release v9.1

README.md

@@ -72,6 +72,13 @@ 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
 
 
+### 9.1
+
+Dockerfiles added: <br />
+ubuntu/v20.04/slivar/v1.0 at date 20221002: from ubuntu:20.04 with samtools and slivar added
+ubuntu/v20.04/samtools/v1.0 at date 20221002: from ubuntu:20.04 with samtools added
+
+
 ### 9.0
 
 Dockerfiles added: <br />

ubuntu/v20.04/extended/v1.0/Dockerfile

+#########################################################################
+##                                                                     ##
+##     Dockerfile                                                      ##
+##     Bash 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>
+
+# Coreutils - GNU core utilities
+# https://www.gnu.org/software/coreutils/
+# v8.25
+
+# gawk - GNU core utilities
+# https://www.gnu.org/software/gawk/
+# v4.1.3
+
+# bc - GNU core utilities
+# https://www.gnu.org/software/bc/
+# v1.06.95
+
+# git - github
+# https://github.com/git/git/archive/refs/tags/
+# v2.7.4
+
+# base image: ubuntu:16.04
+FROM gmillot/ubuntu-base_v20.04:gitlab_v8.5
+# 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="\
+    locales \
+    locales-all \
+    coreutils \
+    gawk \
+    bc \
+    git \
+"
+
+ENV APT_LINUX_LIB=""
+
+
+
+# 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 ; 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 \
+    # end install the packages
+    # cleaning
+    && 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 $APT_GET_LINUX_LIB $APT_LINUX_LIB \
+    >> /building.log
+# https://askubuntu.com/questions/179955/var-lib-apt-lists-is-huge
+# folder filled after running sudo apt-get update (or use the Refresh button in a package manager), a list of packages will get downloaded from the Ubuntu servers. These files are then stored in /var/lib/apt/lists/. You can safely remove the contents of that directory as it is recreated when you refresh the package lists. If you remove the files, but do not run apt-get update to fetch the lists, commands like apt-cache will fail to provide information (since the cache is empty)
+# apt-cache policy print all the indicated package info
+# end cleaning
+
+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

ubuntu/v20.04/samtools/v1.0/Dockerfile

+#########################################################################
+##                                                                     ##
+##     Dockerfile                                                      ##
+##     samtools                                                        ##
+##                                                                     ##
+##     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:16.04
+FROM gmillot/ubuntu-extended_v1.0:gitlab_v9.1
+# 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="\
+    zlib1g \
+    liblzma5 \
+    libncurses5 \
+"
+ENV APT_GET_LINUX_LIB_RM="\
+        wget \
+        gcc \
+        make \
+        libbz2-dev \
+        zlib1g-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        bzip2 \
+"
+
+ENV APT_LINUX_LIB=""
+
+
+
+# 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 ; 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 $APT_GET_LINUX_LIB_RM \
+    | 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 \
+    # end install the packages
+    # samtools install
+    && echo "\n\n\n\n================\n\nsamtools installation\n\n================\n\n\n\n" >> /building.log \
+    && cd /usr/local/ \
+    && wget -O samtools.tar.bz2 https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2 \
+    && tar -xjvf samtools.tar.bz2 \
+    && rm -rf samtools.tar.bz2 \
+    && cd samtools-1.14 \
+    && ./configure \
+    && make \
+    && make install \
+
+    && cd /usr/local \
+    && rm -rf /usr/local/samtools-1.14 \
+    && apt-get remove -y $APT_GET_LINUX_LIB_RM\
+    # end samtools install
+    # cleaning
+    && 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 $APT_GET_LINUX_LIB $APT_LINUX_LIB samtools \
+    >> /building.log \
+    && samtools --version >> /building.log
+# https://askubuntu.com/questions/179955/var-lib-apt-lists-is-huge
+# folder filled after running sudo apt-get update (or use the Refresh button in a package manager), a list of packages will get downloaded from the Ubuntu servers. These files are then stored in /var/lib/apt/lists/. You can safely remove the contents of that directory as it is recreated when you refresh the package lists. If you remove the files, but do not run apt-get update to fetch the lists, commands like apt-cache will fail to provide information (since the cache is empty)
+# apt-cache policy print all the indicated package info
+# end cleaning
+
+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

ubuntu/v20.04/slivar/v2.0/Dockerfile

+#########################################################################
+##                                                                     ##
+##     Dockerfile                                                      ##
+##     Slivar                                                          ##
+##                                                                     ##
+##     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 gmillot/samtools_v1.0:gitlab_v9.1
+# 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="\
+    wget \
+    build-essential \
+"
+ENV APT_GET_LINUX_LIB_RM=""
+
+ENV APT_LINUX_LIB=""
+
+
+
+# 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 \
+    && DEBIAN_FRONTEND="noninteractive" apt-get install -y $APT_GET_LINUX_LIB \
+        | tee -a /building.log
+
+
+RUN echo "\n\n\n\n================\n\slivar install\n\n================\n\n\n\n" >> /building.log \
+    && wget https://github.com/brentp/slivar/releases/download/v0.2.7/slivar \
+    && chmod 755 slivar \
+    | tee -a /building.log \
+
+    # 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 \
+        $APT_GET_LINUX_LIB \
+         >> /building.log \
+    && samtools --version >> /building.log \
+    && echo "slivar version v0.2.7" >> /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