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gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
39 stars 21 forks source link

Conflicting requirements: setuptools<=39.1.0 required by mmsplice, >=41.0.0 required by tensorflow #16

Closed PikalaxALT closed 5 years ago

PikalaxALT commented 5 years ago

Description

Installing mmsplice via pip

What I Did

$ pip install mmsplice
Collecting mmsplice
  Downloading https://files.pythonhosted.org/packages/75/67/c04e48b46c8d32f948b7d4ccd84ef28f209c64fb6986fe776bc989e47cc9/mmsplice-0.2.7-py2.py3-none-any.whl (450kB)
     |████████████████████████████████| 460kB 8.9MB/s
Collecting pyfaidx (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/75/a5/7e2569527b3849ea28d79b4f70d7cf46a47d36459bc59e0efa4e10e8c8b2/pyfaidx-0.5.5.2.tar.gz
Collecting tqdm (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/9f/3d/7a6b68b631d2ab54975f3a4863f3c4e9b26445353264ef01f465dc9b0208/tqdm-4.32.2-py2.py3-none-any.whl (50kB)
     |████████████████████████████████| 51kB 7.9MB/s
Collecting tensorflow (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/de/f0/96fb2e0412ae9692dbf400e5b04432885f677ad6241c088ccc5fe7724d69/tensorflow-1.14.0-cp36-cp36m-manylinux1_x86_64.whl (109.2MB)
     |████████████████████████████████| 109.2MB 27.5MB/s
Collecting setuptools<=39.1.0 (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/8c/10/79282747f9169f21c053c562a0baa21815a8c7879be97abd930dbcf862e8/setuptools-39.1.0-py2.py3-none-any.whl (566kB)
     |████████████████████████████████| 573kB 13.2MB/s
Requirement already satisfied: pandas in ./MAJIQ_2.0/lib/python3.6/site-packages (from mmsplice) (0.24.1)
Collecting sklearn (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/1e/7a/dbb3be0ce9bd5c8b7e3d87328e79063f8b263b2b1bfa4774cb1147bfcd3f/sklearn-0.0.tar.gz
Collecting concise (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/73/06/9b680a74cd7bc682c6da7da04704af89b4ea0eb635d917615e0c7401a686/concise-0.6.6.tar.gz (11.3MB)
     |████████████████████████████████| 11.3MB 14.9MB/s
Collecting cyvcf2==0.9.0 (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/3f/21/29c8dc12e91d55e953f230bf9e96af779b224f6d59f4eacc3dcb80753d34/cyvcf2-0.9.0.tar.gz (1.2MB)
     |████████████████████████████████| 1.2MB 9.6MB/s
Collecting keras (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl (312kB)
     |████████████████████████████████| 317kB 21.5MB/s
Collecting kipoi>=0.4.1 (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/93/df/469e851e562855b69c1c47ca801a14fdd82cd8cc2be9158c07f347635cfd/kipoi-0.6.16-py3-none-any.whl (101kB)
     |████████████████████████████████| 102kB 6.5MB/s
Requirement already satisfied: click in ./MAJIQ_2.0/lib/python3.6/site-packages (from mmsplice) (7.0)
Collecting gffutils (from mmsplice)
  Downloading https://files.pythonhosted.org/packages/b4/ea/54ca403a8d471849606fb432b9afcf73c8c5105ea2dd87b8d38bd5217c5a/gffutils-0.9.tar.gz (1.5MB)
     |████████████████████████████████| 1.5MB 11.4MB/s
Requirement already satisfied: six in ./MAJIQ_2.0/lib/python3.6/site-packages (from pyfaidx->mmsplice) (1.11.0)
Collecting protobuf>=3.6.1 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/dc/0e/e7cdff89745986c984ba58e6ff6541bc5c388dd9ab9d7d312b3b1532584a/protobuf-3.9.0-cp36-cp36m-manylinux1_x86_64.whl (1.2MB)
     |████████████████████████████████| 1.2MB 22.6MB/s
Collecting termcolor>=1.1.0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz
Collecting wheel>=0.26 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/bb/10/44230dd6bf3563b8f227dbf344c908d412ad2ff48066476672f3a72e174e/wheel-0.33.4-py2.py3-none-any.whl
Collecting tensorflow-estimator<1.15.0rc0,>=1.14.0rc0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/3c/d5/21860a5b11caf0678fbc8319341b0ae21a07156911132e0e71bffed0510d/tensorflow_estimator-1.14.0-py2.py3-none-any.whl (488kB)
     |████████████████████████████████| 491kB 22.5MB/s
Collecting grpcio>=1.8.6 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/f2/5d/b434403adb2db8853a97828d3d19f2032e79d630e0d11a8e95d243103a11/grpcio-1.22.0-cp36-cp36m-manylinux1_x86_64.whl (2.2MB)
     |████████████████████████████████| 2.2MB 23.4MB/s
Collecting wrapt>=1.11.1 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/23/84/323c2415280bc4fc880ac5050dddfb3c8062c2552b34c2e512eb4aa68f79/wrapt-1.11.2.tar.gz
Collecting tensorboard<1.15.0,>=1.14.0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/91/2d/2ed263449a078cd9c8a9ba50ebd50123adf1f8cfbea1492f9084169b89d9/tensorboard-1.14.0-py3-none-any.whl (3.1MB)
     |████████████████████████████████| 3.2MB 23.8MB/s
Collecting google-pasta>=0.1.6 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/d0/33/376510eb8d6246f3c30545f416b2263eee461e40940c2a4413c711bdf62d/google_pasta-0.1.7-py3-none-any.whl (52kB)
     |████████████████████████████████| 61kB 9.9MB/s
Collecting gast>=0.2.0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/4e/35/11749bf99b2d4e3cceb4d55ca22590b0d7c2c62b9de38ac4a4a7f4687421/gast-0.2.2.tar.gz
Collecting absl-py>=0.7.0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/da/3f/9b0355080b81b15ba6a9ffcf1f5ea39e307a2778b2f2dc8694724e8abd5b/absl-py-0.7.1.tar.gz (99kB)
     |████████████████████████████████| 102kB 9.3MB/s
Requirement already satisfied: numpy<2.0,>=1.14.5 in ./MAJIQ_2.0/lib/python3.6/site-packages (from tensorflow->mmsplice) (1.16.4)
Collecting keras-preprocessing>=1.0.5 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41kB)
     |████████████████████████████████| 51kB 9.5MB/s
Collecting keras-applications>=1.0.6 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl (50kB)
     |████████████████████████████████| 51kB 9.7MB/s
Collecting astor>=0.6.0 (from tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/d1/4f/950dfae467b384fc96bc6469de25d832534f6b4441033c39f914efd13418/astor-0.8.0-py2.py3-none-any.whl
Requirement already satisfied: pytz>=2011k in ./MAJIQ_2.0/lib/python3.6/site-packages (from pandas->mmsplice) (2018.9)
Requirement already satisfied: python-dateutil>=2.5.0 in ./MAJIQ_2.0/lib/python3.6/site-packages (from pandas->mmsplice) (2.7.5)
Requirement already satisfied: scikit-learn in ./MAJIQ_2.0/lib/python3.6/site-packages (from sklearn->mmsplice) (0.21.2)
Requirement already satisfied: scipy in ./MAJIQ_2.0/lib/python3.6/site-packages (from concise->mmsplice) (1.3.0)
Requirement already satisfied: matplotlib in ./MAJIQ_2.0/lib/python3.6/site-packages (from concise->mmsplice) (3.1.1)
Collecting hyperopt (from concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/63/12/704382c3081df3ae3f9d96fe6afb62efa2fa9749be20c301cd2797fb0b52/hyperopt-0.1.2-py3-none-any.whl (115kB)
     |████████████████████████████████| 122kB 25.4MB/s
Collecting descartes (from concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/e5/b6/1ed2eb03989ae574584664985367ba70cd9cf8b32ee8cad0e8aaeac819f3/descartes-1.1.0-py3-none-any.whl
Collecting shapely (from concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/38/b6/b53f19062afd49bb5abd049aeed36f13bf8d57ef8f3fa07a5203531a0252/Shapely-1.6.4.post2-cp36-cp36m-manylinux1_x86_64.whl (1.5MB)
     |████████████████████████████████| 1.5MB 24.3MB/s
Collecting gtfparse>=1.0.7 (from concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/41/5c/8bd2e9020051ccffc60c56ae70b32a3b649ddac1962e9aa641f93542440e/gtfparse-1.2.0.tar.gz
Requirement already satisfied: h5py in ./MAJIQ_2.0/lib/python3.6/site-packages (from keras->mmsplice) (2.9.0)
Collecting pyyaml (from keras->mmsplice)
  Downloading https://files.pythonhosted.org/packages/a3/65/837fefac7475963d1eccf4aa684c23b95aa6c1d033a2c5965ccb11e22623/PyYAML-5.1.1.tar.gz (274kB)
     |████████████████████████████████| 276kB 24.2MB/s
Collecting future (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/90/52/e20466b85000a181e1e144fd8305caf2cf475e2f9674e797b222f8105f5f/future-0.17.1.tar.gz (829kB)
     |████████████████████████████████| 829kB 23.9MB/s
Requirement already satisfied: jinja2 in ./MAJIQ_2.0/lib/python3.6/site-packages (from kipoi>=0.4.1->mmsplice) (2.10)
Collecting kipoi-utils>=0.1.12 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/8b/84/cfee68e16d4120d5eb23eb6ee67b34f81cbaf1c77d0a60acb6e25a19ff27/kipoi_utils-0.1.12-py3-none-any.whl
Collecting attrs>=17.4.0 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Requirement already satisfied: urllib3>=1.21.1 in ./MAJIQ_2.0/lib/python3.6/site-packages (from kipoi>=0.4.1->mmsplice) (1.24.1)
Collecting deprecation>=2.0.6 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/32/e9/01ffbaf3540ad54476cd7066439d629f1dd73b851cc5c0993ce2c12e1cdd/deprecation-2.0.6-py2.py3-none-any.whl
Collecting related>=0.6.0 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/23/6e/5419d1364d9c408cb4943d1301800bf88b8d91e034c355448b00440ca202/related-0.7.2-py2.py3-none-any.whl
Collecting kipoi-conda>=0.1.6 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/4c/ec/f9436cad99756e2f9981f1ceaba5452257563174c59d785e782d4d981857/kipoi_conda-0.1.6-py3-none-any.whl
Collecting enum34 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/af/42/cb9355df32c69b553e72a2e28daee25d1611d2c0d9c272aa1d34204205b2/enum34-1.1.6-py3-none-any.whl
Collecting colorlog (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/68/4d/892728b0c14547224f0ac40884e722a3d00cb54e7a146aea0b3186806c9e/colorlog-4.0.2-py2.py3-none-any.whl
Collecting cookiecutter>=1.6.0 (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/16/99/1ca3a75978270288354f419e9166666801cf7e7d8df984de44a7d5d8b8d0/cookiecutter-1.6.0-py2.py3-none-any.whl (50kB)
     |████████████████████████████████| 51kB 9.6MB/s
Collecting tinydb (from kipoi>=0.4.1->mmsplice)
  Downloading https://files.pythonhosted.org/packages/d7/f9/0e871cbf0da678cf1780609dc6aef26a5ed544c86733fc1ceaf134fce52c/tinydb-3.13.0-py2.py3-none-any.whl
Collecting argh (from gffutils->mmsplice)
  Downloading https://files.pythonhosted.org/packages/06/1c/e667a7126f0b84aaa1c56844337bf0ac12445d1beb9c8a6199a7314944bf/argh-0.26.2-py2.py3-none-any.whl
Collecting argcomplete (from gffutils->mmsplice)
  Downloading https://files.pythonhosted.org/packages/4d/82/f44c9661e479207348a979b1f6f063625d11dc4ca6256af053719bbb0124/argcomplete-1.10.0-py2.py3-none-any.whl
Collecting simplejson (from gffutils->mmsplice)
  Downloading https://files.pythonhosted.org/packages/e3/24/c35fb1c1c315fc0fffe61ea00d3f88e85469004713dab488dee4f35b0aff/simplejson-3.16.0.tar.gz (81kB)
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Requirement already satisfied: werkzeug>=0.11.15 in ./MAJIQ_2.0/lib/python3.6/site-packages (from tensorboard<1.15.0,>=1.14.0->tensorflow->mmsplice) (0.14.1)
Collecting markdown>=2.6.8 (from tensorboard<1.15.0,>=1.14.0->tensorflow->mmsplice)
  Downloading https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl (87kB)
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Requirement already satisfied: joblib>=0.11 in ./MAJIQ_2.0/lib/python3.6/site-packages (from scikit-learn->sklearn->mmsplice) (0.13.2)
Requirement already satisfied: cycler>=0.10 in ./MAJIQ_2.0/lib/python3.6/site-packages (from matplotlib->concise->mmsplice) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./MAJIQ_2.0/lib/python3.6/site-packages (from matplotlib->concise->mmsplice) (1.0.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./MAJIQ_2.0/lib/python3.6/site-packages (from matplotlib->concise->mmsplice) (2.3.0)
Collecting pymongo (from hyperopt->concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/fb/4a/586826433281ca285f0201235fccf63cc29a30fa78bcd72b6a34e365972d/pymongo-3.8.0-cp36-cp36m-manylinux1_x86_64.whl (416kB)
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Collecting networkx (from hyperopt->concise->mmsplice)
  Downloading https://files.pythonhosted.org/packages/85/08/f20aef11d4c343b557e5de6b9548761811eb16e438cee3d32b1c66c8566b/networkx-2.3.zip (1.7MB)
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Requirement already satisfied: MarkupSafe>=0.23 in ./MAJIQ_2.0/lib/python3.6/site-packages (from jinja2->kipoi>=0.4.1->mmsplice) (1.1.0)
Requirement already satisfied: packaging in ./MAJIQ_2.0/lib/python3.6/site-packages (from deprecation>=2.0.6->kipoi>=0.4.1->mmsplice) (19.0)
Collecting binaryornot>=0.2.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting whichcraft>=0.4.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Requirement already satisfied: requests>=2.18.0 in ./MAJIQ_2.0/lib/python3.6/site-packages (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) (2.21.0)
Collecting poyo>=0.1.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting jinja2-time>=0.1.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Requirement already satisfied: idna<2.9,>=2.5 in ./MAJIQ_2.0/lib/python3.6/site-packages (from requests>=2.18.0->cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) (2.8)
Requirement already satisfied: certifi>=2017.4.17 in ./MAJIQ_2.0/lib/python3.6/site-packages (from requests>=2.18.0->cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) (2018.11.29)
Collecting arrow (from jinja2-time>=0.1.0->cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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<font color=red>ERROR: tensorboard 1.14.0 has requirement setuptools>=41.0.0, but you'll have setuptools 39.1.0 which is incompatible.</font>
Installing collected packages: setuptools, pyfaidx, tqdm, protobuf, termcolor, wheel, tensorflow-estimator, grpcio, wrapt, absl-py, markdown, tensorboard, google-pasta, gast, keras-preprocessing, keras-applications, astor, tensorflow, sklearn, pyyaml, keras, future, pymongo, networkx, hyperopt, descartes, shapely, gtfparse, concise, cyvcf2, attrs, related, kipoi-utils, deprecation, kipoi-conda, enum34, colorlog, binaryornot, whichcraft, poyo, arrow, jinja2-time, cookiecutter, tinydb, kipoi, argh, argcomplete, simplejson, gffutils, mmsplice
  Found existing installation: setuptools 40.9.0
    Uninstalling setuptools-40.9.0:
      Successfully uninstalled setuptools-40.9.0
  Running setup.py install for pyfaidx ... done
  Running setup.py install for termcolor ... done
  Running setup.py install for wrapt ... done
  Running setup.py install for absl-py ... done
  Running setup.py install for gast ... done
  Running setup.py install for sklearn ... done
  Running setup.py install for pyyaml ... done
  Running setup.py install for future ... done
  Running setup.py install for networkx ... done
  Running setup.py install for gtfparse ... done
  Running setup.py install for concise ... done
  Running setup.py install for cyvcf2 ... done
  Running setup.py install for simplejson ... done
  Running setup.py install for gffutils ... done
Successfully installed absl-py-0.7.1 argcomplete-1.10.0 argh-0.26.2 arrow-0.14.2 astor-0.8.0 attrs-19.1.0 binaryornot-0.4.4 colorlog-4.0.2 concise-0.6.6 cookiecutter-1.6.0 cyvcf2-0.9.0 deprecation-2.0.6 descartes-1.1.0 enum34-1.1.6 future-0.17.1 gast-0.2.2 gffutils-0.9 google-pasta-0.1.7 grpcio-1.22.0 gtfparse-1.2.0 hyperopt-0.1.2 jinja2-time-0.2.0 keras-2.2.4 keras-applications-1.0.8 keras-preprocessing-1.1.0 kipoi-0.6.16 kipoi-conda-0.1.6 kipoi-utils-0.1.12 markdown-3.1.1 mmsplice-0.2.7 networkx-2.3 poyo-0.4.2 protobuf-3.9.0 pyfaidx-0.5.5.2 pymongo-3.8.0 pyyaml-5.1.1 related-0.7.2 setuptools-39.1.0 shapely-1.6.4.post2 simplejson-3.16.0 sklearn-0.0 tensorboard-1.14.0 tensorflow-1.14.0 tensorflow-estimator-1.14.0 termcolor-1.1.0 tinydb-3.13.0 tqdm-4.32.2 wheel-0.33.4 whichcraft-0.5.2 wrapt-1.11.2
s6juncheng commented 5 years ago

thanks @PikalaxALT, we will fix this in the next release. Can you successfully install MMSplice?

MuhammedHasan commented 5 years ago

Thanks for reporting the issue.

Latest release of mmsplice==1.0.1 should fix the problem.