diff --git a/README.md b/README.md index 8e92ad2835e4ef1d4cf8054e1306725d35493cc5..435e3b252641ce281161130f1a9d1f2c4d32d028 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,12 @@ 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 +### 9.0 + +Dockerfiles added: <br /> +fedora\v33\immcantation\v1.0 at date 20220928: docker image of immancation + + ### 8.11 Dockerfiles added: <br /> diff --git a/fedora/v33/immcantation/v1.0/Dockerfile b/fedora/v33/immcantation/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..26cc15b9a82f0cd74b129ba4ff0791910f2fc74a --- /dev/null +++ b/fedora/v33/immcantation/v1.0/Dockerfile @@ -0,0 +1,32 @@ +######################################################################### +## ## +## Dockerfile ## +## Ubuntu 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> + +# see https://immcantation.readthedocs.io/en/stable/docker/intro.html +FROM immcantation/suite:4.3.0 + + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENTRYPOINT ["/bin/bash"] diff --git a/python/v3.9.10/changeo_presto/v1.0/Dockerfile b/python/v3.9.10/changeo_presto/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f3fee280f75e4744b65198e6bdf3e008735c7713 --- /dev/null +++ b/python/v3.9.10/changeo_presto/v1.0/Dockerfile @@ -0,0 +1,49 @@ +######################################################################### +## ## +## Dockerfile ## +## changeo_presto ## +## ## +## 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="\ + changeo \ + presto \ +" + + # 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/changeo_presto/v1.0/building.log b/python/v3.9.10/changeo_presto/v1.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..3ede8f5099bcb4f71636585e6e8a9059d5c50dfa --- /dev/null +++ b/python/v3.9.10/changeo_presto/v1.0/building.log @@ -0,0 +1,92 @@ + + + + +================ + +pip install + +================ + + + + +Collecting changeo + Downloading changeo-1.2.0.tar.gz (150 kB) +Collecting presto + Downloading presto-0.7.0.tar.gz (109 kB) +Requirement already satisfied: numpy>=1.8 in /usr/local/lib/python3.9/site-packages (from changeo) (1.22.3) +Collecting scipy>=0.14 + Downloading scipy-1.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.9 MB) +Requirement already satisfied: pandas>=0.24 in /usr/local/lib/python3.9/site-packages (from changeo) (1.4.1) +Requirement already satisfied: biopython>=1.77 in /usr/local/lib/python3.9/site-packages (from changeo) (1.79) +Collecting PyYAML>=5.1 + Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB) +Requirement already satisfied: setuptools>=2.0 in /usr/local/lib/python3.9/site-packages (from changeo) (58.1.0) +Collecting airr>=1.3.1 + Downloading airr-1.4.1.tar.gz (63 kB) +Collecting yamlordereddictloader>=0.4.0 + Downloading yamlordereddictloader-0.4.0.tar.gz (3.3 kB) +Requirement already satisfied: python-dateutil>=2.8.1 in /usr/local/lib/python3.9/site-packages (from pandas>=0.24->changeo) (2.8.2) +Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.9/site-packages (from pandas>=0.24->changeo) (2021.3) +Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas>=0.24->changeo) (1.16.0) +Building wheels for collected packages: changeo, presto, airr, yamlordereddictloader + Building wheel for changeo (setup.py): started + Building wheel for changeo (setup.py): finished with status 'done' + Created wheel for changeo: filename=changeo-1.2.0-py3-none-any.whl size=151660 sha256=1da03d675a1f10a4993486776169a5bbf3e4ca68ba36753db738aba8f7412b70 + Stored in directory: /root/.cache/pip/wheels/32/a1/50/cf5b69a2449ebcb265a1ee6f6b809c4bc4a627aac4248bd626 + Building wheel for presto (setup.py): started + Building wheel for presto (setup.py): finished with status 'done' + Created wheel for presto: filename=presto-0.7.0-py3-none-any.whl size=118994 sha256=cde97b319ba72f3d38928711992fd9a6f6de5876620e6289ccf8bf0d748179b1 + Stored in directory: /root/.cache/pip/wheels/88/30/16/a90689aa0488c9f983dde0e83a40d21ec0f310dde44ffe89d7 + Building wheel for airr (setup.py): started + Building wheel for airr (setup.py): finished with status 'done' + Created wheel for airr: filename=airr-1.4.1-py3-none-any.whl size=46411 sha256=d931840e96e51768b39b2dcc662d9552814f1d02fae65c04feb793b5c6088393 + Stored in directory: /root/.cache/pip/wheels/63/fe/47/0adfcb284d62d9cdfe3bdaee34a5915d66fdb7fe05b4e49917 + Building wheel for yamlordereddictloader (setup.py): started + Building wheel for yamlordereddictloader (setup.py): finished with status 'done' + Created wheel for yamlordereddictloader: filename=yamlordereddictloader-0.4.0-py3-none-any.whl size=4069 sha256=23d83bee7ca69f8e4e1ddf42253b3ad0cc476db714e14d104d40f9aca6434aae + Stored in directory: /root/.cache/pip/wheels/26/be/2c/114a2da8d1eca28fc4ec769eab3304e854a8a2b5ca217ff9c5 +Successfully built changeo presto airr yamlordereddictloader +Installing collected packages: PyYAML, yamlordereddictloader, scipy, presto, airr, changeo +Successfully installed PyYAML-6.0 airr-1.4.1 changeo-1.2.0 presto-0.7.0 scipy-1.9.1 yamlordereddictloader-0.4.0 + + + + +================ + +PIP PACKAGES INSTALLED + +================ + + + + +Package Version +--------------------- --------- +airr 1.4.1 +bio 1.3.3 +biopython 1.79 +biothings-client 0.2.6 +certifi 2021.10.8 +changeo 1.2.0 +charset-normalizer 2.0.12 +idna 3.3 +mygene 3.2.2 +numpy 1.22.3 +pandas 1.4.1 +pip 21.2.4 +presto 0.7.0 +python-dateutil 2.8.2 +pytz 2021.3 +PyYAML 6.0 +regex 2022.3.15 +requests 2.27.1 +scipy 1.9.1 +setuptools 58.1.0 +six 1.16.0 +tqdm 4.63.0 +urllib3 1.26.9 +wheel 0.37.1 +yamlordereddictloader 0.4.0 diff --git a/ubuntu/v20.04/ig_analysis/v1.0/Dockerfile b/ubuntu/v20.04/ig_analysis/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..cb383e6fe7914e53d955652231b9b0c56bcaad33 --- /dev/null +++ b/ubuntu/v20.04/ig_analysis/v1.0/Dockerfile @@ -0,0 +1,102 @@ +######################################################################### +## ## +## Dockerfile ## +## ig_analys ## +## ## +## 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> + + +# base image: ubuntu:20.04 +FROM ubuntu:20.04 +# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENV APT_GET_LINUX_LIB="\ + autoconf \ + automake \ + libblas-dev \ + liblapack-dev \ + libatlas-base-dev \ + wget \ + build-essential \ + git \ +" + +ENV APT_LINUX_LIB="\ + rename \ +" + +# add gensoft deb repo pgp public key to apt trusted ones +# and install modules +WORKDIR /usr/bin/ +# to avoid cd. All the following commands will occurs here. In addition, opening a container will be at this node. + + +# update apt-get +RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > /building.log \ + && apt-get update --fix-missing \ + | tee -a /building.log \ + # install the ubuntu packages + && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \ + && apt-get install -y $APT_GET_LINUX_LIB \ + | tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \ + && apt -y install $APT_LINUX_LIB \ + | tee -a building.log \ + +RUN echo "\n\n\n\n================\n\IgPhyML install\n\n================\n\n\n\n" >> /building.log \ + && cd /usr/bin/ + && git clone https://bitbucket.org/kleinstein/igphyml + | tee -a /building.log \ + && export PATH="/usr/bin/igphyml/src:$PATH" # for igphyml tools + + +RUN echo "\n\n\n\n================\n\IgBlast install\n\n================\n\n\n\n" >> /building.log \ + && cd /usr/bin/ + && git clone https://bitbucket.org/kleinstein/igphyml + | tee -a /building.log \ + && export PATH="/usr/bin/igphyml/src:$PATH" # for igphyml tools + +https://bitbucket.org/kleinstein/immcantation/downloads/ + + + # cleaning +RUN echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> /building.log \ + && apt-get autoremove -y \ + | tee -a /building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> /building.log \ + && apt-get clean \ + | tee -a /building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> /building.log \ + && rm -rf /var/lib/apt/lists/* \ + | tee -a /building.log \ + && echo "\n\n\n\n================\n\ninstalled packages\n\n================\n\n\n\n" >> /building.log \ + && apt-cache policy \ + locales \ + locales-all \ + >> /building.log + +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/bash" , "-l"] +# The -l option (according to the man page) makes "bash act as if it had been invoked as a login shell". Login shells read certain initialization files from your home directory, such as .bash_profile. Variables set in .bash_profile override when bash launches. \ No newline at end of file