TABLE OF CONTENTS
AIM
Dockerfiles that generated the images in dockerhub.
VERSIONS
The different releases are tagged here
LICENCE
These scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose. See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.
CITATION
None
CREDITS
- Gael A. Millot, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
- Eric Deveaud, HPC Core Facility, Institut Pasteur, Paris, France
ACKNOWLEDGEMENTS
The developers & maintainers of the mentioned softwares and packages, including:
Special acknowledgement to:
- Frédéric Lemoine, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
- Bertrand Néron, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
- Yang Cao, Sichuan University, Chengdu, China, for the release of Abalign.
WHAT'S NEW IN
Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below
11.3
Dockerfiles added:
ubuntu\v22.04\smrt\v25.2\v3.0.apptainer at date 20250725
redhat\v8.10 at date 20250725
11.2
Dockerfiles modified:
R/v4.1.2/extended/v4.0 at date 20250710: from gmillot/r_v4.1.2_extended_v3.3:gitlab_v9.9 with saferDev added
11.1
Dockerfiles modified:
ubuntu/v22.04/smrt/v25.2 at date 20250326: from ubuntu/v22.04/ with smrt v25.2 full version (GUI) added
11.0
Dockerfiles added:
ubuntu/v22.04/smrt/v25.2 at date 20250325: from ubuntu/v22.04/ with smrt v25.2 added
10.9
Dockerfiles added:
fedora/v33/immcantation/v2.0 at date 20250128: from immcantation/suite:4.5.0, with lubridate and svglite packages added
10.8
Dockerfiles added:
ubuntu/v20.04/alohomora_merlin_allegro/v1.0 at date 20231212: from ubuntu/v20.04/alohomora_merlin/v2.1:gitlab_v9.5, with allegro soft and alohomora_bch_haplo_20231212 and allegro_20231212.pl script files added
Warning: see section 8.5 below
10.7
Dockerfiles added:
ubuntu/v20.04/alohomora_merlin/v2.2 at date 20231211: from ubuntu/v20.04/alohomora_merlin/v2.1:gitlab_v9.5, with allegro added
Warning: see section 8.5 below
10.6
Dockerfiles modified:
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
10.5
Dockerfiles modified:
ubuntu_v22.4_bcftools_v1.18 at date 20231201: from gmillot/ubuntu_v22.4_bcftools_v1.18:gitlab_v10.4 with pigz added
10.4
Dockerfiles modified:
ubuntu_v22.4_bcftools_v1.18 at date 20231201: from gmillot/ubuntu_v22.4_bcftools_v1.18:gitlab_v10.3 with gzip and tabix added
10.3
Dockerfiles added:
ubuntu_v22.4_bcftools_v1.18 at date 20231128
10.2
Dockerfiles added:
ubuntu/v22.04/base at date 20231114
ubuntu/v22.04/extended/v1.0 at date 20231114: from ubuntu:22.04 with wget git bc gawk coreutils added
ubuntu/v22.04/abalign/v1.0 at date 20231114
python/v3.6.12/base/v1.0 at date 20231114
python/v3.6.12/nanoForkSpeed_basecalling/v1.0 at date 20231114
10.1
Dockerfiles modified:
fedora/v33/immcantation/v1.2 at date 20230407: from gmillot/immcantation_v1.1:gitlab_v10.0 with lubridate added
10.0
Dockerfiles modified:
fedora/v33/immcantation/v1.1 at date 20230407: from gmillot/immcantation_v1.0:gitlab_v9.0 with svglite added
9.9
Dockerfiles modified:
R/v4.1.2/extended/v3.3 at date 20230331: from gmillot/r_v4.1.2_extended_v3.2:gitlab_v9.8 with lemon added
R/v4.1.2/ig_clustering/v1.3 at date 20230331: from gmillot/r_v4.1.2_ig_clustering_v1.2:gitlab_v9.8 with lemon added
9.8
Dockerfiles modified:
R/v4.1.2/extended/v3.2 at date 20230323: from gmillot/r_v4.1.2_extended_v3.1:gitlab_v9.6 with ggrepel added
R/v4.1.2/ig_clustering/v1.2 at date 20230323: from gmillot/r_v4.1.2_ig_clustering_v1.1:gitlab_v9.7 with ggrepel added
9.7
Dockerfiles modified:
R/v4.1.2/ig_clustering/v1.1 at date 20230211: from gmillot/r_v4.1.2_ig_clustering_v1.0:gitlab_v9.3 with svglite added and debugged
9.6
Dockerfiles added:
R/v4.1.2/extended/v3.1 at date 20230211: from gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3 with svglite added
R/v4.1.2/ig_clustering/v1.1 at date 20230211: from gmillot/r_v4.1.2_ig_clustering_v1.0:gitlab_v9.3 with svglite added
9.5
Dockerfiles added:
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:
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
9.3
Dockerfiles added:
R/v4.1.2/extended/v3.0 at date 20221108: from gmillot/r-base_v4.1.2:gitlab_v8.2 used as base for R/v4.1.2/ig_clustering
R/v4.1.2/ig_clustering/v1.0 at date 20221108: from gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3
9.2
Dockerfiles added:
python/3.9.10/changeo_presto/v1.0 at date 20221007: from ubuntu:20.04 & python v3.9.10
9.1
Dockerfiles added:
ubuntu/v20.04/extended/v1.0 at date 20221002: from ubuntu:20.04 with git bc gawk coreutils added
ubuntu/v20.04/slivar/v2.0 at date 20221002: from ubuntu:20.04 with samtools and slivar added
ubuntu/v20.04/samtools/v1.0 at date 20221002: from ubuntu:20.04 with samtools added
ubuntu/v20.04/htslib/v1.0 at date 20221002: from ubuntu:20.04 with samtools added
9.0
Dockerfiles added:
fedora/v33/immcantation/v1.0 at date 20220928: docker image of immancation
8.11
Dockerfiles added:
ubuntu/v20.04/slivar/v1.0 at date 20220705: from ubuntu:20.04 with slivar added
8.10
Dockerfiles 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:
R/v4.1.2/contracted/v1.0 at date 20220622:
v8.8
Dockerfiles 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:
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:
python/v3.6.8/base/v1.0 at date 20220504: FROM python:3.6.8
python/v3.6.8/serpentine/v1.0 at date 20220504: from gmillot/python_v3.8.6_base_v1.0:gitlab_v8.6
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:
ubuntu/v16.04/base at date 20220422
ubuntu/v20.04/base at date 20220422
ubuntu/v20.04/alohomora_merlin/v1.0 at date 20220422
Warning: do not use --entrypoint bash for image alohomora_merlin/v1.0, because modules will not be available.
Just use : sudo docker run -ti d6e1595795cf
Explanation:
ENTRYPOINT=["/usr/bin/bash" , "-l"]
Pourquoi du coup cela marche avec /usr/bin/bash -l ?
Shell de login vs shell classique
Shell de login source les fichiers d’init systemes
Shell classique source les fichiers d’init user
v8.4
Dockerfiles 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
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
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:
python/v3.9.10/extended/v1.0 at date 20220314: using the debian 11 bullseye system
v8.2
Dockerfiles added:
R/v4.1.2/base at date 20220310: using the ubuntu 20.04 system
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
R/v4.1.2/extended v2.0 at date 20220310: v1.0 + 5 packages installed for rmarkdown and pdftools
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:
ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20220114: locales added
v8.0
Dockerfiles added:
ubuntu/v16.04/bedtools/v1.14 at date 20220114
Dockerfiles modified:
ubuntu/v16.04/bash-extended/v4.0 at date 20220114: locales added
ubuntu/v16.04/samtools/v1.14 at date 20220114: locales added
ubuntu/v16.04/bowtie2-extended/v2.0 at date 20220114: locales added
v7.0
Dockerfiles added:
ubuntu/v16.04/bowtie2-extended/v1.0 at date 20220106
ubuntu/v16.04/samtools/v1.14 at date 20220106
v6.4
Dockerfiles added:
R/v4.0.5/extended v2.0 at date 20211228: v1.0 + pandoc added for knitting documents using R
v6.3
Dockerfiles modified:
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:
R/v4.0.5/extended at date 20211213: ggplot2 v3.3.3 to fit with cute and devtools correctly installed
v6.1
Dockerfiles modified:
R/v4.0.5/extended at date 20211212: dependencies=NA instead of dependencies=TRUE (no suggested packages installed)
v6.0
Dockerfiles modified:
R/v4.0.5/extended at date 20211211: location of the library folder forced
v5.1
Dockerfiles modified:
ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20211117: debbugging (CR removed from AlienTrimmer.sh)
v5.0
Dockerfiles modified:
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:
ubuntu/v16.04/bcftools/v1.14 at date 20211108
Dockerfiles modified:
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 |
|
1.3 GB |
| V3.0 |
|
81.7 MB |
v3.0
Dockerfiles added:
ubuntu/v16.04/git/v2.33.1 at date 20211029
ubuntu/v16.04/bash-extended/v2.0 at date 20211029
Dockerfiles modified:
R/v4.0.5/base at date 20211002: comment added to explain the install of procps
v2.0
Dockerfiles added:
ubuntu/v16.04/alien_trimmer/v0.4.0 at date 20211001
v1.0
Dockerfiles added:
ubuntu/v16.04/coreutils/v8.30 at date 20211001
ubuntu/v16.04/gawk/v5.1.0 at date 20211001
ubuntu/v16.04/bc/v1.07 at date 20211001
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
R/v4.0.5/extended at date 20211001