Closed PikalaxALT closed 5 years ago
Installing mmsplice via pip
$ 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) |████████████████████████████████| 81kB 12.3MB/s 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) |████████████████████████████████| 92kB 13.7MB/s 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) |████████████████████████████████| 419kB 23.3MB/s Collecting networkx (from hyperopt->concise->mmsplice) Downloading https://files.pythonhosted.org/packages/85/08/f20aef11d4c343b557e5de6b9548761811eb16e438cee3d32b1c66c8566b/networkx-2.3.zip (1.7MB) |████████████████████████████████| 1.8MB 23.8MB/s 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) Downloading https://files.pythonhosted.org/packages/24/7e/f7b6f453e6481d1e233540262ccbfcf89adcd43606f44a028d7f5fae5eb2/binaryornot-0.4.4-py2.py3-none-any.whl Collecting whichcraft>=0.4.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) Downloading https://files.pythonhosted.org/packages/ab/c6/eb4d1dfbb68168bb01c4394420e5e71d5851e64b910838aa0f14ebd5c7a0/whichcraft-0.5.2-py2.py3-none-any.whl 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) Downloading https://files.pythonhosted.org/packages/e0/16/e00e3001007a5e416ca6a51def6f9e4be6a774bf1c8486d20466f834d113/poyo-0.4.2-py2.py3-none-any.whl Collecting jinja2-time>=0.1.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) Downloading https://files.pythonhosted.org/packages/6a/a1/d44fa38306ffa34a7e1af09632b158e13ec89670ce491f8a15af3ebcb4e4/jinja2_time-0.2.0-py2.py3-none-any.whl Requirement already satisfied: decorator>=4.3.0 in ./MAJIQ_2.0/lib/python3.6/site-packages (from networkx->hyperopt->concise->mmsplice) (4.3.2) Requirement already satisfied: chardet>=3.0.2 in ./MAJIQ_2.0/lib/python3.6/site-packages (from binaryornot>=0.2.0->cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice) (3.0.4) 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) Downloading https://files.pythonhosted.org/packages/a2/6a/a3d20e80ee4fee7c55c022fb28d52239bd01171edd3c137dd1e2ef8b2a20/arrow-0.14.2-py2.py3-none-any.whl <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
thanks @PikalaxALT, we will fix this in the next release. Can you successfully install MMSplice?
Thanks for reporting the issue.
Latest release of mmsplice==1.0.1 should fix the problem.
Description
Installing mmsplice via pip
What I Did