diff --git a/README.md b/README.md index 5d5b812cd1814147eff2b7a3371d95ffec9e7f89..48e3f8ddb3aae31355495a871d41b06b078cd516 100644 --- a/README.md +++ b/README.md @@ -69,6 +69,14 @@ Hub-CDB and Institut Pasteur Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below +### v8.4 + +Dockerfiles added: <br /> +python\v3.9.10\base\v1.0 at date 20220318: using the debian 11 bullseye system. A python base in my repo in case the distant one is lost +python\v3.9.10\extended\v1.1 at date 20220318: same as v1.0 but using the gmillot/python_v3.9.10_base_v1.0:gitlab_v8.4 image +python\v3.9.10\extended\v2.0 at date 20220318: from gmillot/python_v3.9.10_extended_v1.1:gitlab_v8.4 with regex package added + + ### v8.3 Dockerfiles added: <br /> diff --git a/python/v3.9.10/base/v1.0/Dockerfile b/python/v3.9.10/base/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..db4b0c686fbb2f30689b694c39fd8988fcbf147c --- /dev/null +++ b/python/v3.9.10/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:3.9.10 + +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/v3.9.10/base/v1.0/building.log b/python/v3.9.10/base/v1.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..9ec83b37da8a8fdaf0694c55fbacb08a78a9536c --- /dev/null +++ b/python/v3.9.10/base/v1.0/building.log @@ -0,0 +1,18 @@ + + + + +================ + +PIP PACKAGES INSTALLED + +================ + + + + +Package Version +---------- ------- +pip 21.2.4 +setuptools 58.1.0 +wheel 0.37.1 diff --git a/python/v3.9.10/extended/v1.0/Dockerfile b/python/v3.9.10/extended/v1.0/Dockerfile index 6438e14943b10323f50904a5a2463794a4dba6ca..fc81ddd84ccde8813c176ebcff21db8b52b5ccd1 100644 --- a/python/v3.9.10/extended/v1.0/Dockerfile +++ b/python/v3.9.10/extended/v1.0/Dockerfile @@ -1,7 +1,7 @@ ######################################################################### ## ## ## Dockerfile ## -## R base ## +## Python extended ## ## ## ## Gael A. Millot ## ## Bioinformatics and Biostatistics Hub ## diff --git a/python/v3.9.10/extended/v1.1/Dockerfile b/python/v3.9.10/extended/v1.1/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..1697259a9094dbe4d08758ed6bf3333c779fe600 --- /dev/null +++ b/python/v3.9.10/extended/v1.1/Dockerfile @@ -0,0 +1,58 @@ +######################################################################### +## ## +## 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_base_v1.0:gitlab_v8.4 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +# Following packages are in the python base installation +# os.path \ +# os \ +# sys \ +# glob \ +# re \ +# time \ +# csv \ + +ENV PY_LIB="\ + pandas \ + Bio \ +" + + # 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/v1.1/building.log b/python/v3.9.10/extended/v1.1/building.log new file mode 100644 index 0000000000000000000000000000000000000000..dce550a3a16b7c8f0814152c316ab04efe97dd70 --- /dev/null +++ b/python/v3.9.10/extended/v1.1/building.log @@ -0,0 +1,78 @@ + + + + +================ + +pip install + +================ + + + + +Collecting pandas + Downloading pandas-1.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) +Collecting Bio + Downloading bio-1.3.3-py3-none-any.whl (271 kB) +Collecting pytz>=2020.1 + Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) +Collecting numpy>=1.18.5 + Downloading numpy-1.22.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB) +Collecting python-dateutil>=2.8.1 + Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) +Collecting tqdm + Downloading tqdm-4.63.0-py2.py3-none-any.whl (76 kB) +Collecting mygene + Downloading mygene-3.2.2-py2.py3-none-any.whl (5.4 kB) +Collecting biopython>=1.79 + Downloading biopython-1.79-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (2.3 MB) +Collecting requests + Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB) +Collecting six>=1.5 + Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) +Collecting biothings-client>=0.2.6 + Downloading biothings_client-0.2.6-py2.py3-none-any.whl (37 kB) +Collecting idna<4,>=2.5 + Downloading idna-3.3-py3-none-any.whl (61 kB) +Collecting urllib3<1.27,>=1.21.1 + Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB) +Collecting charset-normalizer~=2.0.0 + Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB) +Collecting certifi>=2017.4.17 + Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) +Installing collected packages: urllib3, idna, charset-normalizer, certifi, requests, six, numpy, biothings-client, tqdm, pytz, python-dateutil, mygene, biopython, pandas, Bio +Successfully installed Bio-1.3.3 biopython-1.79 biothings-client-0.2.6 certifi-2021.10.8 charset-normalizer-2.0.12 idna-3.3 mygene-3.2.2 numpy-1.22.3 pandas-1.4.1 python-dateutil-2.8.2 pytz-2021.3 requests-2.27.1 six-1.16.0 tqdm-4.63.0 urllib3-1.26.9 + + + + +================ + +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 +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 +requests 2.27.1 +setuptools 58.1.0 +six 1.16.0 +tqdm 4.63.0 +urllib3 1.26.9 +wheel 0.37.1 diff --git a/python/v3.9.10/extended/v2.0/Dockerfile b/python/v3.9.10/extended/v2.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ab4b35432f1f6cbe0eb23d413dff90d2fd1e980b --- /dev/null +++ b/python/v3.9.10/extended/v2.0/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_v1.1:gitlab_v8.4 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENV PY_LIB="\ + regex \ +" + + # 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/v2.0/building.log b/python/v3.9.10/extended/v2.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..107e447fac3b64cf250ca85e5d2686cf80b552ed --- /dev/null +++ b/python/v3.9.10/extended/v2.0/building.log @@ -0,0 +1,51 @@ + + + + +================ + +pip install + +================ + + + + +Collecting regex + Downloading regex-2022.3.15-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (763 kB) +Installing collected packages: regex +Successfully installed regex-2022.3.15 + + + + +================ + +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 +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