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Commit 574663a3 authored by Gael MILLOT's avatar Gael MILLOT
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release v9.0

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README.md
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...@@ -72,6 +72,12 @@ Hub-CDB Institut Pasteur & DSI Institut Pasteur ...@@ -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 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 ### 8.11
Dockerfiles added: <br /> Dockerfiles added: <br />
......
fedora/v33/immcantation/v1.0/Dockerfile 0 → 100644
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#########################################################################
## ##
## 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"]
python/v3.9.10/changeo_presto/v1.0/Dockerfile 0 → 100644
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#########################################################################
## ##
## 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"]
python/v3.9.10/changeo_presto/v1.0/building.log 0 → 100644
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================
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
ubuntu/v20.04/ig_analysis/v1.0/Dockerfile 0 → 100644
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− 0
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#########################################################################
## ##
## 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
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