diff --git a/README.md b/README.md index 0df30138245fd2e64920d68c781e6b504e313986..0b7e33751f52847e23a55b807d2848334f4fe264 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,12 @@ Special acknowledgement to:<br /> Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below +### 10.6 + +Dockerfiles modified: <br /> +python_v3.9.10_extended_v3.1 at date 20231201: from gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7 with pigz gzip and tabix added<br /> + + ### 10.5 Dockerfiles modified: <br /> diff --git a/python/v3.9.10/extended/v3.2/Dockerfile b/python/v3.9.10/extended/v3.2/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..87ecc162f5e810d084c29db7c3b2f066b70a5c38 --- /dev/null +++ b/python/v3.9.10/extended/v3.2/Dockerfile @@ -0,0 +1,81 @@ +######################################################################### +## ## +## 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_v3.1:gitlab_v8.7 + +LABEL Gael.Millot=gael.millot@pasteur.fr +LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles" + +ENV APT_GET_LINUX_LIB="\ + pigz \ + gzip \ + tabix \ +" + +# 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 +RUN 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 + +# install the locales +RUN apt-get install -y locales \ + | tee -a /building.log + +# Set the locale +RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen \ + && locale-gen \ + | tee -a /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 + + +# 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 + + + +# print installed packages +RUN 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 locales locales-all \ + >> /building.log + + +ENTRYPOINT ["/usr/bin/python3"] diff --git a/python/v3.9.10/extended/v3.2/building.log b/python/v3.9.10/extended/v3.2/building.log new file mode 100644 index 0000000000000000000000000000000000000000..647a799f783705db519a1ef825fa6f6ba0080fcd --- /dev/null +++ b/python/v3.9.10/extended/v3.2/building.log @@ -0,0 +1,177 @@ + + + + +================ + +apt-get update + +================ + + + + +Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] +Get:2 http://security.debian.org/debian-security bullseye-security InRelease [48.4 kB] +Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] +Get:4 http://deb.debian.org/debian bullseye/main amd64 Packages [8062 kB] +Get:5 http://security.debian.org/debian-security bullseye-security/main amd64 Packages [259 kB] +Get:6 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [17.7 kB] +Fetched 8547 kB in 1s (5807 kB/s) +Reading package lists... + + + + +================ + +apt-get install + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +Suggested packages: + less +The following NEW packages will be installed: + pigz tabix +The following packages will be upgraded: + gzip +1 upgraded, 2 newly installed, 0 to remove and 136 not upgraded. +Need to get 535 kB of archives. +After this operation, 1275 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main amd64 gzip amd64 1.10-4+deb11u1 [132 kB] +Get:2 http://deb.debian.org/debian bullseye/main amd64 pigz amd64 2.6-1 [64.0 kB] +Get:3 http://deb.debian.org/debian bullseye/main amd64 tabix amd64 1.11-4 [339 kB] +Fetched 535 kB in 0s (4431 kB/s) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23373 files and directories currently installed.) +Preparing to unpack .../gzip_1.10-4+deb11u1_amd64.deb ... +Unpacking gzip (1.10-4+deb11u1) over (1.10-4) ... +Setting up gzip (1.10-4+deb11u1) ... +Selecting previously unselected package pigz. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23373 files and directories currently installed.) +Preparing to unpack .../archives/pigz_2.6-1_amd64.deb ... +Unpacking pigz (2.6-1) ... +Selecting previously unselected package tabix. +Preparing to unpack .../tabix_1.11-4_amd64.deb ... +Unpacking tabix (1.11-4) ... +Setting up pigz (2.6-1) ... +Setting up tabix (1.11-4) ... +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libc-l10n +The following NEW packages will be installed: + libc-l10n locales +0 upgraded, 2 newly installed, 0 to remove and 136 not upgraded. +Need to get 4947 kB of archives. +After this operation, 20.9 MB of additional disk space will be used. +Get:1 http://security.debian.org/debian-security bullseye-security/main amd64 libc-l10n all 2.31-13+deb11u7 [864 kB] +Get:2 http://security.debian.org/debian-security bullseye-security/main amd64 locales all 2.31-13+deb11u7 [4083 kB] +Fetched 4947 kB in 0s (30.6 MB/s) +Selecting previously unselected package libc-l10n. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23392 files and directories currently installed.) +Preparing to unpack .../libc-l10n_2.31-13+deb11u7_all.deb ... +Unpacking libc-l10n (2.31-13+deb11u7) ... +Selecting previously unselected package locales. +Preparing to unpack .../locales_2.31-13+deb11u7_all.deb ... +Unpacking locales (2.31-13+deb11u7) ... +Setting up libc-l10n (2.31-13+deb11u7) ... +Setting up locales (2.31-13+deb11u7) ... +debconf: unable to initialize frontend: Dialog +debconf: (TERM is not set, so the dialog frontend is not usable.) +debconf: falling back to frontend: Readline +Generating locales (this might take a while)... +Generation complete. +Generating locales (this might take a while)... + en_US.UTF-8... done +Generation complete. + + + + +================ + +apt-get autoremove + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +0 upgraded, 0 newly installed, 0 to remove and 136 not upgraded. + + + + +================ + +apt-get clean + +================ + + + + + + + + +================ + +rm + +================ + + + + + + + + +================ + +installed packages + +================ + + + + +pigz: + Installed: 2.6-1 + Candidate: 2.6-1 + Version table: + *** 2.6-1 100 + 100 /var/lib/dpkg/status +gzip: + Installed: 1.10-4+deb11u1 + Candidate: 1.10-4+deb11u1 + Version table: + *** 1.10-4+deb11u1 100 + 100 /var/lib/dpkg/status +tabix: + Installed: 1.11-4 + Candidate: 1.11-4 + Version table: + *** 1.11-4 100 + 100 /var/lib/dpkg/status +locales: + Installed: 2.31-13+deb11u7 + Candidate: 2.31-13+deb11u7 + Version table: + *** 2.31-13+deb11u7 100 + 100 /var/lib/dpkg/status +locales-all: + Installed: (none) + Candidate: (none) + Version table: