From b7048cea8aaa64e03da4705fd617aba1488c917a Mon Sep 17 00:00:00 2001
From: gmillot <gael.millot@pasteur.fr>
Date: Wed, 15 Nov 2023 17:45:30 +0100
Subject: [PATCH] release v10.2: added ubuntu v22.04 base,extended; abalignv2;
python v3.6.12; nanoForkSpeed_basecalling
---
README.md | 113 ++-
python/v3.6.12/base/v1.0/Dockerfile | 66 ++
python/v3.6.12/base/v1.0/building.log | 98 ++
.../nanoForkSpeed_basecalling/v1.0/Dockerfile | 94 ++
ubuntu/v20.04/base/{building2.log => .log} | 0
ubuntu/v22.04/abalign/building.log | 308 ++++++
ubuntu/v22.04/abalign/v1.0/Dockerfile | 68 ++
ubuntu/v22.04/base/.log | 33 +
ubuntu/v22.04/base/Dockerfile | 32 +
ubuntu/v22.04/extended/v1.0/Dockerfile | 140 +++
ubuntu/v22.04/extended/v1.0/building.log | 949 ++++++++++++++++++
11 files changed, 1849 insertions(+), 52 deletions(-)
create mode 100644 python/v3.6.12/base/v1.0/Dockerfile
create mode 100644 python/v3.6.12/base/v1.0/building.log
create mode 100644 python/v3.6.12/nanoForkSpeed_basecalling/v1.0/Dockerfile
rename ubuntu/v20.04/base/{building2.log => .log} (100%)
create mode 100644 ubuntu/v22.04/abalign/building.log
create mode 100644 ubuntu/v22.04/abalign/v1.0/Dockerfile
create mode 100644 ubuntu/v22.04/base/.log
create mode 100644 ubuntu/v22.04/base/Dockerfile
create mode 100644 ubuntu/v22.04/extended/v1.0/Dockerfile
create mode 100644 ubuntu/v22.04/extended/v1.0/building.log
diff --git a/README.md b/README.md
index 4cb28f9..afe1789 100644
--- a/README.md
+++ b/README.md
@@ -71,17 +71,26 @@ 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
+### 10.2
+
+Dockerfiles added: <br />
+ubuntu/v22.04/base at date 20231114 <br />
+ubuntu/v22.04/extended/v1.0 at date 20231114: from ubuntu:22.04 with wget git bc gawk coreutils added<br />
+ubuntu/v22.04/abalign/v1.0 at date 20231114
+python/v3.6.12/base/v1.0 at date 20231114 <br />
+python/v3.6.12/nanoForkSpeed_basecalling/v1.0 at date 20231114
+
### 10.1
Dockerfiles modified: <br />
-fedora\v33\immcantation\v1.2 at date 20230407: from gmillot/immcantation_v1.1:gitlab_v10.0 with lubridate added<br />
+fedora/v33/immcantation/v1.2 at date 20230407: from gmillot/immcantation_v1.1:gitlab_v10.0 with lubridate added<br />
### 10.0
Dockerfiles modified: <br />
-fedora\v33\immcantation\v1.1 at date 20230407: from gmillot/immcantation_v1.0:gitlab_v9.0 with svglite added<br />
+fedora/v33/immcantation/v1.1 at date 20230407: from gmillot/immcantation_v1.0:gitlab_v9.0 with svglite added<br />
### 9.9
@@ -114,14 +123,14 @@ R/v4.1.2/ig_clustering/v1.1 at date 20230211: from gmillot/r_v4.1.2_ig_clusterin
### 9.5
Dockerfiles added: <br />
-ubuntu\v20.04\alohomora_merlin\v2.1 at date 20230122: from ubuntu:20.04, idem gmillot/alohomora_merlin_v2.0:gitlab_v9.4 with problem of locales solved
+ubuntu/v20.04/alohomora_merlin/v2.1 at date 20230122: from ubuntu:20.04, idem gmillot/alohomora_merlin_v2.0:gitlab_v9.4 with problem of locales solved
Warning: see section 8.5 below
### 9.4
Dockerfiles added: <br />
-ubuntu\v20.04\alohomora_merlin\v2.0 at date 20221231: from ubuntu:20.04, idem gmillot/alohomora_merlin_v1.0:gitlab_v8.5 with R added
+ubuntu/v20.04/alohomora_merlin/v2.0 at date 20221231: from ubuntu:20.04, idem gmillot/alohomora_merlin_v1.0:gitlab_v8.5 with R added
Warning: see section 8.5 below
@@ -150,7 +159,7 @@ ubuntu/v20.04/htslib/v1.0 at date 20221002: from ubuntu:20.04 with samtools adde
### 9.0
Dockerfiles added: <br />
-fedora\v33\immcantation\v1.0 at date 20220928: docker image of immancation
+fedora/v33/immcantation/v1.0 at date 20220928: docker image of immancation
### 8.11
@@ -162,43 +171,43 @@ ubuntu/v20.04/slivar/v1.0 at date 20220705: from ubuntu:20.04 with slivar added
### 8.10
Dockerfiles added: <br />
-R\v4.1.2\extended\v1.1 at date 20220628: for slitherine, from gmillot/r-base_v4.1.2:gitlab_v8.2 with notably HiCcompare added
+R/v4.1.2/extended/v1.1 at date 20220628: for slitherine, from gmillot/r-base_v4.1.2:gitlab_v8.2 with notably HiCcompare added
### v8.9
Dockerfiles added: <br />
-R\v4.1.2\contracted\v1.0 at date 20220622:
+R/v4.1.2/contracted/v1.0 at date 20220622:
### v8.8
Dockerfiles added: <br />
-R\v4.1.2\extended\v2.1 at date 20220607: from gmillot/r_v4.1.2_extended_v2.0:gitlab_v8.2 with qqman package added
+R/v4.1.2/extended/v2.1 at date 20220607: from gmillot/r_v4.1.2_extended_v2.0:gitlab_v8.2 with qqman package added
### v8.7
Dockerfiles added: <br />
-python\v3.9.10\extended\v3.1 at date 20220504: from gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 with cyvcf2 and scipy packages added
+python/v3.9.10/extended/v3.1 at date 20220504: from gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 with cyvcf2 and scipy packages added
### v8.6
Dockerfiles added: <br />
-python\v3.6.8\base\v1.0 at date 20220504: FROM python:3.6.8<br />
-python\v3.6.8\serpentine\v1.0 at date 20220504: from gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6<br />
-python\v3.9.10\extended\v3.0 at date 20220504: from gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 with cyvcf2 package added
+python/v3.6.8/base/v1.0 at date 20220504: FROM python:3.6.8<br />
+python/v3.6.8/serpentine/v1.0 at date 20220504: from gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6<br />
+python/v3.9.10/extended/v3.0 at date 20220504: from gmillot/python_v3.9.10_extended_v2.0:gitlab_v8.4 with cyvcf2 package added
### v8.5
Dockerfiles added: <br />
-ubuntu\v16.04\base at date 20220422 <br />
-ubuntu\v20.04\base at date 20220422 <br />
-ubuntu\v20.04\alohomora_merlin\v1.0 at date 20220422
+ubuntu/v16.04/base at date 20220422 <br />
+ubuntu/v20.04/base at date 20220422 <br />
+ubuntu/v20.04/alohomora_merlin/v1.0 at date 20220422
<br />
-Warning: do not use --entrypoint bash for image alohomora_merlin\v1.0, because modules will not be available.<br />
+Warning: do not use --entrypoint bash for image alohomora_merlin/v1.0, because modules will not be available.<br />
Just use : sudo docker run -ti d6e1595795cf<br />
<br /><br />
Explanation:<br />
@@ -213,131 +222,131 @@ Shell classique source les fichiers d’init user
### 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 <br />
-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 <br />
-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
+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 <br />
+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 <br />
+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 />
-python\v3.9.10\extended\v1.0 at date 20220314: using the debian 11 bullseye system
+python/v3.9.10/extended/v1.0 at date 20220314: using the debian 11 bullseye system
### v8.2
Dockerfiles added: <br />
-R\v4.1.2\base at date 20220310: using the ubuntu 20.04 system <br />
-R\v4.1.2\extended v1.0 at date 20220310: base + 238 packages installed but 40 of them could not be properly installed due to a too much recent R version. Thus, plan a v1.1 later <br />
-R\v4.1.2\extended v2.0 at date 20220310: v1.0 + 5 packages installed for rmarkdown and pdftools <br />
-R\v4.0.5\extended v3.0 at date 20220308: v2.0 + pdftools but is not working because of the unstable debian system used
+R/v4.1.2/base at date 20220310: using the ubuntu 20.04 system <br />
+R/v4.1.2/extended v1.0 at date 20220310: base + 238 packages installed but 40 of them could not be properly installed due to a too much recent R version. Thus, plan a v1.1 later <br />
+R/v4.1.2/extended v2.0 at date 20220310: v1.0 + 5 packages installed for rmarkdown and pdftools <br />
+R/v4.0.5/extended v3.0 at date 20220308: v2.0 + pdftools but is not working because of the unstable debian system used
### v8.1
Dockerfiles modified: <br />
-ubuntu\v16.04\alien_trimmer\v0.4.0 at date 20220114: locales added <br />
+ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20220114: locales added <br />
### v8.0
Dockerfiles added: <br />
-ubuntu\v16.04\bedtools\v1.14 at date 20220114 <br />
+ubuntu/v16.04/bedtools/v1.14 at date 20220114 <br />
Dockerfiles modified: <br />
-ubuntu\v16.04\bash-extended\v4.0 at date 20220114: locales added <br />
-ubuntu\v16.04\samtools\v1.14 at date 20220114: locales added <br />
-ubuntu\v16.04\bowtie2-extended\v2.0 at date 20220114: locales added
+ubuntu/v16.04/bash-extended/v4.0 at date 20220114: locales added <br />
+ubuntu/v16.04/samtools/v1.14 at date 20220114: locales added <br />
+ubuntu/v16.04/bowtie2-extended/v2.0 at date 20220114: locales added
### v7.0
Dockerfiles added: <br />
-ubuntu\v16.04\bowtie2-extended\v1.0 at date 20220106 <br />
-ubuntu\v16.04\samtools\v1.14 at date 20220106
+ubuntu/v16.04/bowtie2-extended/v1.0 at date 20220106 <br />
+ubuntu/v16.04/samtools/v1.14 at date 20220106
### v6.4
Dockerfiles added: <br />
-R\v4.0.5\extended v2.0 at date 20211228: v1.0 + pandoc added for knitting documents using R
+R/v4.0.5/extended v2.0 at date 20211228: v1.0 + pandoc added for knitting documents using R
### v6.3
Dockerfiles modified: <br />
-R\v4.0.5\extended v1.0 at date 20211228: 1) log of the building execution + table of the installed packages available in the image, 2) version frozen for the ubuntu and R packages, 3) name of the image improved
+R/v4.0.5/extended v1.0 at date 20211228: 1) log of the building execution + table of the installed packages available in the image, 2) version frozen for the ubuntu and R packages, 3) name of the image improved
### v6.2
Dockerfiles debugged: <br />
-R\v4.0.5\extended at date 20211213: ggplot2 v3.3.3 to fit with cute and devtools correctly installed
+R/v4.0.5/extended at date 20211213: ggplot2 v3.3.3 to fit with cute and devtools correctly installed
### v6.1
Dockerfiles modified: <br />
-R\v4.0.5\extended at date 20211212: dependencies=NA instead of dependencies=TRUE (no suggested packages installed)
+R/v4.0.5/extended at date 20211212: dependencies=NA instead of dependencies=TRUE (no suggested packages installed)
### v6.0
Dockerfiles modified: <br />
-R\v4.0.5\extended at date 20211211: location of the library folder forced
+R/v4.0.5/extended at date 20211211: location of the library folder forced
### v5.1
Dockerfiles modified: <br />
-ubuntu\v16.04\alien_trimmer\v0.4.0 at date 20211117: debbugging (CR removed from AlienTrimmer.sh)
+ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20211117: debbugging (CR removed from AlienTrimmer.sh)
### v5.0
Dockerfiles modified: <br />
-ubuntu\v16.04\alien_trimmer\v0.4.0 at date 20211117: backbone is older but lighter (bash-extended_v3.0:gitlab_v4.0 instead of bash-extended_v1.0:gitlab_v1.0)
+ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20211117: backbone is older but lighter (bash-extended_v3.0:gitlab_v4.0 instead of bash-extended_v1.0:gitlab_v1.0)
### v4.0
Dockerfiles added: <br />
-ubuntu\v16.04\bcftools\v1.14 at date 20211108 <br />
+ubuntu/v16.04/bcftools/v1.14 at date 20211108 <br />
<br />
Dockerfiles modified: <br />
-ubuntu\v16.04\bash-extended\v3.0 at date 20211108: installation made using apt-get install, instead of installing the source code. Warning, this v3.0 has older versions of added packages:
+ubuntu/v16.04/bash-extended/v3.0 at date 20211108: installation made using apt-get install, instead of installing the source code. Warning, this v3.0 has older versions of added packages:
| Version | Packages | Size |
| --- | --- | --- |
-| **V2.0** |<ul><li>coreutils\v8.30<br /></li><li>gawk\v5.1.0<br /></li><li>bc\v1.07<br /></li><li>git\v2.33.1<br /></li></li>| 1.3 GB |
-| **V3.0** |<ul><li>coreutils\v8.25<br /></li><li>gawk\v4.1.3<br /></li><li>bc\v1.06.95<br /></li><li>git\v2.7.4<br /></li></li>| 81.7 MB |
+| **V2.0** |<ul><li>coreutils/v8.30<br /></li><li>gawk/v5.1.0<br /></li><li>bc/v1.07<br /></li><li>git/v2.33.1<br /></li></li>| 1.3 GB |
+| **V3.0** |<ul><li>coreutils/v8.25<br /></li><li>gawk/v4.1.3<br /></li><li>bc/v1.06.95<br /></li><li>git/v2.7.4<br /></li></li>| 81.7 MB |
### v3.0
Dockerfiles added: <br />
-ubuntu\v16.04\git\v2.33.1 at date 20211029 <br />
-ubuntu\v16.04\bash-extended\v2.0 at date 20211029 <br />
+ubuntu/v16.04/git/v2.33.1 at date 20211029 <br />
+ubuntu/v16.04/bash-extended/v2.0 at date 20211029 <br />
<br />
Dockerfiles modified: <br />
-R\v4.0.5\base at date 20211002: comment added to explain the install of procps
+R/v4.0.5/base at date 20211002: comment added to explain the install of procps
### v2.0
Dockerfiles added: <br />
-ubuntu\v16.04\alien_trimmer\v0.4.0 at date 20211001
+ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20211001
### v1.0
Dockerfiles added: <br />
-ubuntu\v16.04\coreutils\v8.30 at date 20211001<br />
-ubuntu\v16.04\gawk\v5.1.0 at date 20211001<br />
-ubuntu\v16.04\bc\v1.07 at date 20211001<br />
-ubuntu\v16.04\bash-extended\v1.0 at date 20211001, which contains coreutils\v8.30, gawk\v5.1.0 and bc\v1.07
+ubuntu/v16.04/coreutils/v8.30 at date 20211001<br />
+ubuntu/v16.04/gawk/v5.1.0 at date 20211001<br />
+ubuntu/v16.04/bc/v1.07 at date 20211001<br />
+ubuntu/v16.04/bash-extended/v1.0 at date 20211001, which contains coreutils/v8.30, gawk/v5.1.0 and bc/v1.07
-R\v4.0.5\base at date 20211001<br />
-R\v4.0.5\extended at date 20211001
+R/v4.0.5/base at date 20211001<br />
+R/v4.0.5/extended at date 20211001
diff --git a/python/v3.6.12/base/v1.0/Dockerfile b/python/v3.6.12/base/v1.0/Dockerfile
new file mode 100644
index 0000000..afeb284
--- /dev/null
+++ b/python/v3.6.12/base/v1.0/Dockerfile
@@ -0,0 +1,66 @@
+#########################################################################
+## ##
+## 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:3.6.12
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+# 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 \
+ wget \
+ build-essential \
+ | tee -a /building.log
+
+
+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
+
+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/v3.6.12/base/v1.0/building.log b/python/v3.6.12/base/v1.0/building.log
new file mode 100644
index 0000000..a79cad9
--- /dev/null
+++ b/python/v3.6.12/base/v1.0/building.log
@@ -0,0 +1,98 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Get:1 http://deb.debian.org/debian buster InRelease [122 kB]
+Get:2 http://security.debian.org/debian-security buster/updates InRelease [34.8 kB]
+Get:3 http://deb.debian.org/debian buster-updates InRelease [56.6 kB]
+Get:4 http://security.debian.org/debian-security buster/updates/main amd64 Packages [550 kB]
+Get:5 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB]
+Get:6 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B]
+Fetched 8681 kB in 8s (1022 kB/s)
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+wget is already the newest version (1.20.1-1.1).
+The following NEW packages will be installed:
+ build-essential
+0 upgraded, 1 newly installed, 0 to remove and 168 not upgraded.
+Need to get 7576 B of archives.
+After this operation, 20.5 kB of additional disk space will be used.
+Get:1 http://deb.debian.org/debian buster/main amd64 build-essential amd64 12.6 [7576 B]
+Fetched 7576 B in 0s (30.9 kB/s)
+Selecting previously unselected package build-essential.
+(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%
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(Reading database ... 70%
(Reading database ... 75%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 24611 files and directories currently installed.)
+Preparing to unpack .../build-essential_12.6_amd64.deb ...
+Unpacking build-essential (12.6) ...
+Setting up build-essential (12.6) ...
+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 168 not upgraded.
+Need to get 4904 kB of archives.
+After this operation, 20.8 MB of additional disk space will be used.
+Get:1 http://security.debian.org/debian-security buster/updates/main amd64 libc-l10n all 2.28-10+deb10u2 [846 kB]
+Get:2 http://security.debian.org/debian-security buster/updates/main amd64 locales all 2.28-10+deb10u2 [4058 kB]
+Fetched 4904 kB in 4s (1170 kB/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%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 24620 files and directories currently installed.)
+Preparing to unpack .../libc-l10n_2.28-10+deb10u2_all.deb ...
+Unpacking libc-l10n (2.28-10+deb10u2) ...
+Selecting previously unselected package locales.
+Preparing to unpack .../locales_2.28-10+deb10u2_all.deb ...
+Unpacking locales (2.28-10+deb10u2) ...
+Setting up libc-l10n (2.28-10+deb10u2) ...
+Setting up locales (2.28-10+deb10u2) ...
+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.
+
+
+
+
+================
+
+PIP PACKAGES INSTALLED
+
+================
+
+
+
+
+Package Version
+---------- -------
+pip 21.0.1
+setuptools 53.0.0
+wheel 0.36.2
diff --git a/python/v3.6.12/nanoForkSpeed_basecalling/v1.0/Dockerfile b/python/v3.6.12/nanoForkSpeed_basecalling/v1.0/Dockerfile
new file mode 100644
index 0000000..61ed104
--- /dev/null
+++ b/python/v3.6.12/nanoForkSpeed_basecalling/v1.0/Dockerfile
@@ -0,0 +1,94 @@
+#########################################################################
+## ##
+## 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 and python v3.6.12
+FROM gmillot/python_v3.6.12_base_v1.0:gitlab_v10.2
+# 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 PY_LIB_PRE="\
+ numpy==1.19.2\n \
+"
+
+ENV PY_LIB="\
+ cached-property==1.5.2\n \
+ cycler==0.10.0\n \
+ h5py==3.1.0\n \
+ joblib==1.0.0\n \
+ kiwisolver==1.3.1\n \
+ mappy==2.17\n \
+ matplotlib==3.3.3\n \
+ megalodon==2.2.9\n \
+ ont-fast5-api==3.1.6\n \
+ ont-pyguppy-client-lib==4.4.1\n \
+ packaging==20.8\n \
+ pandas==1.1.5\n \
+ pillow==8.1.0\n \
+ progressbar33==2.4\n \
+ pyparsing==2.4.7\n \
+ pysam==0.16.0.1\n \
+ python-dateutil==2.8.1\n \
+ pytz==2020.5\n \
+ scikit-learn==0.24.0\n \
+ scipy==1.5.4\n \
+ seaborn==0.11.1\n \
+ sklearn==0.0\n \
+ threadpoolctl==2.1.0\n \
+ tqdm==4.56.0 \
+"
+
+# 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.
+
+RUN echo "\n\n\n\n================\n\npre pip install\n\n================\n\n\n\n" >> /building.log \
+ && echo "$PY_LIB_PRE" > caca.txt \
+ && pip install -r caca.txt >> /building.log \
+ && rm caca.txt
+
+RUN echo "\n\n\n\n================\n\npip install\n\n================\n\n\n\n" >> /building.log \
+ && echo "$PY_LIB" > caca.txt \
+ && pip install -v -r caca.txt >> /building.log \
+ && rm caca.txt
+
+RUN echo "\n\n\n\n================\n\nubuntu installed packages\n\n================\n\n\n\n" >> /building.log \
+ && apt-cache policy \
+ locales \
+ locales-all \
+ $APT_GET_LINUX_LIB \
+ >> /building.log
+
+
+RUN echo "\n\n\n\n================\n\npip installed packages\n\n================\n\n\n\n" >> /building.log \
+ && pip list >> /building.log
+ # end install the packages
+ # inactivated packages because are in the base installation
+
+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
diff --git a/ubuntu/v20.04/base/building2.log b/ubuntu/v20.04/base/.log
similarity index 100%
rename from ubuntu/v20.04/base/building2.log
rename to ubuntu/v20.04/base/.log
diff --git a/ubuntu/v22.04/abalign/building.log b/ubuntu/v22.04/abalign/building.log
new file mode 100644
index 0000000..56e0db1
--- /dev/null
+++ b/ubuntu/v22.04/abalign/building.log
@@ -0,0 +1,308 @@
+
+
+
+
+================
+
+abalign installation
+
+================
+
+
+
+
+Archive: Abalign_V2_Linux_Term.zip
+ creating: Abalign_V2_Linux_Term/
+ inflating: Abalign_V2_Linux_Term/Abalign
+ inflating: Abalign_V2_Linux_Term/LICENSE
+ creating: Abalign_V2_Linux_Term/lib/
+ creating: Abalign_V2_Linux_Term/lib/jgenedatabase/
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Bostaurus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Camelusdromedarius_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Camelusdromedarius_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Camelusdromedarius_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Camelusdromedarius_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Canislupusfamiliaris_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Caprahircus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Caprahircus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Caprahircus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Caprahircus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Daniorerio_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Daniorerio_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Daniorerio_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Daniorerio_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Equuscaballus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Feliscatus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Feliscatus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Feliscatus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Feliscatus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gallusgallus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gorillagorillagorilla_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gorillagorillagorilla_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gorillagorillagorilla_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Gorillagorillagorilla_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Homosapiens_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Lemurcatta_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacafascicularis_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacafascicularis_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacafascicularis_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacafascicularis_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Macacamulatta_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Musmusculus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oncorhynchusmykiss_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oncorhynchusmykiss_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oncorhynchusmykiss_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oncorhynchusmykiss_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ornithorhynchusanatinus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ornithorhynchusanatinus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ornithorhynchusanatinus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ornithorhynchusanatinus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Oryctolaguscuniculus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ovisaries_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ovisaries_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ovisaries_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Ovisaries_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Rattusnorvegicus_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Salmosalar_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Salmosalar_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Salmosalar_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Salmosalar_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Susscrofa_IGKLJgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Vicugnapacos_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Vicugnapacos_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Vicugnapacos_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/Vicugnapacos_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGHJgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGHJgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGHJgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGHJgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGKLJgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGKLJgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGKLJgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/jgenedatabase/all_IGKLJgene_ml.txt
+ creating: Abalign_V2_Linux_Term/lib/vgenedatabase/
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Bostaurus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Camelusdromedarius_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Camelusdromedarius_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Camelusdromedarius_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Camelusdromedarius_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Canislupusfamiliaris_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Caprahircus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Caprahircus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Caprahircus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Caprahircus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Daniorerio_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Daniorerio_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Daniorerio_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Daniorerio_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Equuscaballus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Feliscatus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Feliscatus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Feliscatus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Feliscatus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gallusgallus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gorillagorillagorilla_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gorillagorillagorilla_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gorillagorillagorilla_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Gorillagorillagorilla_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Homosapiens_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Lemurcatta_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacafascicularis_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacafascicularis_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacafascicularis_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacafascicularis_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Macacamulatta_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Musmusculus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oncorhynchusmykiss_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oncorhynchusmykiss_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oncorhynchusmykiss_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oncorhynchusmykiss_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ornithorhynchusanatinus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ornithorhynchusanatinus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ornithorhynchusanatinus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ornithorhynchusanatinus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Oryctolaguscuniculus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ovisaries_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ovisaries_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ovisaries_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Ovisaries_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Rattusnorvegicus_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Salmosalar_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Salmosalar_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Salmosalar_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Salmosalar_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Susscrofa_IGKLVgene_ml.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Vicugnapacos_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Vicugnapacos_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Vicugnapacos_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/Vicugnapacos_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGHVgene_ch.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGHVgene_gh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGHVgene_kh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGHVgene_mh.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGKLVgene_cl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGKLVgene_gl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGKLVgene_kl.txt
+ inflating: Abalign_V2_Linux_Term/lib/vgenedatabase/all_IGKLVgene_ml.txt
+Reading package lists...
+Building dependency tree...
+Reading state information...
+locales is already the newest version (2.35-0ubuntu3.4).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Generating locales (this might take a while)...
+ en_US.UTF-8... done
+Generation complete.
diff --git a/ubuntu/v22.04/abalign/v1.0/Dockerfile b/ubuntu/v22.04/abalign/v1.0/Dockerfile
new file mode 100644
index 0000000..18f2582
--- /dev/null
+++ b/ubuntu/v22.04/abalign/v1.0/Dockerfile
@@ -0,0 +1,68 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## abalign ##
+## ##
+## 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>
+
+# Abalign
+# http://cao.labshare.cn/abalign/index.html
+# v2
+
+FROM gmillot/ubuntu_v22.04_extended_v1.0:gitlab_v10.2
+
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+RUN echo "\n\n\n\n================\n\nabalign installation\n\n================\n\n\n\n" > /building.log \
+ && cd /bin \
+ && wget http://cao.labshare.cn/abalign/download/Abalign_V2_Linux_Term.zip | tee -a /building.log \
+ && unzip Abalign_V2_Linux_Term.zip | tee -a /building.log \
+ && rm -rf Abalign_V2_Linux_Term.zip \
+ && cd Abalign_V2_Linux_Term
+
+
+# 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
+
+WORKDIR /bin/Abalign_V2_Linux_Term/
+
+
+# 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
+
+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
diff --git a/ubuntu/v22.04/base/.log b/ubuntu/v22.04/base/.log
new file mode 100644
index 0000000..3451fb6
--- /dev/null
+++ b/ubuntu/v22.04/base/.log
@@ -0,0 +1,33 @@
+#0 building with "default" instance using docker driver
+
+#1 [internal] load .dockerignore
+#1 transferring context: 2B done
+#1 DONE 0.1s
+
+#2 [internal] load build definition from Dockerfile
+#2 transferring dockerfile: 1.41kB 0.0s done
+#2 DONE 0.1s
+
+#3 [internal] load metadata for docker.io/library/ubuntu:22.04
+#3 DONE 12.4s
+
+#4 [1/1] FROM docker.io/library/ubuntu:22.04@sha256:2b7412e6465c3c7fc5bb21d3e6f1917c167358449fecac8176c6e496e5c1f05f
+#4 resolve docker.io/library/ubuntu:22.04@sha256:2b7412e6465c3c7fc5bb21d3e6f1917c167358449fecac8176c6e496e5c1f05f 0.0s done
+#4 sha256:2b7412e6465c3c7fc5bb21d3e6f1917c167358449fecac8176c6e496e5c1f05f 1.13kB / 1.13kB done
+#4 sha256:c9cf959fd83770dfdefd8fb42cfef0761432af36a764c077aed54bbc5bb25368 424B / 424B done
+#4 sha256:e4c58958181a5925816faa528ce959e487632f4cfd192f8132f71b32df2744b4 2.30kB / 2.30kB done
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 0B / 29.54MB 0.1s
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 3.15MB / 29.54MB 0.2s
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 17.83MB / 29.54MB 0.4s
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 23.07MB / 29.54MB 0.5s
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 25.17MB / 29.54MB 0.6s
+#4 sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 29.54MB / 29.54MB 0.7s done
+#4 extracting sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e
+#4 extracting sha256:aece8493d3972efa43bfd4ee3cdba659c0f787f8f59c82fb3e48c87cbb22a12e 0.8s done
+#4 DONE 1.7s
+
+#5 exporting to image
+#5 exporting layers done
+#5 writing image sha256:904e960655268311da7710b676aaea5ec7709a2b0738f3fe8a70dac8e4ab468a done
+#5 naming to docker.io/gmillot/ubuntu-base_v22.04:gitlab_v10.2 done
+#5 DONE 0.0s
diff --git a/ubuntu/v22.04/base/Dockerfile b/ubuntu/v22.04/base/Dockerfile
new file mode 100644
index 0000000..df8f63e
--- /dev/null
+++ b/ubuntu/v22.04/base/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>
+
+
+FROM ubuntu:22.04
+
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+ENTRYPOINT ["/bin/bash"]
diff --git a/ubuntu/v22.04/extended/v1.0/Dockerfile b/ubuntu/v22.04/extended/v1.0/Dockerfile
new file mode 100644
index 0000000..9851490
--- /dev/null
+++ b/ubuntu/v22.04/extended/v1.0/Dockerfile
@@ -0,0 +1,140 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## Ubuntu 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/
+# v8.32-4
+
+# gawk - GNU core utilities
+# https://www.gnu.org/software/gawk/
+# v5.1.0
+
+# bc - GNU core utilities
+# https://www.gnu.org/software/bc/
+# v1.07.1
+
+# git - github
+# https://github.com/git/git/archive/refs/tags/
+# v2.34.1
+
+# build-essential
+# https://packages.ubuntu.com/jammy/build-essential
+# v12.9
+
+# wget
+# https://packages.ubuntu.com/jammy/wget
+# v1.21.2
+
+# p7zip-full
+# https://packages.ubuntu.com/jammy/p7zip-full
+# v16.02+dfsg-8
+
+# zip
+# https://packages.ubuntu.com/jammy/zip
+# v3.0-12build2
+
+# unzip
+# https://packages.ubuntu.com/jammy/unzip
+# v6.0-26ubuntu3.1
+
+# tar
+# https://packages.ubuntu.com/jammy/tar
+# v1.34+dfsg
+
+
+
+
+FROM ubuntu:22.04
+
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+ENV APT_GET_LINUX_LIB="\
+ wget \
+ build-essential \
+ coreutils \
+ gawk \
+ bc \
+ git \
+ p7zip-full \
+ zip \
+ unzip \
+ tar \
+"
+
+
+# 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
+
+
+# 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
+
+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
diff --git a/ubuntu/v22.04/extended/v1.0/building.log b/ubuntu/v22.04/extended/v1.0/building.log
new file mode 100644
index 0000000..af46f13
--- /dev/null
+++ b/ubuntu/v22.04/extended/v1.0/building.log
@@ -0,0 +1,949 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Get:1 http://archive.ubuntu.com/ubuntu jammy InRelease [270 kB]
+Get:2 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB]
+Get:3 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [109 kB]
+Get:4 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
+Get:5 http://archive.ubuntu.com/ubuntu jammy/main amd64 Packages [1792 kB]
+Get:6 http://archive.ubuntu.com/ubuntu jammy/restricted amd64 Packages [164 kB]
+Get:7 http://archive.ubuntu.com/ubuntu jammy/universe amd64 Packages [17.5 MB]
+Get:8 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1203 kB]
+Get:9 http://archive.ubuntu.com/ubuntu jammy/multiverse amd64 Packages [266 kB]
+Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1472 kB]
+Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1276 kB]
+Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [49.8 kB]
+Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [1430 kB]
+Get:14 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [1009 kB]
+Get:15 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [32.6 kB]
+Get:16 http://archive.ubuntu.com/ubuntu jammy-backports/main amd64 Packages [78.3 kB]
+Get:17 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [44.0 kB]
+Get:18 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [1404 kB]
+Fetched 28.3 MB in 3s (8938 kB/s)
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+coreutils is already the newest version (8.32-4.1ubuntu1).
+tar is already the newest version (1.34+dfsg-1ubuntu0.1.22.04.1).
+The following additional packages will be installed:
+ binutils binutils-common binutils-x86-64-linux-gnu bzip2 ca-certificates cpp
+ cpp-11 dirmngr dpkg-dev fakeroot fontconfig-config fonts-dejavu-core g++
+ g++-11 gcc gcc-11 gcc-11-base git-man gnupg gnupg-l10n gnupg-utils gpg
+ gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm less
+ libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl
+ libasan6 libassuan0 libatomic1 libbinutils libbrotli1 libbsd0 libc-dev-bin
+ libc-devtools libc6-dev libcbor0.8 libcc1-0 libcrypt-dev libctf-nobfd0
+ libctf0 libcurl3-gnutls libdeflate0 libdpkg-perl libedit2 liberror-perl
+ libexpat1 libfakeroot libfido2-1 libfile-fcntllock-perl libfontconfig1
+ libfreetype6 libgcc-11-dev libgd3 libgdbm-compat4 libgdbm6 libgomp1 libisl23
+ libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libksba8 libldap-2.5-0
+ libldap-common liblocale-gettext-perl liblsan0 libmd0 libmpc3 libmpfr6
+ libnghttp2-14 libnpth0 libnsl-dev libperl5.34 libpng16-16 libpsl5
+ libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules
+ libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh-4 libstdc++-11-dev
+ libtiff5 libtirpc-dev libtsan0 libubsan1 libwebp7 libx11-6 libx11-data
+ libxau6 libxcb1 libxdmcp6 libxext6 libxmuu1 libxpm4 linux-libc-dev
+ lto-disabled-list make manpages manpages-dev netbase openssh-client openssl
+ p7zip patch perl perl-modules-5.34 pinentry-curses publicsuffix
+ readline-common rpcsvc-proto ucf xauth xz-utils
+Suggested packages:
+ binutils-doc bzip2-doc cpp-doc gcc-11-locales dbus-user-session
+ libpam-systemd pinentry-gnome3 tor debian-keyring g++-multilib
+ g++-11-multilib gcc-11-doc gawk-doc gcc-multilib autoconf automake libtool
+ flex bison gdb gcc-doc gcc-11-multilib gettext-base git-daemon-run
+ | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs
+ git-mediawiki git-svn parcimonie xloadimage scdaemon glibc-doc bzr
+ libgd-tools gdbm-l10n libsasl2-modules-gssapi-mit
+ | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp
+ libsasl2-modules-sql libstdc++-11-doc make-doc man-browser keychain
+ libpam-ssh monkeysphere ssh-askpass p7zip-rar ed diffutils-doc perl-doc
+ libterm-readline-gnu-perl | libterm-readline-perl-perl
+ libtap-harness-archive-perl pinentry-doc readline-doc
+The following NEW packages will be installed:
+ bc binutils binutils-common binutils-x86-64-linux-gnu build-essential bzip2
+ ca-certificates cpp cpp-11 dirmngr dpkg-dev fakeroot fontconfig-config
+ fonts-dejavu-core g++ g++-11 gawk gcc gcc-11 gcc-11-base git git-man gnupg
+ gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf
+ gpgsm less libalgorithm-diff-perl libalgorithm-diff-xs-perl
+ libalgorithm-merge-perl libasan6 libassuan0 libatomic1 libbinutils
+ libbrotli1 libbsd0 libc-dev-bin libc-devtools libc6-dev libcbor0.8 libcc1-0
+ libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libdeflate0 libdpkg-perl
+ libedit2 liberror-perl libexpat1 libfakeroot libfido2-1
+ libfile-fcntllock-perl libfontconfig1 libfreetype6 libgcc-11-dev libgd3
+ libgdbm-compat4 libgdbm6 libgomp1 libisl23 libitm1 libjbig0 libjpeg-turbo8
+ libjpeg8 libksba8 libldap-2.5-0 libldap-common liblocale-gettext-perl
+ liblsan0 libmd0 libmpc3 libmpfr6 libnghttp2-14 libnpth0 libnsl-dev
+ libperl5.34 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1
+ libsasl2-2 libsasl2-modules libsasl2-modules-db libsigsegv2 libsqlite3-0
+ libssh-4 libstdc++-11-dev libtiff5 libtirpc-dev libtsan0 libubsan1 libwebp7
+ libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxmuu1 libxpm4
+ linux-libc-dev lto-disabled-list make manpages manpages-dev netbase
+ openssh-client openssl p7zip p7zip-full patch perl perl-modules-5.34
+ pinentry-curses publicsuffix readline-common rpcsvc-proto ucf unzip wget
+ xauth xz-utils zip
+0 upgraded, 130 newly installed, 0 to remove and 11 not upgraded.
+Need to get 94.2 MB of archives.
+After this operation, 331 MB of additional disk space will be used.
+Get:1 http://archive.ubuntu.com/ubuntu jammy/main amd64 liblocale-gettext-perl amd64 1.07-4build3 [17.1 kB]
+Get:2 http://archive.ubuntu.com/ubuntu jammy/main amd64 libmpfr6 amd64 4.1.0-3build3 [1425 kB]
+Get:3 http://archive.ubuntu.com/ubuntu jammy/main amd64 readline-common all 8.1.2-1 [53.5 kB]
+Get:4 http://archive.ubuntu.com/ubuntu jammy/main amd64 libreadline8 amd64 8.1.2-1 [153 kB]
+Get:5 http://archive.ubuntu.com/ubuntu jammy/main amd64 libsigsegv2 amd64 2.13-1ubuntu3 [14.6 kB]
+Get:6 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gawk amd64 1:5.1.0-1ubuntu0.1 [447 kB]
+Get:7 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 perl-modules-5.34 all 5.34.0-3ubuntu1.2 [2977 kB]
+Get:8 http://archive.ubuntu.com/ubuntu jammy/main amd64 libgdbm6 amd64 1.23-1 [33.9 kB]
+Get:9 http://archive.ubuntu.com/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.23-1 [6606 B]
+Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libperl5.34 amd64 5.34.0-3ubuntu1.2 [4818 kB]
+Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 perl amd64 5.34.0-3ubuntu1.2 [232 kB]
+Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 openssl amd64 3.0.2-0ubuntu1.12 [1182 kB]
+Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 ca-certificates all 20230311ubuntu0.22.04.1 [155 kB]
+Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 less amd64 590-1ubuntu0.22.04.1 [143 kB]
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+Get:18 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libsqlite3-0 amd64 3.37.2-2ubuntu0.1 [641 kB]
+Get:19 http://archive.ubuntu.com/ubuntu jammy/main amd64 netbase all 6.3 [12.9 kB]
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+Get:44 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libctf0 amd64 2.38-4ubuntu2.3 [103 kB]
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+Get:47 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libc-dev-bin amd64 2.35-0ubuntu3.4 [20.3 kB]
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+Get:78 http://archive.ubuntu.com/ubuntu jammy/main amd64 lto-disabled-list all 24 [12.5 kB]
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+Get:80 http://archive.ubuntu.com/ubuntu jammy/main amd64 build-essential amd64 12.9ubuntu3 [4744 B]
+Get:81 http://archive.ubuntu.com/ubuntu jammy/main amd64 libassuan0 amd64 2.5.5-1build1 [38.2 kB]
+Get:82 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gpgconf amd64 2.2.27-3ubuntu2.1 [94.2 kB]
+Get:83 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libksba8 amd64 1.6.0-2ubuntu0.2 [119 kB]
+Get:84 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-3ubuntu1.2 [20.5 kB]
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+Get:86 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-0ubuntu0.22.04.1 [183 kB]
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+Get:88 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 dirmngr amd64 2.2.27-3ubuntu2.1 [293 kB]
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+Get:90 http://archive.ubuntu.com/ubuntu jammy/main amd64 fakeroot amd64 1.28-1ubuntu1 [60.4 kB]
+Get:91 http://archive.ubuntu.com/ubuntu jammy/main amd64 fonts-dejavu-core all 2.37-2build1 [1041 kB]
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+Get:94 http://archive.ubuntu.com/ubuntu jammy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB]
+Get:95 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libssh-4 amd64 0.9.6-2ubuntu0.22.04.1 [185 kB]
+Get:96 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libcurl3-gnutls amd64 7.81.0-1ubuntu1.14 [284 kB]
+Get:97 http://archive.ubuntu.com/ubuntu jammy/main amd64 liberror-perl all 0.17029-1 [26.5 kB]
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+Get:100 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gnupg-l10n all 2.2.27-3ubuntu2.1 [54.4 kB]
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+Get:102 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gpg amd64 2.2.27-3ubuntu2.1 [519 kB]
+Get:103 http://archive.ubuntu.com/ubuntu jammy/main amd64 pinentry-curses amd64 1.1.1-1build2 [34.4 kB]
+Get:104 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gpg-agent amd64 2.2.27-3ubuntu2.1 [209 kB]
+Get:105 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gpg-wks-client amd64 2.2.27-3ubuntu2.1 [62.7 kB]
+Get:106 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gpg-wks-server amd64 2.2.27-3ubuntu2.1 [57.5 kB]
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+Preparing to unpack .../119-libsasl2-modules_2.1.27+dfsg2-3ubuntu1.2_amd64.deb ...
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+Preparing to unpack .../121-p7zip_16.02+dfsg-8_amd64.deb ...
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+Selecting previously unselected package zip.
+Preparing to unpack .../124-zip_3.0-12build2_amd64.deb ...
+Unpacking zip (3.0-12build2) ...
+Setting up libksba8:amd64 (1.6.0-2ubuntu0.2) ...
+Setting up libexpat1:amd64 (2.4.7-1ubuntu0.2) ...
+Setting up gcc-11-base:amd64 (11.4.0-1ubuntu1~22.04) ...
+Setting up libxau6:amd64 (1:1.0.9-1build5) ...
+Setting up lto-disabled-list (24) ...
+Setting up libpsl5:amd64 (0.21.0-1.2build2) ...
+Setting up wget (1.21.2-2ubuntu1) ...
+Setting up gawk (1:5.1.0-1ubuntu0.1) ...
+Setting up manpages (5.10-1ubuntu1) ...
+Setting up unzip (6.0-26ubuntu3.1) ...
+Setting up libcbor0.8:amd64 (0.8.0-2ubuntu1) ...
+Setting up libbrotli1:amd64 (1.0.9-2build6) ...
+Setting up libsqlite3-0:amd64 (3.37.2-2ubuntu0.1) ...
+Setting up libsasl2-modules:amd64 (2.1.27+dfsg2-3ubuntu1.2) ...
+Setting up binutils-common:amd64 (2.38-4ubuntu2.3) ...
+Setting up libnghttp2-14:amd64 (1.43.0-1build3) ...
+Setting up libdeflate0:amd64 (1.10-2) ...
+Setting up less (590-1ubuntu0.22.04.1) ...
+Setting up linux-libc-dev:amd64 (5.15.0-88.98) ...
+Setting up bc (1.07.1-3build1) ...
+Setting up libctf-nobfd0:amd64 (2.38-4ubuntu2.3) ...
+Setting up libnpth0:amd64 (1.6-3build2) ...
+Setting up libassuan0:amd64 (2.5.5-1build1) ...
+Setting up libgomp1:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up perl-modules-5.34 (5.34.0-3ubuntu1.2) ...
+Setting up bzip2 (1.0.8-5build1) ...
+Setting up libldap-common (2.5.16+dfsg-0ubuntu0.22.04.1) ...
+Setting up libjbig0:amd64 (2.1-3.1ubuntu0.22.04.1) ...
+Setting up libfakeroot:amd64 (1.28-1ubuntu1) ...
+Setting up libasan6:amd64 (11.4.0-1ubuntu1~22.04) ...
+Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg2-3ubuntu1.2) ...
+Setting up fakeroot (1.28-1ubuntu1) ...
+update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/fakeroot.1.gz because associated file /usr/share/man/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/faked.1.gz because associated file /usr/share/man/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/es/man1/fakeroot.1.gz because associated file /usr/share/man/es/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/es/man1/faked.1.gz because associated file /usr/share/man/es/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/fr/man1/fakeroot.1.gz because associated file /usr/share/man/fr/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/fr/man1/faked.1.gz because associated file /usr/share/man/fr/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/sv/man1/fakeroot.1.gz because associated file /usr/share/man/sv/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/sv/man1/faked.1.gz because associated file /usr/share/man/sv/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
+Setting up zip (3.0-12build2) ...
+Setting up libtirpc-dev:amd64 (1.3.2-2ubuntu0.1) ...
+Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
+Setting up libx11-data (2:1.7.5-1ubuntu0.3) ...
+Setting up make (4.3-4.1build1) ...
+Setting up gnupg-l10n (2.2.27-3ubuntu2.1) ...
+Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ...
+Setting up xz-utils (5.2.5-2ubuntu1) ...
+update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzma.1.gz because associated file /usr/share/man/man1/xz.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/unlzma.1.gz because associated file /usr/share/man/man1/unxz.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzcat.1.gz because associated file /usr/share/man/man1/xzcat.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzmore.1.gz because associated file /usr/share/man/man1/xzmore.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzless.1.gz because associated file /usr/share/man/man1/xzless.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzdiff.1.gz because associated file /usr/share/man/man1/xzdiff.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzcmp.1.gz because associated file /usr/share/man/man1/xzcmp.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzgrep.1.gz because associated file /usr/share/man/man1/xzgrep.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzegrep.1.gz because associated file /usr/share/man/man1/xzegrep.1.gz (of link group lzma) doesn't exist
+update-alternatives: warning: skip creation of /usr/share/man/man1/lzfgrep.1.gz because associated file /usr/share/man/man1/xzfgrep.1.gz (of link group lzma) doesn't exist
+Setting up libquadmath0:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up libpng16-16:amd64 (1.6.37-3build5) ...
+Setting up libmpc3:amd64 (1.2.1-2build1) ...
+Setting up libatomic1:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up patch (2.7.6-7build2) ...
+Setting up fonts-dejavu-core (2.37-2build1) ...
+Setting up ucf (3.0043) ...
+Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ...
+Setting up libsasl2-2:amd64 (2.1.27+dfsg2-3ubuntu1.2) ...
+Setting up libssh-4:amd64 (0.9.6-2ubuntu0.22.04.1) ...
+Setting up libwebp7:amd64 (1.2.2-2ubuntu0.22.04.2) ...
+Setting up libubsan1:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up libmd0:amd64 (1.0.4-1build1) ...
+Setting up libnsl-dev:amd64 (1.3.0-2build2) ...
+Setting up libcrypt-dev:amd64 (1:4.4.27-1) ...
+Setting up gpgconf (2.2.27-3ubuntu2.1) ...
+Setting up git-man (1:2.34.1-1ubuntu1.10) ...
+Setting up netbase (6.3) ...
+Setting up libbinutils:amd64 (2.38-4ubuntu2.3) ...
+Setting up libfido2-1:amd64 (1.10.0-1) ...
+Setting up libisl23:amd64 (0.24-2build1) ...
+Setting up libc-dev-bin (2.35-0ubuntu3.4) ...
+Setting up openssl (3.0.2-0ubuntu1.12) ...
+Setting up libbsd0:amd64 (0.11.5-1) ...
+Setting up publicsuffix (20211207.1025-1) ...
+Setting up libcc1-0:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up liblocale-gettext-perl (1.07-4build3) ...
+Setting up gpg (2.2.27-3ubuntu2.1) ...
+Setting up liblsan0:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up p7zip (16.02+dfsg-8) ...
+Setting up libitm1:amd64 (12.3.0-1ubuntu1~22.04) ...
+Setting up libgdbm6:amd64 (1.23-1) ...
+Setting up gnupg-utils (2.2.27-3ubuntu2.1) ...
+Setting up libtsan0:amd64 (11.4.0-1ubuntu1~22.04) ...
+Setting up libctf0:amd64 (2.38-4ubuntu2.3) ...
+Setting up libjpeg8:amd64 (8c-2ubuntu10) ...
+Setting up pinentry-curses (1.1.1-1build2) ...
+Setting up cpp-11 (11.4.0-1ubuntu1~22.04) ...
+Setting up manpages-dev (5.10-1ubuntu1) ...
+Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ...
+Setting up libxcb1:amd64 (1.14-3ubuntu3) ...
+Setting up gpg-agent (2.2.27-3ubuntu2.1) ...
+Setting up fontconfig-config (2.13.1-4.2ubuntu5) ...
+Setting up libedit2:amd64 (3.1-20210910-1build1) ...
+Setting up gpgsm (2.2.27-3ubuntu2.1) ...
+Setting up p7zip-full (16.02+dfsg-8) ...
+Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-0ubuntu0.22.04.1) ...
+Setting up dirmngr (2.2.27-3ubuntu2.1) ...
+Setting up ca-certificates (20230311ubuntu0.22.04.1) ...
+Updating certificates in /etc/ssl/certs...
+137 added, 0 removed; done.
+Setting up libfreetype6:amd64 (2.11.1+dfsg-1ubuntu0.2) ...
+Setting up libgdbm-compat4:amd64 (1.23-1) ...
+Setting up gpg-wks-server (2.2.27-3ubuntu2.1) ...
+Setting up libgcc-11-dev:amd64 (11.4.0-1ubuntu1~22.04) ...
+Setting up cpp (4:11.2.0-1ubuntu1) ...
+Setting up libc6-dev:amd64 (2.35-0ubuntu3.4) ...
+Setting up libx11-6:amd64 (2:1.7.5-1ubuntu0.3) ...
+Setting up libtiff5:amd64 (4.3.0-6ubuntu0.6) ...
+Setting up libfontconfig1:amd64 (2.13.1-4.2ubuntu5) ...
+Setting up libxmuu1:amd64 (2:1.1.3-3) ...
+Setting up binutils-x86-64-linux-gnu (2.38-4ubuntu2.3) ...
+Setting up libperl5.34:amd64 (5.34.0-3ubuntu1.2) ...
+Setting up libxpm4:amd64 (1:3.5.12-1ubuntu0.22.04.2) ...
+Setting up gpg-wks-client (2.2.27-3ubuntu2.1) ...
+Setting up openssh-client (1:8.9p1-3ubuntu0.4) ...
+update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/rsh.1.gz because associated file /usr/share/man/man1/ssh.1.gz (of link group rsh) doesn't exist
+update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/rlogin.1.gz because associated file /usr/share/man/man1/slogin.1.gz (of link group rlogin) doesn't exist
+update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/rcp.1.gz because associated file /usr/share/man/man1/scp.1.gz (of link group rcp) doesn't exist
+Setting up libxext6:amd64 (2:1.3.4-1build1) ...
+Setting up libcurl3-gnutls:amd64 (7.81.0-1ubuntu1.14) ...
+Setting up binutils (2.38-4ubuntu2.3) ...
+Setting up perl (5.34.0-3ubuntu1.2) ...
+Setting up libgd3:amd64 (2.3.0-2ubuntu2) ...
+Setting up libdpkg-perl (1.21.1ubuntu2.2) ...
+Setting up libstdc++-11-dev:amd64 (11.4.0-1ubuntu1~22.04) ...
+Setting up gcc-11 (11.4.0-1ubuntu1~22.04) ...
+Setting up xauth (1:1.1-1build2) ...
+Setting up gnupg (2.2.27-3ubuntu2.1) ...
+Setting up libc-devtools (2.35-0ubuntu3.4) ...
+Setting up g++-11 (11.4.0-1ubuntu1~22.04) ...
+Setting up libfile-fcntllock-perl (0.22-3build7) ...
+Setting up libalgorithm-diff-perl (1.201-1) ...
+Setting up gcc (4:11.2.0-1ubuntu1) ...
+Setting up dpkg-dev (1.21.1ubuntu2.2) ...
+Setting up liberror-perl (0.17029-1) ...
+Setting up git (1:2.34.1-1ubuntu1.10) ...
+Setting up g++ (4:11.2.0-1ubuntu1) ...
+update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist
+Setting up build-essential (12.9ubuntu3) ...
+Setting up libalgorithm-diff-xs-perl (0.04-6build3) ...
+Setting up libalgorithm-merge-perl (0.08-3) ...
+Processing triggers for libc-bin (2.35-0ubuntu3.4) ...
+Processing triggers for ca-certificates (20230311ubuntu0.22.04.1) ...
+Updating certificates in /etc/ssl/certs...
+0 added, 0 removed; done.
+Running hooks in /etc/ca-certificates/update.d...
+done.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following NEW packages will be installed:
+ locales
+0 upgraded, 1 newly installed, 0 to remove and 11 not upgraded.
+Need to get 4245 kB of archives.
+After this operation, 17.5 MB of additional disk space will be used.
+Get:1 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 locales all 2.35-0ubuntu3.4 [4245 kB]
+Fetched 4245 kB in 0s (22.5 MB/s)
+Selecting previously unselected package locales.
+(Reading database ...
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(Reading database ... 15384 files and directories currently installed.)
+Preparing to unpack .../locales_2.35-0ubuntu3.4_all.deb ...
+Unpacking locales (2.35-0ubuntu3.4) ...
+Setting up locales (2.35-0ubuntu3.4) ...
+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 11 not upgraded.
+
+
+
+
+================
+
+apt-get clean
+
+================
+
+
+
+
+
+
+
+
+================
+
+rm
+
+================
+
+
+
+
+
+
+
+
+================
+
+installed packages
+
+================
+
+
+
+
+wget:
+ Installed: 1.21.2-2ubuntu1
+ Candidate: 1.21.2-2ubuntu1
+ Version table:
+ *** 1.21.2-2ubuntu1 100
+ 100 /var/lib/dpkg/status
+build-essential:
+ Installed: 12.9ubuntu3
+ Candidate: 12.9ubuntu3
+ Version table:
+ *** 12.9ubuntu3 100
+ 100 /var/lib/dpkg/status
+coreutils:
+ Installed: 8.32-4.1ubuntu1
+ Candidate: 8.32-4.1ubuntu1
+ Version table:
+ *** 8.32-4.1ubuntu1 100
+ 100 /var/lib/dpkg/status
+gawk:
+ Installed: 1:5.1.0-1ubuntu0.1
+ Candidate: 1:5.1.0-1ubuntu0.1
+ Version table:
+ *** 1:5.1.0-1ubuntu0.1 100
+ 100 /var/lib/dpkg/status
+bc:
+ Installed: 1.07.1-3build1
+ Candidate: 1.07.1-3build1
+ Version table:
+ *** 1.07.1-3build1 100
+ 100 /var/lib/dpkg/status
+git:
+ Installed: 1:2.34.1-1ubuntu1.10
+ Candidate: 1:2.34.1-1ubuntu1.10
+ Version table:
+ *** 1:2.34.1-1ubuntu1.10 100
+ 100 /var/lib/dpkg/status
+p7zip-full:
+ Installed: 16.02+dfsg-8
+ Candidate: 16.02+dfsg-8
+ Version table:
+ *** 16.02+dfsg-8 100
+ 100 /var/lib/dpkg/status
+zip:
+ Installed: 3.0-12build2
+ Candidate: 3.0-12build2
+ Version table:
+ *** 3.0-12build2 100
+ 100 /var/lib/dpkg/status
+unzip:
+ Installed: 6.0-26ubuntu3.1
+ Candidate: 6.0-26ubuntu3.1
+ Version table:
+ *** 6.0-26ubuntu3.1 100
+ 100 /var/lib/dpkg/status
+tar:
+ Installed: 1.34+dfsg-1ubuntu0.1.22.04.1
+ Candidate: 1.34+dfsg-1ubuntu0.1.22.04.1
+ Version table:
+ *** 1.34+dfsg-1ubuntu0.1.22.04.1 100
+ 100 /var/lib/dpkg/status
+locales:
+ Installed: 2.35-0ubuntu3.4
+ Candidate: 2.35-0ubuntu3.4
+ Version table:
+ *** 2.35-0ubuntu3.4 100
+ 100 /var/lib/dpkg/status
+locales-all:
+ Installed: (none)
+ Candidate: (none)
+ Version table:
--
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