 coverage-4.0.3 docutils-0.12 funcsigs-1.0.2 gnureadline-6.3.3 imagesize-0.7.1 ipdb-0.10.0 ipdbplugin-1.4.5 ipython-4.2.0 ipython-genutils-0.1.0 lazy-object-proxy-1.2.2 mock-2.0.0 nose-1.3.7 nosexcover-1.0.10 pathlib2-2.1.0 pbr-1.9.1 pep8-1.7.0 pexpect-4.0.1 pickleshare-0.7.2 ptyprocess-0.5.1 pylint-1.5.5 python-termstyle-0.1.10 pytz-2016.4 pyzmq-15.2.0 rednose-1.1.1 simplegeneric-0.8.1 singledispatch-3.4.0.3 snowballstemmer-1.2.1 sphinx-1.4.1 sphinx-bootstrap-theme-0.4.9 tornado-4.3 traitlets-4.2.1 wrapt-1.10.8 | |
| (ve) pbsmrtpipe $> make test-sanity | |
| python -c "import pbsmrtpipe.loader as L; L.load_all()" | |
| nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/tests/test_pb_pipelines_sanity.py | |
| Test that all pipelines are well defined ... ok | |
| ---------------------------------------------------------------------- | |
| Ran 1 test in 1.179s | |
| OK | |
| python -c "import pbsmrtpipe.loader as L; L.load_and_validate_chunk_operators()" | |
| python -c "import pbsmrtpipe.loader as L; L.load_all()" | |
| mkdir -p extras/pipeline-templates-avro | |
| pbsmrtpipe show-templates --output-templates-avro extras/pipeline-templates-avro | |
| ************************************ | |
| 48 Registered Pipelines (name -> id) | |
| ************************************ | |
| 1. Example Dev 01 pipeline pbsmrtpipe.pipelines.dev_01 | |
| 2. Example Dev 01 Subread DataSet pipeline pbsmrtpipe.pipelines.dev_01_ds | |
| 3. Example Dev 01 crashing pipeline pbsmrtpipe.pipelines.dev_01_fail | |
| 4. Example Dev 02 pipeline pbsmrtpipe.pipelines.dev_02 | |
| 5. Example Dev 03 pipelines pbsmrtpipe.pipelines.dev_03 | |
| 6. Example Dev 04 pbsmrtpipe.pipelines.dev_04 | |
| 7. Pipeline that leverages a python static tasks pbsmrtpipe.pipelines.dev_04_w_static_task | |
| 8. Reference Set Report pbsmrtpipe.pipelines.dev_diagnostic | |
| 9. Dev Hello Distributed Workflow Pipeline pbsmrtpipe.pipelines.dev_dist | |
| 10. Dev Local Hello Pipeline pbsmrtpipe.pipelines.dev_local | |
| 11. Dev Local Hello Chunkable Pipeline pbsmrtpipe.pipelines.dev_local_chunk | |
| 12. Dev local Task for Chunking pipelines pbsmrtpipe.pipelines.dev_local_fasta_chunk | |
| 13. Base Modification Detection pbsmrtpipe.pipelines.ds_modification_detection | |
| 14. Base Modification and Motif Analysis pbsmrtpipe.pipelines.ds_modification_motif_analysis | |
| 15. XI- Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_cmd | |
| 16. X - Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_lean | |
| 17. Internal Condition JSON Dev Test pbsmrtpipe.pipelines.internal_cond_dev | |
| 18. Internal Condition JSON Dev Test 2 pbsmrtpipe.pipelines.internal_cond_dev2 | |
| 19. Internal Consensus Read Mapping pbsmrtpipe.pipelines.pb_ccs_align | |
| 20. Internal CCS Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_ccs | |
| 21. Internal LAA Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_laa | |
| 22. Internal Iso-Seq pipeline pbsmrtpipe.pipelines.pb_isoseq | |
| 23. Internal Iso-Seq clustering pipeline pbsmrtpipe.pipelines.pb_isoseq_cluster | |
| 24. PacBio Internal Modification Analysis pbsmrtpipe.pipelines.pb_modification_detection | |
| 25. PacBio Internal Modification and Motif Analysis pbsmrtpipe.pipelines.pb_modification_motif_analysis | |
| 26. Falcon Pipeline pbsmrtpipe.pipelines.pipe_falcon | |
| 27. Falcon FOFN Pipeline pbsmrtpipe.pipelines.pipe_falcon_with_fofn | |
| 28. Polished Falcon Pipeline pbsmrtpipe.pipelines.polished_falcon | |
| 29. Assembly (HGAP 4) pbsmrtpipe.pipelines.polished_falcon_fat | |
| 30. Assembly (HGAP 4) without reports pbsmrtpipe.pipelines.polished_falcon_lean | |
| 31. RS movie Align pbsmrtpipe.pipelines.sa3_align | |
| 32. SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align | |
| 33. Unrolled Template SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align_unrolled | |
| 34. Barcoding pbsmrtpipe.pipelines.sa3_ds_barcode | |
| 35. Circular Consensus Sequences (CCS 2) pbsmrtpipe.pipelines.sa3_ds_ccs | |
| 36. CCS Mapping pbsmrtpipe.pipelines.sa3_ds_ccs_align | |
| 37. Convert FASTA to ReferenceSet pbsmrtpipe.pipelines.sa3_ds_fasta_to_reference | |
| 38. Genomic Consensus pbsmrtpipe.pipelines.sa3_ds_genomic_consensus | |
| 39. Iso-Seq pbsmrtpipe.pipelines.sa3_ds_isoseq | |
| 40. Iso-Seq Classify Only pbsmrtpipe.pipelines.sa3_ds_isoseq_classify | |
| 41. Long Amplicon Analysis (LAA 2) pbsmrtpipe.pipelines.sa3_ds_laa | |
| 42. Basic Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing | |
| 43. Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing_fat | |
| 44. Convert BAM to FASTX pbsmrtpipe.pipelines.sa3_ds_subreads_to_fastx | |
| 45. RS Movie to Subread DataSet pbsmrtpipe.pipelines.sa3_fetch | |
| 46. Convert RS to BAM pbsmrtpipe.pipelines.sa3_hdfsubread_to_subread | |
| 47. RS movie Resequencing pbsmrtpipe.pipelines.sa3_resequencing | |
| 48. Site Acceptance Test (SAT) pbsmrtpipe.pipelines.sa3_sat | |
| mkdir -p extras/pipeline-templates-json | |
| pbsmrtpipe show-templates --output-templates-json extras/pipeline-templates-json | |
| ************************************ | |
| 48 Registered Pipelines (name -> id) | |
| ************************************ | |
| 1. Example Dev 01 pipeline pbsmrtpipe.pipelines.dev_01 | |
| 2. Example Dev 01 Subread DataSet pipeline pbsmrtpipe.pipelines.dev_01_ds | |
| 3. Example Dev 01 crashing pipeline pbsmrtpipe.pipelines.dev_01_fail | |
| 4. Example Dev 02 pipeline pbsmrtpipe.pipelines.dev_02 | |
| 5. Example Dev 03 pipelines pbsmrtpipe.pipelines.dev_03 | |
| 6. Example Dev 04 pbsmrtpipe.pipelines.dev_04 | |
| 7. Pipeline that leverages a python static tasks pbsmrtpipe.pipelines.dev_04_w_static_task | |
| 8. Reference Set Report pbsmrtpipe.pipelines.dev_diagnostic | |
| 9. Dev Hello Distributed Workflow Pipeline pbsmrtpipe.pipelines.dev_dist | |
| 10. Dev Local Hello Pipeline pbsmrtpipe.pipelines.dev_local | |
| 11. Dev Local Hello Chunkable Pipeline pbsmrtpipe.pipelines.dev_local_chunk | |
| 12. Dev local Task for Chunking pipelines pbsmrtpipe.pipelines.dev_local_fasta_chunk | |
| 13. Base Modification Detection pbsmrtpipe.pipelines.ds_modification_detection | |
| 14. Base Modification and Motif Analysis pbsmrtpipe.pipelines.ds_modification_motif_analysis | |
| 15. XI- Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_cmd | |
| 16. X - Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_lean | |
| 17. Internal Condition JSON Dev Test pbsmrtpipe.pipelines.internal_cond_dev | |
| 18. Internal Condition JSON Dev Test 2 pbsmrtpipe.pipelines.internal_cond_dev2 | |
| 19. Internal Consensus Read Mapping pbsmrtpipe.pipelines.pb_ccs_align | |
| 20. Internal CCS Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_ccs | |
| 21. Internal LAA Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_laa | |
| 22. Internal Iso-Seq pipeline pbsmrtpipe.pipelines.pb_isoseq | |
| 23. Internal Iso-Seq clustering pipeline pbsmrtpipe.pipelines.pb_isoseq_cluster | |
| 24. PacBio Internal Modification Analysis pbsmrtpipe.pipelines.pb_modification_detection | |
| 25. PacBio Internal Modification and Motif Analysis pbsmrtpipe.pipelines.pb_modification_motif_analysis | |
| 26. Falcon Pipeline pbsmrtpipe.pipelines.pipe_falcon | |
| 27. Falcon FOFN Pipeline pbsmrtpipe.pipelines.pipe_falcon_with_fofn | |
| 28. Polished Falcon Pipeline pbsmrtpipe.pipelines.polished_falcon | |
| 29. Assembly (HGAP 4) pbsmrtpipe.pipelines.polished_falcon_fat | |
| 30. Assembly (HGAP 4) without reports pbsmrtpipe.pipelines.polished_falcon_lean | |
| 31. RS movie Align pbsmrtpipe.pipelines.sa3_align | |
| 32. SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align | |
| 33. Unrolled Template SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align_unrolled | |
| 34. Barcoding pbsmrtpipe.pipelines.sa3_ds_barcode | |
| 35. Circular Consensus Sequences (CCS 2) pbsmrtpipe.pipelines.sa3_ds_ccs | |
| 36. CCS Mapping pbsmrtpipe.pipelines.sa3_ds_ccs_align | |
| 37. Convert FASTA to ReferenceSet pbsmrtpipe.pipelines.sa3_ds_fasta_to_reference | |
| 38. Genomic Consensus pbsmrtpipe.pipelines.sa3_ds_genomic_consensus | |
| 39. Iso-Seq pbsmrtpipe.pipelines.sa3_ds_isoseq | |
| 40. Iso-Seq Classify Only pbsmrtpipe.pipelines.sa3_ds_isoseq_classify | |
| 41. Long Amplicon Analysis (LAA 2) pbsmrtpipe.pipelines.sa3_ds_laa | |
| 42. Basic Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing | |
| 43. Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing_fat | |
| 44. Convert BAM to FASTX pbsmrtpipe.pipelines.sa3_ds_subreads_to_fastx | |
| 45. RS Movie to Subread DataSet pbsmrtpipe.pipelines.sa3_fetch | |
| 46. Convert RS to BAM pbsmrtpipe.pipelines.sa3_hdfsubread_to_subread | |
| 47. RS movie Resequencing pbsmrtpipe.pipelines.sa3_resequencing | |
| 48. Site Acceptance Test (SAT) pbsmrtpipe.pipelines.sa3_sat | |
| (ve) pbsmrtpipe $> make test-suite | |
| python -c "import pbsmrtpipe.loader as L; L.load_all()" | |
| nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/tests/test_pb_pipelines_sanity.py | |
| Test that all pipelines are well defined ... ok | |
| ---------------------------------------------------------------------- | |
| Ran 1 test in 1.190s | |
| OK | |
| python -c "import pbsmrtpipe.loader as L; L.load_and_validate_chunk_operators()" | |
| python -c "import pbsmrtpipe.loader as L; L.load_all()" | |
| mkdir -p extras/pipeline-templates-avro | |
| pbsmrtpipe show-templates --output-templates-avro extras/pipeline-templates-avro | |
| ************************************ | |
| 48 Registered Pipelines (name -> id) | |
| ************************************ | |
| 1. Example Dev 01 pipeline pbsmrtpipe.pipelines.dev_01 | |
| 2. Example Dev 01 Subread DataSet pipeline pbsmrtpipe.pipelines.dev_01_ds | |
| 3. Example Dev 01 crashing pipeline pbsmrtpipe.pipelines.dev_01_fail | |
| 4. Example Dev 02 pipeline pbsmrtpipe.pipelines.dev_02 | |
| 5. Example Dev 03 pipelines pbsmrtpipe.pipelines.dev_03 | |
| 6. Example Dev 04 pbsmrtpipe.pipelines.dev_04 | |
| 7. Pipeline that leverages a python static tasks pbsmrtpipe.pipelines.dev_04_w_static_task | |
| 8. Reference Set Report pbsmrtpipe.pipelines.dev_diagnostic | |
| 9. Dev Hello Distributed Workflow Pipeline pbsmrtpipe.pipelines.dev_dist | |
| 10. Dev Local Hello Pipeline pbsmrtpipe.pipelines.dev_local | |
| 11. Dev Local Hello Chunkable Pipeline pbsmrtpipe.pipelines.dev_local_chunk | |
| 12. Dev local Task for Chunking pipelines pbsmrtpipe.pipelines.dev_local_fasta_chunk | |
| 13. Base Modification Detection pbsmrtpipe.pipelines.ds_modification_detection | |
| 14. Base Modification and Motif Analysis pbsmrtpipe.pipelines.ds_modification_motif_analysis | |
| 15. XI- Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_cmd | |
| 16. X - Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_lean | |
| 17. Internal Condition JSON Dev Test pbsmrtpipe.pipelines.internal_cond_dev | |
| 18. Internal Condition JSON Dev Test 2 pbsmrtpipe.pipelines.internal_cond_dev2 | |
| 19. Internal Consensus Read Mapping pbsmrtpipe.pipelines.pb_ccs_align | |
| 20. Internal CCS Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_ccs | |
| 21. Internal LAA Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_laa | |
| 22. Internal Iso-Seq pipeline pbsmrtpipe.pipelines.pb_isoseq | |
| 23. Internal Iso-Seq clustering pipeline pbsmrtpipe.pipelines.pb_isoseq_cluster | |
| 24. PacBio Internal Modification Analysis pbsmrtpipe.pipelines.pb_modification_detection | |
| 25. PacBio Internal Modification and Motif Analysis pbsmrtpipe.pipelines.pb_modification_motif_analysis | |
| 26. Falcon Pipeline pbsmrtpipe.pipelines.pipe_falcon | |
| 27. Falcon FOFN Pipeline pbsmrtpipe.pipelines.pipe_falcon_with_fofn | |
| 28. Polished Falcon Pipeline pbsmrtpipe.pipelines.polished_falcon | |
| 29. Assembly (HGAP 4) pbsmrtpipe.pipelines.polished_falcon_fat | |
| 30. Assembly (HGAP 4) without reports pbsmrtpipe.pipelines.polished_falcon_lean | |
| 31. RS movie Align pbsmrtpipe.pipelines.sa3_align | |
| 32. SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align | |
| 33. Unrolled Template SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align_unrolled | |
| 34. Barcoding pbsmrtpipe.pipelines.sa3_ds_barcode | |
| 35. Circular Consensus Sequences (CCS 2) pbsmrtpipe.pipelines.sa3_ds_ccs | |
| 36. CCS Mapping pbsmrtpipe.pipelines.sa3_ds_ccs_align | |
| 37. Convert FASTA to ReferenceSet pbsmrtpipe.pipelines.sa3_ds_fasta_to_reference | |
| 38. Genomic Consensus pbsmrtpipe.pipelines.sa3_ds_genomic_consensus | |
| 39. Iso-Seq pbsmrtpipe.pipelines.sa3_ds_isoseq | |
| 40. Iso-Seq Classify Only pbsmrtpipe.pipelines.sa3_ds_isoseq_classify | |
| 41. Long Amplicon Analysis (LAA 2) pbsmrtpipe.pipelines.sa3_ds_laa | |
| 42. Basic Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing | |
| 43. Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing_fat | |
| 44. Convert BAM to FASTX pbsmrtpipe.pipelines.sa3_ds_subreads_to_fastx | |
| 45. RS Movie to Subread DataSet pbsmrtpipe.pipelines.sa3_fetch | |
| 46. Convert RS to BAM pbsmrtpipe.pipelines.sa3_hdfsubread_to_subread | |
| 47. RS movie Resequencing pbsmrtpipe.pipelines.sa3_resequencing | |
| 48. Site Acceptance Test (SAT) pbsmrtpipe.pipelines.sa3_sat | |
| mkdir -p extras/pipeline-templates-json | |
| pbsmrtpipe show-templates --output-templates-json extras/pipeline-templates-json | |
| ************************************ | |
| 48 Registered Pipelines (name -> id) | |
| ************************************ | |
| 1. Example Dev 01 pipeline pbsmrtpipe.pipelines.dev_01 | |
| 2. Example Dev 01 Subread DataSet pipeline pbsmrtpipe.pipelines.dev_01_ds | |
| 3. Example Dev 01 crashing pipeline pbsmrtpipe.pipelines.dev_01_fail | |
| 4. Example Dev 02 pipeline pbsmrtpipe.pipelines.dev_02 | |
| 5. Example Dev 03 pipelines pbsmrtpipe.pipelines.dev_03 | |
| 6. Example Dev 04 pbsmrtpipe.pipelines.dev_04 | |
| 7. Pipeline that leverages a python static tasks pbsmrtpipe.pipelines.dev_04_w_static_task | |
| 8. Reference Set Report pbsmrtpipe.pipelines.dev_diagnostic | |
| 9. Dev Hello Distributed Workflow Pipeline pbsmrtpipe.pipelines.dev_dist | |
| 10. Dev Local Hello Pipeline pbsmrtpipe.pipelines.dev_local | |
| 11. Dev Local Hello Chunkable Pipeline pbsmrtpipe.pipelines.dev_local_chunk | |
| 12. Dev local Task for Chunking pipelines pbsmrtpipe.pipelines.dev_local_fasta_chunk | |
| 13. Base Modification Detection pbsmrtpipe.pipelines.ds_modification_detection | |
| 14. Base Modification and Motif Analysis pbsmrtpipe.pipelines.ds_modification_motif_analysis | |
| 15. XI- Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_cmd | |
| 16. X - Experimental Assembly (HGAP 5) without reports pbsmrtpipe.pipelines.hgap_lean | |
| 17. Internal Condition JSON Dev Test pbsmrtpipe.pipelines.internal_cond_dev | |
| 18. Internal Condition JSON Dev Test 2 pbsmrtpipe.pipelines.internal_cond_dev2 | |
| 19. Internal Consensus Read Mapping pbsmrtpipe.pipelines.pb_ccs_align | |
| 20. Internal CCS Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_ccs | |
| 21. Internal LAA Pipeline with SubreadSet Barcoding pbsmrtpipe.pipelines.pb_ds_barcode_laa | |
| 22. Internal Iso-Seq pipeline pbsmrtpipe.pipelines.pb_isoseq | |
| 23. Internal Iso-Seq clustering pipeline pbsmrtpipe.pipelines.pb_isoseq_cluster | |
| 24. PacBio Internal Modification Analysis pbsmrtpipe.pipelines.pb_modification_detection | |
| 25. PacBio Internal Modification and Motif Analysis pbsmrtpipe.pipelines.pb_modification_motif_analysis | |
| 26. Falcon Pipeline pbsmrtpipe.pipelines.pipe_falcon | |
| 27. Falcon FOFN Pipeline pbsmrtpipe.pipelines.pipe_falcon_with_fofn | |
| 28. Polished Falcon Pipeline pbsmrtpipe.pipelines.polished_falcon | |
| 29. Assembly (HGAP 4) pbsmrtpipe.pipelines.polished_falcon_fat | |
| 30. Assembly (HGAP 4) without reports pbsmrtpipe.pipelines.polished_falcon_lean | |
| 31. RS movie Align pbsmrtpipe.pipelines.sa3_align | |
| 32. SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align | |
| 33. Unrolled Template SubreadSet Mapping pbsmrtpipe.pipelines.sa3_ds_align_unrolled | |
| 34. Barcoding pbsmrtpipe.pipelines.sa3_ds_barcode | |
| 35. Circular Consensus Sequences (CCS 2) pbsmrtpipe.pipelines.sa3_ds_ccs | |
| 36. CCS Mapping pbsmrtpipe.pipelines.sa3_ds_ccs_align | |
| 37. Convert FASTA to ReferenceSet pbsmrtpipe.pipelines.sa3_ds_fasta_to_reference | |
| 38. Genomic Consensus pbsmrtpipe.pipelines.sa3_ds_genomic_consensus | |
| 39. Iso-Seq pbsmrtpipe.pipelines.sa3_ds_isoseq | |
| 40. Iso-Seq Classify Only pbsmrtpipe.pipelines.sa3_ds_isoseq_classify | |
| 41. Long Amplicon Analysis (LAA 2) pbsmrtpipe.pipelines.sa3_ds_laa | |
| 42. Basic Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing | |
| 43. Resequencing pbsmrtpipe.pipelines.sa3_ds_resequencing_fat | |
| 44. Convert BAM to FASTX pbsmrtpipe.pipelines.sa3_ds_subreads_to_fastx | |
| 45. RS Movie to Subread DataSet pbsmrtpipe.pipelines.sa3_fetch | |
| 46. Convert RS to BAM pbsmrtpipe.pipelines.sa3_hdfsubread_to_subread | |
| 47. RS movie Resequencing pbsmrtpipe.pipelines.sa3_resequencing | |
| 48. Site Acceptance Test (SAT) pbsmrtpipe.pipelines.sa3_sat | |
| nosetests --verbose --with-xunit --logging-conf nose.cfg pbsmrtpipe/pb_tasks/tests/*.py pbsmrtpipe/tests/test_*.py | |
| test_run_e2e (test_dev_simple.PbTestApp) ... ok | |
| test_run_e2e (test_dev_simple.TestDevSimpleTaskDefaults) ... ok | |
| test_run_e2e (test_dev_simple.TestTestDevSimpleTask) ... ok | |
| test_binding_format (test_bgraph.TestBindingFormat) ... ok | |
| test_binding_str_format (test_bgraph.TestBindingFormat) ... ok | |
| test_to_xml (test_bgraph.TestConvertBindingStrToXml) ... ok | |
| test_basic (test_cluster.TestCluster) ... ok | |
| test_load_cluster_templates (test_cluster.TestCluster) ... ok | |
| test_load_templates (test_cluster.TestCluster) ... ok | |
| test_render_cluster_templates (test_cluster.TestCluster) ... ok | |
| test_cluster_template_bad_template_type (test_cluster.TestClusterTemplate) ... ok | |
| test_cluster_template_str (test_cluster.TestClusterTemplate) ... ok | |
| test_validate_load_by_python_module_name (test_cluster.TestValidateClusterTemplate) ... ok | |
| test_validate_pbs_relative_path (test_cluster.TestValidateClusterTemplate) ... ok | |
| test_validate_sge_pacbio_relative_path (test_cluster.TestValidateClusterTemplate) ... ok | |
| test_validate_sge_relative_path (test_cluster.TestValidateClusterTemplate) ... ok | |
| test_hello (test_cluster_templates.TestHelloClusterWorld) ... SKIP: Cluster is not accessible | |
| test_sanity (test_cluster_templates.TestInstalledClusterTemplates) ... ok | |
| Crude cram-esque test test if installed pbsmrtpipe exe's are ... ok | |
| test_01 (test_dataset_io.DatasetFastaTest) ... ok | |
| test_01 (test_dataset_io.DatasetFastqTest) ... ok | |
| test_01 (test_dataset_io.DatasetFofnTest) ... ok | |
| test_01 (test_dataset_io.DatasetRegionFofnTest) ... ok | |
| test_01 (test_dataset_io.DatasetRegionMovieFofnTest) ... ok | |
| test_run_driver (test_driver.LocalHelloDevTest) ... ok | |
| test_run_driver (test_driver.MyTest) ... SKIP: No qsub exe found. | |
| test_cluster_pool (test_engine.TestClusterProcessPoolManager) ... SKIP: Unable to find cluster exe 'qsub' | |
| test_backticks (test_engine.TestUtilFuncs) ... ok | |
| test_convert_dot_to_svg (test_external_tools.TestExternalTools) ... ok | |
| test_hello_world_job (test_integration.TestHelloWorldCluster) ... SKIP: Cluster is not accessible | |
| test_run (test_integration.TestHelloWorldDistributed) ... SKIP: No qsub exe found. | |
| test_run (test_integration.TestHelloWorldWorkflow) ... ok | |
| test_help (test_integration.TestIntegrationHelp) ... ok | |
| test_run (test_integration_dev.Dev01DriverIntegration) ... ok | |
| test_run (test_integration_dev.Dev01FailureModeIntegration) ... ok | |
| test_run (test_integration_dev.Dev02DriverIntegration) ... ok | |
| test_run (test_integration_dev.Dev02FailureModeIntegration) ... ok | |
| test_run (test_integration_dev.Dev03DriverIntegration) ... ok | |
| test_run (test_integration_dev.Dev04DriverIntegration) ... ok | |
| test_run (test_integration_dev.DevDistDriverIntegration) ... SKIP: No qsub exe found. | |
| test_run (test_integration_dev.DevLocalChunkDriverIntegration) ... SKIP: No qsub exe found. | |
| test_run (test_integration_dev.DevLocalDriverIntegration) ... ok | |
| test_run (test_integration_dev.DevLocalWithStaticTaskDriverIntegration) ... ok | |
| test_loading (test_operators.TestLoadingOperators) ... ok | |
| test_nbindings (test_pb_io.TestBindingParsing) ... ok | |
| test_sanity_load_installed_operators (test_pb_io.TestLoadOperators) ... ok | |
| test_01 (test_pb_io.TestParsingFetchPresetXml) ... ok | |
| test_to_dict (test_pb_io.TestParsingFetchPresetXml) ... ok | |
| test_to_wopts (test_pb_io.TestParsingFetchPresetXml) ... ok | |
| test_workflow_level_opts_from_defaults (test_pb_io.TestParsingFetchPresetXml) ... ok | |
| test_workflow_level_opts_from_dict (test_pb_io.TestParsingFetchPresetXml) ... ok | |
| test_01 (test_pb_io.TestParsingPresetXml) ... ok | |
| test_to_dict (test_pb_io.TestParsingPresetXml) ... ok | |
| test_to_wopts (test_pb_io.TestParsingPresetXml) ... ok | |
| test_workflow_level_opts_from_defaults (test_pb_io.TestParsingPresetXml) ... ok | |
| test_workflow_level_opts_from_dict (test_pb_io.TestParsingPresetXml) ... ok | |
| test_load_preset (test_pb_io.TestWriteSchemaOptsToXML) ... ok | |
| test_to_xml (test_pb_io.TestWriteSchemaOptsToXML) ... ok | |
| Test that all pipelines are well defined ... ok | |
| test_load_static_tasks (test_pb_task_static_sanity.TestSanity) ... ok | |
| test_file_type_eq (test_pb_tasks_core.TestLoading) ... ok | |
| test_loading_di_tasks (test_pb_tasks_core.TestLoading) ... ok | |
| test_task_manifest_serialization (test_pb_tasks_core.TestLoading) ... ok | |
| test_01 (test_report_renderer.TestCliReportRender) ... SKIP: Pbreports is not installed. | |
| test_01 (test_report_renderer.TestRenderReportIndex) ... SKIP: Pbreports is not installed. | |
| test_01 (test_schemas.TestPipelinTemplate) ... ok | |
| test_sanity_dynamic_task_loading (test_task_sanity.TestDynamicTaskLoading) ... ok | |
| test_parsing_cfg_to_butler (test_testkit_butler.TestParsingButlerTaskCfg) ... ok | |
| test_parsing_cfg_to_butler (test_testkit_butler.TestParsingButlerWorkflowCfg) ... ok | |
| test_parsing_cfg_to_butler (test_testkit_butler.TestParsingButlerWorkflowCfgWithPrefix) ... ok | |
| test_parsing_preset_xml (test_testkit_butler.TestParsingButlerWorkflowCfgWithPrefix) ... ok | |
| test_01 (test_tools_runner.TestHelloRunnableTask) ... ok | |
| test_01 (test_tools_runner.TestRunnableTask) ... ok | |
| test_can_find_and_load_template (test_utils.TestLoadJinjaTemplate) ... ok | |
| test_bad_which (test_utils.TestUtils) ... SKIP: Unable to find test /pbi/dept/secondary/siv/testdata | |
| test_which (test_utils.TestUtils) ... SKIP: Unable to find test /pbi/dept/secondary/siv/testdata | |
| test_version (test_version.TestVersion) ... ok | |
| ---------------------------------------------------------------------- | |
| XML: /Users/mkocher/tmp/test-ve/pbsmrtpipe/nosetests.xml | |
| ---------------------------------------------------------------------- | |
| Ran 77 tests in 61.368s | |
| OK (SKIP=11) | |
| cd testkit-data && fab cleaner && pbtestkit-multirunner --debug --nworkers 8 dev.fofn | |
| Found 13 job dirs. Cleaned 0 job dirs. | |
| Done. | |
| [INFO] 2016-05-20 10:36:21,763Z [pbsmrtpipe.testkit.multirunner _pacbio_main_runner 128] Using pbcommand v0.3.25 | |
| [INFO] 2016-05-20 10:36:21,763Z [pbsmrtpipe.testkit.multirunner _pacbio_main_runner 129] completed setting up logger with <function setup_log at 0x101248320> | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _pacbio_main_runner 130] log opts {'file_name': None, 'level': 10} | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 50] Parsed file /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev.fofn. Found 7 configs. | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01_ds/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_03/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_04/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_diagnostic/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_chunk/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner _testkit_cfg_fofn_to_files 52] /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_fasta_chunk/testkit.cfg | |
| [INFO] 2016-05-20 10:36:21,764Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 96] Starting with nworkers 7 and 7 butler cfg files | |
| [DEBUG] 2016-05-20 10:36:21,781Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,782Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01_ds/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,782Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_03/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,782Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_04/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,783Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_diagnostic/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,783Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_chunk/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:21,783Z [pbsmrtpipe.engine backticks 45] Running on Michaels-MacBook-Pro.local with cmd 'pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_fasta_chunk/testkit.cfg' | |
| [DEBUG] 2016-05-20 10:36:25,562Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 3.78 sec (0.06 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_diagnostic/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:25,579Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 3.80 sec (0.06 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01_ds/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:29,619Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 7.84 sec (0.13 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_chunk/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:29,621Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 7.84 sec (0.13 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_03/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:29,672Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 7.89 sec (0.13 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:31,618Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 9.84 sec (0.16 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_04/testkit.cfg | |
| [DEBUG] 2016-05-20 10:36:49,704Z [pbsmrtpipe.engine backticks 66] Successful output (Return code = 0) in 27.92 sec (0.47 min) of pbtestkit-runner --debug /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_fasta_chunk/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 123] Results: | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 7 sec (0.13 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 3 sec (0.06 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_01_ds/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 7 sec (0.13 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_03/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 9 sec (0.16 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_04/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 3 sec (0.06 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_diagnostic/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 7 sec (0.13 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_chunk/testkit.cfg | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 126] exit code 0 in 27 sec (0.47 min). job /Users/mkocher/tmp/test-ve/pbsmrtpipe/testkit-data/dev_local_fasta_chunk/testkit.cfg | |
| Completed 7 jobs in 27 sec (0.47 min) 0 failed. | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner run_testkit_cfgs 136] Completed 7 jobs in 27 sec (0.47 min) 0 failed. | |
| [INFO] 2016-05-20 10:36:49,751Z [pbsmrtpipe.testkit.multirunner _pacbio_main_runner 153] exiting with return code 0 in 27.99 sec. | |
| (ve) pbsmrtpipe $> |
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I see your installation has 11 tiemes skips. IS your installation correct ? How about your test with your own sequel cell data,such as CCS ,Isoseq?