diff --git a/README.md b/README.md index 9811174390375bcb786a66a8f544704d29b89f4e..1bffb13f8be7a53605aec4f83b9a796c54104e0f 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,14 @@ Hub-CDB Institut Pasteur & DSI Institut Pasteur Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below +### v8.6 + +Dockerfiles added: <br /> +python\v3.6.8\base\v1.0 at date 20220504: FROM python:3.6.8 +python\v3.6.8\serpentine\v1.0 at date 20220504: from gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6 +python\v3.9.10\extended\v3.0 at date 20220504: from gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 with cyvcf2 package added + + ### v8.5 Dockerfiles added: <br /> diff --git a/python/v3.6.8/base/v1.0/Dockerfile b/python/v3.6.8/base/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..1a8705a9512b1b2f9225f4f4f7fa10e5095882d0 --- /dev/null +++ b/python/v3.6.8/base/v1.0/Dockerfile @@ -0,0 +1,41 @@ +######################################################################### +## ## +## Dockerfile ## +## Python base ## +## ## +## Gael A. Millot ## +## Bioinformatics and Biostatistics Hub ## +## Computational Biology Department ## +## Institut Pasteur Paris ## +## ## +######################################################################### + + +# to see the log of the building: +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# cat building.log + +# to export the log file of the image building from the container: +# sudo docker images +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# exit +# sudo docker container ls -a # to get all the active containers +# sudo docker cp <containerNAMES>:/building.log </host/path/target> + + +FROM python:3.6.8 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +RUN echo "\n\n\n\n================\n\nPIP PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \ + && pip list >> /building.log \ + # end install the packages + # inactivated packages because are in the base installation + +ENV LC_ALL en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV LC_NUMERIC en_US.UTF-8 + +ENTRYPOINT ["/usr/bin/python3"] diff --git a/python/v3.6.8/base/v1.0/building2.log b/python/v3.6.8/base/v1.0/building2.log new file mode 100644 index 0000000000000000000000000000000000000000..351b98876835574d8b35401c80b065882c0a4930 --- /dev/null +++ b/python/v3.6.8/base/v1.0/building2.log @@ -0,0 +1,137 @@ +#1 [internal] load build definition from Dockerfile +#1 sha256:1ea32d86db224fe297045bfb80357f4217a800e82f1fdc735891b1461725280f +#1 transferring dockerfile: 1.79kB 0.0s done +#1 DONE 0.0s + +#2 [internal] load .dockerignore +#2 sha256:4140a9584d4f6b0cdf93cbff20f793bf39e878d6446d620dfd716ef73ca26d17 +#2 transferring context: 2B done +#2 DONE 0.0s + +#3 [internal] load metadata for docker.io/library/python:3.6.8 +#3 sha256:ee07e0303bd08c1ee97b32d9c6ade02e5edf0a355cb184d0a9e362c7a86561c4 +#3 ... + +#4 [auth] library/python:pull token for registry-1.docker.io +#4 sha256:1667b51744f495e1f87951272c53e4a1369ee8c3d8085f136095b4b1fab857d1 +#4 DONE 0.0s + +#3 [internal] load metadata for docker.io/library/python:3.6.8 +#3 sha256:ee07e0303bd08c1ee97b32d9c6ade02e5edf0a355cb184d0a9e362c7a86561c4 +#3 DONE 1.4s + +#5 [1/2] FROM docker.io/library/python:3.6.8@sha256:f20a9bfddd87c238c3d2316b4179222f219090cbb25d5b6975070d4dd4b75004 +#5 sha256:bd1d82c5fd332f4f14b23d3d0a3e51068fdcf785aae752b0001a2022490a20da +#5 resolve docker.io/library/python:3.6.8@sha256:f20a9bfddd87c238c3d2316b4179222f219090cbb25d5b6975070d4dd4b75004 done +#5 sha256:f20a9bfddd87c238c3d2316b4179222f219090cbb25d5b6975070d4dd4b75004 2.38kB / 2.38kB done +#5 sha256:48c06762acf0bb8fa6a7f10686f3430cc3d149cf798556c138a82ded6c61e438 7.38kB / 7.38kB done +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 0B / 45.34MB 0.1s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 0B / 10.79MB 0.1s +#5 sha256:e2b625c433e2e3c9a72eb92483c7e6ebe32163e320258f6a60badc44d9eb2806 2.22kB / 2.22kB done +#5 sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab 0B / 4.34MB 0.1s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 3.15MB / 45.34MB 0.2s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 6.29MB / 45.34MB 0.3s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 9.44MB / 45.34MB 0.5s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 1.05MB / 10.79MB 0.5s +#5 sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab 3.15MB / 4.34MB 0.5s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 3.15MB / 10.79MB 0.6s +#5 sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab 4.19MB / 4.34MB 0.6s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 13.63MB / 45.34MB 0.7s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 5.24MB / 10.79MB 0.7s +#5 sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab 4.34MB / 4.34MB 0.7s done +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 0B / 50.07MB 0.7s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 17.83MB / 45.34MB 0.9s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 9.44MB / 10.79MB 0.9s +#5 sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 10.79MB / 10.79MB 1.0s done +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 3.15MB / 50.07MB 1.0s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 0B / 215.08MB 1.0s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 22.02MB / 45.34MB 1.1s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 25.17MB / 45.34MB 1.3s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 8.39MB / 50.07MB 1.3s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 28.31MB / 45.34MB 1.5s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 11.53MB / 50.07MB 1.5s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 32.51MB / 45.34MB 1.8s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 15.73MB / 50.07MB 1.8s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 11.53MB / 215.08MB 1.9s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 35.65MB / 45.34MB 2.0s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 18.87MB / 50.07MB 2.0s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 38.80MB / 45.34MB 2.2s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 22.02MB / 50.07MB 2.2s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 42.99MB / 45.34MB 2.5s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 26.21MB / 50.07MB 2.5s +#5 sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 45.34MB / 45.34MB 2.6s done +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 30.41MB / 50.07MB 2.7s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 24.12MB / 215.08MB 2.7s +#5 extracting sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 0.1s +#5 sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 0B / 5.75MB 2.7s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 34.60MB / 50.07MB 2.9s +#5 sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 2.10MB / 5.75MB 3.0s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 37.75MB / 50.07MB 3.1s +#5 sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 3.15MB / 5.75MB 3.1s +#5 sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 4.19MB / 5.75MB 3.2s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 40.89MB / 50.07MB 3.3s +#5 sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 5.75MB / 5.75MB 3.2s done +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 0B / 20.98MB 3.3s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 36.70MB / 215.08MB 3.4s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 44.04MB / 50.07MB 3.5s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 47.19MB / 50.07MB 3.7s +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 4.19MB / 20.98MB 3.7s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 50.07MB / 50.07MB 3.9s +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 7.34MB / 20.98MB 3.9s +#5 sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 50.07MB / 50.07MB 3.9s done +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 9.44MB / 20.98MB 4.0s +#5 sha256:ad0713808ef687d1e541819f50497506f5dce12604d1af54dbae153d61d5cf21 0B / 240B 4.0s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 48.23MB / 215.08MB 4.1s +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 11.53MB / 20.98MB 4.1s +#5 sha256:ad0713808ef687d1e541819f50497506f5dce12604d1af54dbae153d61d5cf21 240B / 240B 4.0s done +#5 sha256:7ba59390457320287875a9c381fee7936b50ecfd21abfe3c50278ac2f39b9786 0B / 1.82MB 4.1s +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 13.63MB / 20.98MB 4.2s +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 16.78MB / 20.98MB 4.4s +#5 sha256:7ba59390457320287875a9c381fee7936b50ecfd21abfe3c50278ac2f39b9786 1.82MB / 1.82MB 4.3s done +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 19.92MB / 20.98MB 4.5s +#5 extracting sha256:6f2f362378c5a6fd915d96d11dda1e0223ccf213bf121ace56ae0f6616ea1dc8 1.8s done +#5 sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 20.98MB / 20.98MB 4.6s done +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 63.96MB / 215.08MB 4.7s +#5 extracting sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e +#5 extracting sha256:494c27a8a6b820f9167ec7e368b3a9bb47d7029f4dc8c97c67091f3757a5bc4e 0.3s done +#5 extracting sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 77.59MB / 215.08MB 5.2s +#5 extracting sha256:7596bb83081b6c8410df557d538a0ae45922cbf81e469c6f4cfa835247cb24ab 0.2s done +#5 extracting sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 89.13MB / 215.08MB 6.3s +#5 extracting sha256:372744b62d49eba993652ee4a1201801fe278b687d85489101e07e7b9a4900e0 2.0s done +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 100.66MB / 215.08MB 7.7s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 113.25MB / 215.08MB 8.4s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 124.78MB / 215.08MB 9.9s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 138.41MB / 215.08MB 10.5s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 150.99MB / 215.08MB 11.6s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 163.58MB / 215.08MB 12.5s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 175.11MB / 215.08MB 13.0s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 188.74MB / 215.08MB 13.5s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 200.28MB / 215.08MB 14.2s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 215.08MB / 215.08MB 14.9s +#5 sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 215.08MB / 215.08MB 15.0s done +#5 extracting sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 +#5 extracting sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 5.1s +#5 extracting sha256:615db220d76c063138a2e6c5849703a7a80d682a682f7e1a841e6e7ed5f43879 6.8s done +#5 extracting sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e +#5 extracting sha256:1865698adfb04b47d1aa53e0f8dac0a511d78285cb4dda39b4f3b0b3b091bb2e 0.2s done +#5 extracting sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 +#5 extracting sha256:7159b3304cc0ff68a7903c2660aa37fdae97a02164449400c6ef283a6aaf3879 0.7s done +#5 extracting sha256:ad0713808ef687d1e541819f50497506f5dce12604d1af54dbae153d61d5cf21 done +#5 extracting sha256:7ba59390457320287875a9c381fee7936b50ecfd21abfe3c50278ac2f39b9786 +#5 extracting sha256:7ba59390457320287875a9c381fee7936b50ecfd21abfe3c50278ac2f39b9786 0.1s done +#5 DONE 23.3s + +#6 [2/2] RUN echo "\n\n\n\n================\n\nPIP PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log && pip list >> /building.log ENV LC_ALL en_US.UTF-8 +#6 sha256:a378f6322ddb7d1a3630e088674cbf0828d5a6a881068098789bcf350b01ec49 +#6 1.167 WARNING: You are using pip version 19.1.1, however version 21.3.1 is available. +#6 1.167 You should consider upgrading via the 'pip install --upgrade pip' command. +#6 DONE 1.6s + +#7 exporting to image +#7 sha256:e8c613e07b0b7ff33893b694f7759a10d42e180f2b4dc349fb57dc6b71dcab00 +#7 exporting layers 0.1s done +#7 writing image sha256:c254f2d4e4274928cf226aacd0202206da862df9e2f26f188be9e91e443fbbef done +#7 naming to docker.io/gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6 done +#7 DONE 0.1s diff --git a/python/v3.6.8/serpentine/v1.0/Dockerfile b/python/v3.6.8/serpentine/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..d9bfb54d5eb012cca174762e435ad39c096a16e3 --- /dev/null +++ b/python/v3.6.8/serpentine/v1.0/Dockerfile @@ -0,0 +1,51 @@ +######################################################################### +## ## +## Dockerfile ## +## Python Serpentine ## +## ## +## Gael A. Millot ## +## Bioinformatics and Biostatistics Hub ## +## Computational Biology Department ## +## Institut Pasteur Paris ## +## ## +######################################################################### + + +# to see the log of the building: +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# cat building.log + +# to export the log file of the image building from the container: +# sudo docker images +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# exit +# sudo docker container ls -a # to get all the active containers +# sudo docker cp <containerNAMES>:/building.log </host/path/target> + + +FROM gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENV PY_LIB="\ + numpy \ + pandas \ + python-dateutil \ + serpentine \ +" + + # install the packages +RUN echo "\n\n\n\n================\n\npip install\n\n================\n\n\n\n" > /building.log \ + && pip install $PY_LIB | tee -a /building.log \ + && echo "\n\n\n\n================\n\nPIP PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \ + && pip list >> /building.log \ + # end install the packages + # inactivated packages because are in the base installation + +ENV LC_ALL en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV LC_NUMERIC en_US.UTF-8 + +ENTRYPOINT ["/usr/bin/python3"] diff --git a/python/v3.6.8/serpentine/v1.0/building2.log b/python/v3.6.8/serpentine/v1.0/building2.log new file mode 100644 index 0000000000000000000000000000000000000000..82a2b1722bebeef57ff561c0b123d673f5391453 --- /dev/null +++ b/python/v3.6.8/serpentine/v1.0/building2.log @@ -0,0 +1,69 @@ +#1 [internal] load build definition from Dockerfile +#1 sha256:802ecf842ea158e19ad9ba548a328ee0935ea8461d681647109ff69d721fa95c +#1 transferring dockerfile: 2.04kB done +#1 DONE 0.0s + +#2 [internal] load .dockerignore +#2 sha256:d7e5947f6e6e366ab2b4550e1a5f2c3102b993ab9a47646fbc83eb92d70d0800 +#2 transferring context: 2B done +#2 DONE 0.0s + +#3 [internal] load metadata for docker.io/gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6 +#3 sha256:b33fb8206f76ae5277e0b7a6b7832917f038f6329acdcc9d5d94ced4b75de867 +#3 DONE 0.0s + +#4 [1/2] FROM docker.io/gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6 +#4 sha256:8bf9463c98b06add90fdabce14f04cb3bd6309d32bfeeffe6e8e94f3a9677ccf +#4 DONE 0.0s + +#5 [2/2] RUN echo "\n\n\n\n================\n\npip install\n\n================\n\n\n\n" > /building.log && pip install numpy pandas python-dateutil serpentine | tee -a /building.log && echo "\n\n\n\n================\n\nPIP PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log && pip list >> /building.log ENV LC_ALL en_US.UTF-8 +#5 sha256:318f4b1ddaad250e573f4eb75f894bac720550ae59380bc9f95a3d6bdae0ebba +#5 0.468 Collecting numpy +#5 1.045 Downloading https://files.pythonhosted.org/packages/14/32/d3fa649ad7ec0b82737b92fefd3c4dd376b0bb23730715124569f38f3a08/numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8MB) +#5 1.656 Collecting pandas +#5 1.952 Downloading https://files.pythonhosted.org/packages/c3/e2/00cacecafbab071c787019f00ad84ca3185952f6bb9bca9550ed83870d4d/pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5MB) +#5 2.425 Collecting python-dateutil +#5 2.453 Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247kB) +#5 2.469 Collecting serpentine +#5 2.565 Downloading https://files.pythonhosted.org/packages/d8/a4/09b9d406ef9c0d03358349cb6ed3dc8bdfe33b9c33be236509cc57e9690c/serpentine-0.1.3-py3-none-any.whl +#5 2.576 Collecting pytz>=2017.2 (from pandas) +#5 2.721 Downloading https://files.pythonhosted.org/packages/60/2e/dec1cc18c51b8df33c7c4d0a321b084cf38e1733b98f9d15018880fb4970/pytz-2022.1-py2.py3-none-any.whl (503kB) +#5 2.806 Collecting six>=1.5 (from python-dateutil) +#5 2.832 Downloading https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl +#5 2.840 Collecting docopt (from serpentine) +#5 2.859 Downloading https://files.pythonhosted.org/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz +#5 3.153 Collecting scipy (from serpentine) +#5 3.455 Downloading https://files.pythonhosted.org/packages/c8/89/63171228d5ced148f5ced50305c89e8576ffc695a90b58fe5bb602b910c2/scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9MB) +#5 4.472 Collecting matplotlib (from serpentine) +#5 4.732 Downloading https://files.pythonhosted.org/packages/09/03/b7b30fa81cb687d1178e085d0f01111ceaea3bf81f9330c937fb6f6c8ca0/matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5MB) +#5 5.190 Collecting pillow>=6.2.0 (from matplotlib->serpentine) +#5 5.681 Downloading https://files.pythonhosted.org/packages/7d/2a/2fc11b54e2742db06297f7fa7f420a0e3069fdcf0e4b57dfec33f0b08622/Pillow-8.4.0.tar.gz (49.4MB) +#5 7.849 Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 (from matplotlib->serpentine) +#5 7.936 Downloading https://files.pythonhosted.org/packages/d9/41/d9cfb4410589805cd787f8a82cddd13142d9bf7449d12adf2d05a4a7d633/pyparsing-3.0.8-py3-none-any.whl (98kB) +#5 7.952 Collecting kiwisolver>=1.0.1 (from matplotlib->serpentine) +#5 8.047 Downloading https://files.pythonhosted.org/packages/a7/1b/cbd8ae738719b5f41592a12057ef5442e2ed5f5cb5451f8fc7e9f8875a1a/kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1MB) +#5 8.096 Collecting cycler>=0.10 (from matplotlib->serpentine) +#5 8.111 Downloading https://files.pythonhosted.org/packages/5c/f9/695d6bedebd747e5eb0fe8fad57b72fdf25411273a39791cde838d5a8f51/cycler-0.11.0-py3-none-any.whl +#5 8.118 Building wheels for collected packages: docopt, pillow +#5 8.118 Building wheel for docopt (setup.py): started +#5 8.359 Building wheel for docopt (setup.py): finished with status 'done' +#5 8.360 Stored in directory: /root/.cache/pip/wheels/9b/04/dd/7daf4150b6d9b12949298737de9431a324d4b797ffd63f526e +#5 8.365 Building wheel for pillow (setup.py): started +#5 22.71 Building wheel for pillow (setup.py): finished with status 'done' +#5 22.71 Stored in directory: /root/.cache/pip/wheels/a7/69/9a/bba9fca6782340f88dbc378893095722a663cbc618e58fe401 +#5 22.79 Successfully built docopt pillow +#5 22.81 Installing collected packages: numpy, pytz, six, python-dateutil, pandas, docopt, scipy, pillow, pyparsing, kiwisolver, cycler, matplotlib, serpentine +#5 28.88 Successfully installed cycler-0.11.0 docopt-0.6.2 kiwisolver-1.3.1 matplotlib-3.3.4 numpy-1.19.5 pandas-1.1.5 pillow-8.4.0 pyparsing-3.0.8 python-dateutil-2.8.2 pytz-2022.1 scipy-1.5.4 serpentine-0.1.3 six-1.16.0 +#5 29.07 WARNING: You are using pip version 19.1.1, however version 21.3.1 is available. +#5 29.07 You should consider upgrading via the 'pip install --upgrade pip' command. +#5 29.34 WARNING: You are using pip version 19.1.1, however version 21.3.1 is available. +#5 29.34 You should consider upgrading via the 'pip install --upgrade pip' command. +#5 DONE 29.5s + +#6 exporting to image +#6 sha256:e8c613e07b0b7ff33893b694f7759a10d42e180f2b4dc349fb57dc6b71dcab00 +#6 exporting layers +#6 exporting layers 1.6s done +#6 writing image sha256:87f8bebc2272a1411bbdee4e76b74c32444498c63bcf2ec2ab3d4d19c3a65d98 done +#6 naming to docker.io/gmillot/python_v3.8.6_serpentine_v1.0:gitlab_v8.6 done +#6 DONE 1.6s diff --git a/python/v3.9.10/extended/v3.0/Dockerfile b/python/v3.9.10/extended/v3.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..5fbf71c177fa9b776e9463dc50db72c49f85569a --- /dev/null +++ b/python/v3.9.10/extended/v3.0/Dockerfile @@ -0,0 +1,48 @@ +######################################################################### +## ## +## Dockerfile ## +## Python extended ## +## ## +## Gael A. Millot ## +## Bioinformatics and Biostatistics Hub ## +## Computational Biology Department ## +## Institut Pasteur Paris ## +## ## +######################################################################### + + +# to see the log of the building: +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# cat building.log + +# to export the log file of the image building from the container: +# sudo docker images +# sudo docker run -ti --entrypoint bash <IMAGE_NAME> +# exit +# sudo docker container ls -a # to get all the active containers +# sudo docker cp <containerNAMES>:/building.log </host/path/target> + + +FROM gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENV PY_LIB="\ + cyvcf2 \ +" + + # install the packages +RUN echo "\n\n\n\n================\n\npip install\n\n================\n\n\n\n" > /building.log \ + && pip install $PY_LIB | tee -a /building.log \ + && echo "\n\n\n\n================\n\nPIP PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \ + && pip list >> /building.log \ + # end install the packages + # inactivated packages because are in the base installation + +ENV LC_ALL en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV LC_NUMERIC en_US.UTF-8 + +ENTRYPOINT ["/usr/bin/python3"] diff --git a/python/v3.9.10/extended/v3.0/building.log b/python/v3.9.10/extended/v3.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..91293757d61edc6d59f3d447e0f6cce5aaa78544 --- /dev/null +++ b/python/v3.9.10/extended/v3.0/building.log @@ -0,0 +1,62 @@ + + + + +================ + +pip install + +================ + + + + +Collecting cyvcf2 + Downloading cyvcf2-0.30.15-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.8 MB) +Requirement already satisfied: numpy in /usr/local/lib/python3.9/site-packages (from cyvcf2) (1.22.3) +Collecting click + Downloading click-8.1.3-py3-none-any.whl (96 kB) +Collecting coloredlogs + Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) +Collecting humanfriendly>=9.1 + Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB) +Installing collected packages: humanfriendly, coloredlogs, click, cyvcf2 +Successfully installed click-8.1.3 coloredlogs-15.0.1 cyvcf2-0.30.15 humanfriendly-10.0 + + + + +================ + +PIP PACKAGES INSTALLED + +================ + + + + +Package Version +------------------ --------- +bio 1.3.3 +biopython 1.79 +biothings-client 0.2.6 +certifi 2021.10.8 +charset-normalizer 2.0.12 +click 8.1.3 +coloredlogs 15.0.1 +cyvcf2 0.30.15 +humanfriendly 10.0 +idna 3.3 +mygene 3.2.2 +numpy 1.22.3 +pandas 1.4.1 +pip 21.2.4 +python-dateutil 2.8.2 +pytz 2021.3 +regex 2022.3.15 +requests 2.27.1 +setuptools 58.1.0 +six 1.16.0 +tqdm 4.63.0 +urllib3 1.26.9 +wheel 0.37.1