From b2737f4f8acc2a1179ff69b838d483ff9ea42de6 Mon Sep 17 00:00:00 2001
From: gmillot <gael.millot@pasteur.fr>
Date: Tue, 9 Nov 2021 18:29:23 +0100
Subject: [PATCH] test
---
R/v4.0.5/base/Dockerfile | 32 +-
R/v4.0.5/extended/Dockerfile | 554 +++++++++---------
README.md | 198 +++----
.../alien_trimmer/v0.4.0/AlienTrimmer.sh | 2 +-
ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile | 72 +--
ubuntu/v16.04/bash-extended/v1.0/Dockerfile | 118 ++--
ubuntu/v16.04/bash-extended/v2.0/Dockerfile | 160 ++---
ubuntu/v16.04/bc/v1.07/Dockerfile | 72 +--
ubuntu/v16.04/bcftools/v1.14/Dockerfile | 37 ++
ubuntu/v16.04/coreutils/v8.30/Dockerfile | 74 +--
ubuntu/v16.04/gawk/v5.1.0/Dockerfile | 72 +--
ubuntu/v16.04/git/v2.33.1/Dockerfile | 74 +--
12 files changed, 751 insertions(+), 714 deletions(-)
create mode 100644 ubuntu/v16.04/bcftools/v1.14/Dockerfile
diff --git a/R/v4.0.5/base/Dockerfile b/R/v4.0.5/base/Dockerfile
index ed34473..5865d0b 100644
--- a/R/v4.0.5/base/Dockerfile
+++ b/R/v4.0.5/base/Dockerfile
@@ -1,16 +1,16 @@
-# R
-# https://cran.r-project.org/
-# v4.0.5
-
-# base image: r-base:4.0.5, see https://hub.docker.com/_/r-base for details
-FROM r-base:4.0.5
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/r-base:4.0.5 iw not correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update \
-&& apt-get install -y procps
-## nextflow needs procps for usage stats, cpu and process memory. Normally, this package is present by default in ubuntu. But in the R base image, it seems that there is a problem, the reason why it is installed here
-
-ENTRYPOINT ["/usr/bin/R"]
+# R
+# https://cran.r-project.org/
+# v4.0.5
+
+# base image: r-base:4.0.5, see https://hub.docker.com/_/r-base for details
+FROM r-base:4.0.5
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/r-base:4.0.5 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update \
+&& apt-get install -y procps
+## nextflow needs procps for usage stats, cpu and process memory. Normally, this package is present by default in ubuntu. But in the R base image, it seems that there is a problem, the reason why it is installed here
+
+ENTRYPOINT ["/usr/bin/R"]
diff --git a/R/v4.0.5/extended/Dockerfile b/R/v4.0.5/extended/Dockerfile
index f1233b7..ffdeb40 100644
--- a/R/v4.0.5/extended/Dockerfile
+++ b/R/v4.0.5/extended/Dockerfile
@@ -1,277 +1,277 @@
-
-# to get all the packages:
-## open a R session
-## use
-# lib_path = "C:/Program Files/R/R-4.0.5/library"
-# ip = as.data.frame(installed.packages(lib.loc = lib_path)[,c(1,3:4)])
-# ip = ip[is.na(ip$Priority),1:2,drop=FALSE]
-# ip
-
-
-# R v4.0.5 with packages:
-# Package Version
-# SARTools 1.7.3
-# abind 1.4-5
-# annotate 1.68.0
-# AnnotationDbi 1.52.0
-# askpass 1.1
-# assertthat 0.2.1
-# backports 1.2.1
-# base64enc 0.1-3
-# BH 1.75.0-0
-# Biobase 2.50.0
-# BiocGenerics 0.36.0
-# BiocManager 1.30.12
-# BiocParallel 1.24.1
-# BiocVersion 3.12.0
-# Biostrings 2.58.0
-# bit 4.0.4
-# bit64 4.0.5
-# bitops 1.0-6
-# blob 1.2.1
-# brew 1.0-6
-# brio 1.1.1
-# broom 0.7.6
-# cachem 1.0.4
-# Cairo 1.5-12.2
-# callr 3.6.0
-# car 3.0-10
-# carData 3.0-4
-# caTools 1.18.2
-# cellranger 1.1.0
-# CGHbase 1.50.0
-# CGHcall 2.52.0
-# cli 2.4.0
-# clipr 0.7.1
-# colorspace 2.0-0
-# commonmark 1.7
-# conquer 1.0.2
-# corrplot 0.84
-# covr 3.5.1
-# cpp11 0.2.7
-# crayon 1.4.1
-# credentials 1.3.0
-# crosstalk 1.1.1
-# curl 4.3
-# data.table 1.14.0
-# DBI 1.1.1
-# dbplyr 2.1.1
-# DelayedArray 0.16.3
-# desc 1.3.0
-# DESeq2 1.30.1
-# devtools 2.4.2
-# diffobj 0.3.4
-# digest 0.6.27
-# DNAcopy 1.64.0
-# dplyr 1.0.5
-# DT 0.17
-# dtplyr 1.1.0
-# edgeR 3.32.1
-# ellipsis 0.3.1
-# emmeans 1.5.5-1
-# estimability 1.3
-# evaluate 0.14
-# ExPosition 2.8.23
-# fansi 0.4.2
-# farver 2.1.0
-# fastmap 1.1.0
-# forcats 0.5.1
-# formatR 1.8
-# fs 1.5.0
-# futile.logger 1.4.3
-# futile.options 1.0.1
-# future 1.21.0
-# future.apply 1.7.0
-# gargle 1.1.0
-# genefilter 1.72.1
-# geneplotter 1.68.0
-# generics 0.1.0
-# GenomeInfoDb 1.26.4
-# GenomeInfoDbData 1.2.4
-# GenomicRanges 1.42.0
-# gert 1.3.0
-# GGally 2.1.1
-# ggdendro 0.1.22
-# ggplot2 3.3.3
-# ggrepel 0.9.1
-# gh 1.2.0
-# gitcreds 0.1.1
-# githubinstall 0.2.2
-# globals 0.14.0
-# glue 1.4.2
-# googledrive 1.0.1
-# googlesheets4 0.3.0
-# gplots 3.1.1
-# gridExtra 2.3
-# gtable 0.3.0
-# gtools 3.8.2
-# haven 2.3.1
-# HiCcompare 1.12.0
-# highr 0.8
-# hms 1.0.0
-# htmltools 0.5.1.1
-# htmlwidgets 1.5.3
-# httr 1.4.2
-# ids 1.0.1
-# impute 1.64.0
-# ini 0.3.1
-# InteractionSet 1.18.1
-# IRanges 2.24.1
-# isoband 0.2.4
-# jpeg 0.1-8.1
-# jsonlite 1.7.2
-# kableExtra 1.3.4
-# knitr 1.31
-# labeling 0.4.2
-# lambda.r 1.2.4
-# later 1.1.0.1
-# lazyeval 0.2.2
-# lemon 0.4.5
-# lifecycle 1.0.0
-# limma 3.46.0
-# listenv 0.8.0
-# lme4 1.1-26
-# lmerTest 3.1-3
-# locfit 1.5-9.4
-# lubridate 1.7.10
-# magrittr 2.0.1
-# maptools 1.1-1
-# markdown 1.1
-# marray 1.68.0
-# MatrixGenerics 1.2.1
-# MatrixModels 0.5-0
-# matrixStats 0.58.0
-# memoise 2.0.0
-# mime 0.1
-# minqa 1.2.4
-# mockery 0.4.2
-# modelr 0.1.8
-# munsell 0.5.0
-# mvtnorm 1.1-1
-# nloptr 1.2.2.2
-# numDeriv 2016.8-1.1
-# openssl 1.4.3
-# openxlsx 4.2.3
-# parallelly 1.24.0
-# pbkrtest 0.5.1
-# pheatmap 1.0.12
-# pillar 1.6.0
-# pkgbuild 1.2.0
-# pkgconfig 2.0.3
-# pkgload 1.2.1
-# plogr 0.2.0
-# plyr 1.8.6
-# png 0.1-7
-# praise 1.0.0
-# prettyGraphs 2.1.6
-# prettyunits 1.1.1
-# processx 3.5.0
-# progress 1.2.2
-# promises 1.2.0.1
-# ps 1.6.0
-# pspearman 0.3-0
-# purrr 0.3.4
-# QDNAseq 1.26.0
-# quantreg 5.85
-# R.methodsS3 1.8.1
-# R.oo 1.24.0
-# R.utils 2.10.1
-# R6 2.5.0
-# rappdirs 0.3.3
-# rcmdcheck 1.3.3
-# RColorBrewer 1.1-2
-# Rcpp 1.0.6
-# RcppArmadillo 0.10.2.2.0
-# RcppEigen 0.3.3.9.1
-# RCurl 1.98-1.3
-# readr 1.4.0
-# readxl 1.3.1
-# rematch 1.0.1
-# rematch2 2.1.2
-# remotes 2.3.0
-# reprex 2.0.0
-# reshape 0.8.8
-# reshape2 1.4.4
-# reticulate 1.19
-# rex 1.2.0
-# rhdf5 2.34.0
-# rhdf5filters 1.2.0
-# Rhdf5lib 1.12.1
-# Rhtslib 1.22.0
-# rio 0.5.26
-# rlang 0.4.10
-# rmarkdown 2.7
-# roxygen2 7.1.1
-# rprojroot 2.0.2
-# Rsamtools 2.6.0
-# RSQLite 2.2.5
-# rstudioapi 0.13
-# rversions 2.0.2
-# rvest 1.0.0
-# S4Vectors 0.28.1
-# SARTools 1.7.3
-# scales 1.1.1
-# selectr 0.4-2
-# sessioninfo 1.1.1
-# snow 0.4-3
-# snowfall 1.84-6.1
-# sp 1.4-5
-# SparseM 1.81
-# statmod 1.4.35
-# stringi 1.5.3
-# stringr 1.4.0
-# SummarizedExperiment 1.20.0
-# SuppDists 1.1-9.5
-# svglite 2.0.0
-# sys 3.4
-# systemfonts 1.0.1
-# testthat 3.0.2
-# tibble 3.1.0
-# tidyr 1.1.3
-# tidyselect 1.1.0
-# tidyverse 1.3.1
-# tinytex 0.31
-# translations 4.0.5
-# usethis 2.0.1
-# utf8 1.2.1
-# uuid 0.1-4
-# vctrs 0.3.7
-# viridisLite 0.3.0
-# waldo 0.2.5
-# webshot 0.5.2
-# whisker 0.4
-# withr 2.4.1
-# xfun 0.22
-# XML 3.99-0.6
-# xml2 1.3.2
-# xopen 1.0.0
-# xtable 1.8-4
-# XVector 0.30.0
-# yaml 2.2.1
-# zip 2.1.1
-# zlibbioc 1.36.0
-
-
-
-
-
-# base image: r-base:4.0.5
-FROM gmillot/r-base_v4.0.5:gitlab_v1.0
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. Here, the image is present locally, or distantly on the gmillot repo. Thus, gmillot/r-base:4.0.5 is correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-ENV CRANREPO="'https://cran.irsn.fr/'"
-# use the code above to get the list of the installed packages
-ENV RLIB="'SARTools' 'abind' 'annotate' 'AnnotationDbi' 'askpass' 'assertthat' 'backports' 'base64enc' 'BH' 'Biobase' 'BiocGenerics' 'BiocManager' 'BiocParallel' 'BiocVersion' 'Biostrings' 'bit' 'bit64' 'bitops' 'blob' 'brew' 'brio' 'broom' 'cachem' 'Cairo' 'callr' 'car' 'carData' 'caTools' 'cellranger' 'CGHbase' 'CGHcall' 'cli' 'clipr' 'colorspace' 'commonmark' 'conquer' 'corrplot' 'covr' 'cpp11' 'crayon' 'credentials' 'crosstalk' 'curl' 'data.table' 'DBI' 'dbplyr' 'DelayedArray' 'desc' 'DESeq2' 'devtools' 'diffobj' 'digest' 'DNAcopy' 'dplyr' 'DT' 'dtplyr' 'edgeR' 'ellipsis' 'emmeans' 'estimability' 'evaluate' 'ExPosition' 'fansi' 'farver' 'fastmap' 'forcats' 'formatR' 'fs' 'futile.logger' 'futile.options' 'future' 'future.apply' 'gargle' 'genefilter' 'geneplotter' 'generics' 'GenomeInfoDb' 'GenomeInfoDbData' 'GenomicRanges' 'gert' 'GGally' 'ggdendro' 'ggplot2' 'ggrepel' 'gh' 'gitcreds' 'githubinstall' 'globals' 'glue' 'googledrive' 'googlesheets4' 'gplots' 'gridExtra' 'gtable' 'gtools' 'haven' 'HiCcompare' 'highr' 'hms' 'htmltools' 'htmlwidgets' 'httr' 'ids' 'impute' 'ini' 'InteractionSet' 'IRanges' 'isoband' 'jpeg' 'jsonlite' 'kableExtra' 'knitr' 'labeling' 'lambda.r' 'later' 'lazyeval' 'lemon' 'lifecycle' 'limma' 'listenv' 'lme4' 'lmerTest' 'locfit' 'lubridate' 'magrittr' 'maptools' 'markdown' 'marray' 'MatrixGenerics' 'MatrixModels' 'matrixStats' 'memoise' 'mime' 'minqa' 'mockery' 'modelr' 'munsell' 'mvtnorm' 'nloptr' 'numDeriv' 'openssl' 'openxlsx' 'parallelly' 'pbkrtest' 'pheatmap' 'pillar' 'pkgbuild' 'pkgconfig' 'pkgload' 'plogr' 'plyr' 'png' 'praise' 'prettyGraphs' 'prettyunits' 'processx' 'progress' 'promises' 'ps' 'pspearman' 'purrr' 'QDNAseq' 'quantreg' 'R.methodsS3' 'R.oo' 'R.utils' 'R6' 'rappdirs' 'rcmdcheck' 'RColorBrewer' 'Rcpp' 'RcppArmadillo' 'RcppEigen' 'RCurl' 'readr' 'readxl' 'rematch' 'rematch2' 'remotes' 'reprex' 'reshape' 'reshape2' 'reticulate' 'rex' 'rhdf5' 'rhdf5filters' 'Rhdf5lib' 'Rhtslib' 'rio' 'rlang' 'rmarkdown' 'roxygen2' 'rprojroot' 'Rsamtools' 'RSQLite' 'rstudioapi' 'rversions' 'rvest' 'S4Vectors' 'SARTools' 'scales' 'selectr' 'sessioninfo' 'snow' 'snowfall' 'sp' 'SparseM' 'statmod' 'stringi' 'stringr' 'SummarizedExperiment' 'SuppDists' 'svglite' 'sys' 'systemfonts' 'testthat' 'tibble' 'tidyr' 'tidyselect' 'tidyverse' 'tinytex' 'translations' 'usethis' 'utf8' 'uuid' 'vctrs' 'viridisLite' 'waldo' 'webshot' 'whisker' 'withr' 'xfun' 'XML' 'xml2' 'xopen' 'xtable' 'XVector' 'yaml' 'zip' 'zlibbioc'"
-
-# nextflow needs procps for usage stats, cpu and process memory. Normally, this package is present by default in ubuntu. But in the R base image, it seems that there is a problem
-RUN apt-get update && apt-get install -y procps \
- && for i in $RLIB ; do R -e "install.packages(pkgs = $i, repo=$CRANREPO)" ; done \
- && apt-get autoremove -y \
- && apt-get clean \
- && rm -rf /var/lib/apt/lists/*
-
-
-ENTRYPOINT ["/usr/bin/R"]
+
+# to get all the packages:
+## open a R session
+## use
+# lib_path = "C:/Program Files/R/R-4.0.5/library"
+# ip = as.data.frame(installed.packages(lib.loc = lib_path)[,c(1,3:4)])
+# ip = ip[is.na(ip$Priority),1:2,drop=FALSE]
+# ip
+
+
+# R v4.0.5 with packages:
+# Package Version
+# SARTools 1.7.3
+# abind 1.4-5
+# annotate 1.68.0
+# AnnotationDbi 1.52.0
+# askpass 1.1
+# assertthat 0.2.1
+# backports 1.2.1
+# base64enc 0.1-3
+# BH 1.75.0-0
+# Biobase 2.50.0
+# BiocGenerics 0.36.0
+# BiocManager 1.30.12
+# BiocParallel 1.24.1
+# BiocVersion 3.12.0
+# Biostrings 2.58.0
+# bit 4.0.4
+# bit64 4.0.5
+# bitops 1.0-6
+# blob 1.2.1
+# brew 1.0-6
+# brio 1.1.1
+# broom 0.7.6
+# cachem 1.0.4
+# Cairo 1.5-12.2
+# callr 3.6.0
+# car 3.0-10
+# carData 3.0-4
+# caTools 1.18.2
+# cellranger 1.1.0
+# CGHbase 1.50.0
+# CGHcall 2.52.0
+# cli 2.4.0
+# clipr 0.7.1
+# colorspace 2.0-0
+# commonmark 1.7
+# conquer 1.0.2
+# corrplot 0.84
+# covr 3.5.1
+# cpp11 0.2.7
+# crayon 1.4.1
+# credentials 1.3.0
+# crosstalk 1.1.1
+# curl 4.3
+# data.table 1.14.0
+# DBI 1.1.1
+# dbplyr 2.1.1
+# DelayedArray 0.16.3
+# desc 1.3.0
+# DESeq2 1.30.1
+# devtools 2.4.2
+# diffobj 0.3.4
+# digest 0.6.27
+# DNAcopy 1.64.0
+# dplyr 1.0.5
+# DT 0.17
+# dtplyr 1.1.0
+# edgeR 3.32.1
+# ellipsis 0.3.1
+# emmeans 1.5.5-1
+# estimability 1.3
+# evaluate 0.14
+# ExPosition 2.8.23
+# fansi 0.4.2
+# farver 2.1.0
+# fastmap 1.1.0
+# forcats 0.5.1
+# formatR 1.8
+# fs 1.5.0
+# futile.logger 1.4.3
+# futile.options 1.0.1
+# future 1.21.0
+# future.apply 1.7.0
+# gargle 1.1.0
+# genefilter 1.72.1
+# geneplotter 1.68.0
+# generics 0.1.0
+# GenomeInfoDb 1.26.4
+# GenomeInfoDbData 1.2.4
+# GenomicRanges 1.42.0
+# gert 1.3.0
+# GGally 2.1.1
+# ggdendro 0.1.22
+# ggplot2 3.3.3
+# ggrepel 0.9.1
+# gh 1.2.0
+# gitcreds 0.1.1
+# githubinstall 0.2.2
+# globals 0.14.0
+# glue 1.4.2
+# googledrive 1.0.1
+# googlesheets4 0.3.0
+# gplots 3.1.1
+# gridExtra 2.3
+# gtable 0.3.0
+# gtools 3.8.2
+# haven 2.3.1
+# HiCcompare 1.12.0
+# highr 0.8
+# hms 1.0.0
+# htmltools 0.5.1.1
+# htmlwidgets 1.5.3
+# httr 1.4.2
+# ids 1.0.1
+# impute 1.64.0
+# ini 0.3.1
+# InteractionSet 1.18.1
+# IRanges 2.24.1
+# isoband 0.2.4
+# jpeg 0.1-8.1
+# jsonlite 1.7.2
+# kableExtra 1.3.4
+# knitr 1.31
+# labeling 0.4.2
+# lambda.r 1.2.4
+# later 1.1.0.1
+# lazyeval 0.2.2
+# lemon 0.4.5
+# lifecycle 1.0.0
+# limma 3.46.0
+# listenv 0.8.0
+# lme4 1.1-26
+# lmerTest 3.1-3
+# locfit 1.5-9.4
+# lubridate 1.7.10
+# magrittr 2.0.1
+# maptools 1.1-1
+# markdown 1.1
+# marray 1.68.0
+# MatrixGenerics 1.2.1
+# MatrixModels 0.5-0
+# matrixStats 0.58.0
+# memoise 2.0.0
+# mime 0.1
+# minqa 1.2.4
+# mockery 0.4.2
+# modelr 0.1.8
+# munsell 0.5.0
+# mvtnorm 1.1-1
+# nloptr 1.2.2.2
+# numDeriv 2016.8-1.1
+# openssl 1.4.3
+# openxlsx 4.2.3
+# parallelly 1.24.0
+# pbkrtest 0.5.1
+# pheatmap 1.0.12
+# pillar 1.6.0
+# pkgbuild 1.2.0
+# pkgconfig 2.0.3
+# pkgload 1.2.1
+# plogr 0.2.0
+# plyr 1.8.6
+# png 0.1-7
+# praise 1.0.0
+# prettyGraphs 2.1.6
+# prettyunits 1.1.1
+# processx 3.5.0
+# progress 1.2.2
+# promises 1.2.0.1
+# ps 1.6.0
+# pspearman 0.3-0
+# purrr 0.3.4
+# QDNAseq 1.26.0
+# quantreg 5.85
+# R.methodsS3 1.8.1
+# R.oo 1.24.0
+# R.utils 2.10.1
+# R6 2.5.0
+# rappdirs 0.3.3
+# rcmdcheck 1.3.3
+# RColorBrewer 1.1-2
+# Rcpp 1.0.6
+# RcppArmadillo 0.10.2.2.0
+# RcppEigen 0.3.3.9.1
+# RCurl 1.98-1.3
+# readr 1.4.0
+# readxl 1.3.1
+# rematch 1.0.1
+# rematch2 2.1.2
+# remotes 2.3.0
+# reprex 2.0.0
+# reshape 0.8.8
+# reshape2 1.4.4
+# reticulate 1.19
+# rex 1.2.0
+# rhdf5 2.34.0
+# rhdf5filters 1.2.0
+# Rhdf5lib 1.12.1
+# Rhtslib 1.22.0
+# rio 0.5.26
+# rlang 0.4.10
+# rmarkdown 2.7
+# roxygen2 7.1.1
+# rprojroot 2.0.2
+# Rsamtools 2.6.0
+# RSQLite 2.2.5
+# rstudioapi 0.13
+# rversions 2.0.2
+# rvest 1.0.0
+# S4Vectors 0.28.1
+# SARTools 1.7.3
+# scales 1.1.1
+# selectr 0.4-2
+# sessioninfo 1.1.1
+# snow 0.4-3
+# snowfall 1.84-6.1
+# sp 1.4-5
+# SparseM 1.81
+# statmod 1.4.35
+# stringi 1.5.3
+# stringr 1.4.0
+# SummarizedExperiment 1.20.0
+# SuppDists 1.1-9.5
+# svglite 2.0.0
+# sys 3.4
+# systemfonts 1.0.1
+# testthat 3.0.2
+# tibble 3.1.0
+# tidyr 1.1.3
+# tidyselect 1.1.0
+# tidyverse 1.3.1
+# tinytex 0.31
+# translations 4.0.5
+# usethis 2.0.1
+# utf8 1.2.1
+# uuid 0.1-4
+# vctrs 0.3.7
+# viridisLite 0.3.0
+# waldo 0.2.5
+# webshot 0.5.2
+# whisker 0.4
+# withr 2.4.1
+# xfun 0.22
+# XML 3.99-0.6
+# xml2 1.3.2
+# xopen 1.0.0
+# xtable 1.8-4
+# XVector 0.30.0
+# yaml 2.2.1
+# zip 2.1.1
+# zlibbioc 1.36.0
+
+
+
+
+
+# base image: r-base:4.0.5
+FROM gmillot/r-base_v4.0.5:gitlab_v1.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. Here, the image is present locally, or distantly on the gmillot repo. Thus, gmillot/r-base:4.0.5 is correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+ENV CRANREPO="'https://cran.irsn.fr/'"
+# use the code above to get the list of the installed packages
+ENV RLIB="'SARTools' 'abind' 'annotate' 'AnnotationDbi' 'askpass' 'assertthat' 'backports' 'base64enc' 'BH' 'Biobase' 'BiocGenerics' 'BiocManager' 'BiocParallel' 'BiocVersion' 'Biostrings' 'bit' 'bit64' 'bitops' 'blob' 'brew' 'brio' 'broom' 'cachem' 'Cairo' 'callr' 'car' 'carData' 'caTools' 'cellranger' 'CGHbase' 'CGHcall' 'cli' 'clipr' 'colorspace' 'commonmark' 'conquer' 'corrplot' 'covr' 'cpp11' 'crayon' 'credentials' 'crosstalk' 'curl' 'data.table' 'DBI' 'dbplyr' 'DelayedArray' 'desc' 'DESeq2' 'devtools' 'diffobj' 'digest' 'DNAcopy' 'dplyr' 'DT' 'dtplyr' 'edgeR' 'ellipsis' 'emmeans' 'estimability' 'evaluate' 'ExPosition' 'fansi' 'farver' 'fastmap' 'forcats' 'formatR' 'fs' 'futile.logger' 'futile.options' 'future' 'future.apply' 'gargle' 'genefilter' 'geneplotter' 'generics' 'GenomeInfoDb' 'GenomeInfoDbData' 'GenomicRanges' 'gert' 'GGally' 'ggdendro' 'ggplot2' 'ggrepel' 'gh' 'gitcreds' 'githubinstall' 'globals' 'glue' 'googledrive' 'googlesheets4' 'gplots' 'gridExtra' 'gtable' 'gtools' 'haven' 'HiCcompare' 'highr' 'hms' 'htmltools' 'htmlwidgets' 'httr' 'ids' 'impute' 'ini' 'InteractionSet' 'IRanges' 'isoband' 'jpeg' 'jsonlite' 'kableExtra' 'knitr' 'labeling' 'lambda.r' 'later' 'lazyeval' 'lemon' 'lifecycle' 'limma' 'listenv' 'lme4' 'lmerTest' 'locfit' 'lubridate' 'magrittr' 'maptools' 'markdown' 'marray' 'MatrixGenerics' 'MatrixModels' 'matrixStats' 'memoise' 'mime' 'minqa' 'mockery' 'modelr' 'munsell' 'mvtnorm' 'nloptr' 'numDeriv' 'openssl' 'openxlsx' 'parallelly' 'pbkrtest' 'pheatmap' 'pillar' 'pkgbuild' 'pkgconfig' 'pkgload' 'plogr' 'plyr' 'png' 'praise' 'prettyGraphs' 'prettyunits' 'processx' 'progress' 'promises' 'ps' 'pspearman' 'purrr' 'QDNAseq' 'quantreg' 'R.methodsS3' 'R.oo' 'R.utils' 'R6' 'rappdirs' 'rcmdcheck' 'RColorBrewer' 'Rcpp' 'RcppArmadillo' 'RcppEigen' 'RCurl' 'readr' 'readxl' 'rematch' 'rematch2' 'remotes' 'reprex' 'reshape' 'reshape2' 'reticulate' 'rex' 'rhdf5' 'rhdf5filters' 'Rhdf5lib' 'Rhtslib' 'rio' 'rlang' 'rmarkdown' 'roxygen2' 'rprojroot' 'Rsamtools' 'RSQLite' 'rstudioapi' 'rversions' 'rvest' 'S4Vectors' 'SARTools' 'scales' 'selectr' 'sessioninfo' 'snow' 'snowfall' 'sp' 'SparseM' 'statmod' 'stringi' 'stringr' 'SummarizedExperiment' 'SuppDists' 'svglite' 'sys' 'systemfonts' 'testthat' 'tibble' 'tidyr' 'tidyselect' 'tidyverse' 'tinytex' 'translations' 'usethis' 'utf8' 'uuid' 'vctrs' 'viridisLite' 'waldo' 'webshot' 'whisker' 'withr' 'xfun' 'XML' 'xml2' 'xopen' 'xtable' 'XVector' 'yaml' 'zip' 'zlibbioc'"
+
+# nextflow needs procps for usage stats, cpu and process memory. Normally, this package is present by default in ubuntu. But in the R base image, it seems that there is a problem
+RUN apt-get update && apt-get install -y procps \
+ && for i in $RLIB ; do R -e "install.packages(pkgs = $i, repo=$CRANREPO)" ; done \
+ && apt-get autoremove -y \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+
+ENTRYPOINT ["/usr/bin/R"]
diff --git a/README.md b/README.md
index 4d67f63..a96650e 100644
--- a/README.md
+++ b/README.md
@@ -1,99 +1,99 @@
-
-<br /><br />
-## TABLE OF CONTENTS
-
- - [AIM](#aim)
- - [VERSIONS](#versions)
- - [LICENCE](#licence)
- - [CITATION](#citation)
- - [CREDITS](#credits)
- - [ACKNOWLEDGEMENTS](#Acknowledgements)
- - [WHAT'S NEW IN](#what's-new-in)
-
-
-
-<br /><br />
-## AIM
-
-Dockerfiles that generated the images in [dockerhub](https://hub.docker.com/u/gmillot).
-
-
-
-<br /><br />
-## VERSIONS
-
-The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/dockerfiles/-/tags)
-
-
-
-<br /><br />
-## 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.
-
-
-
-<br /><br />
-## CITATION
-
-None
-
-
-
-<br /><br />
-## CREDITS
-
-[Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, Paris, France
-
-
-
-<br /><br />
-## ACKNOWLEDGEMENTS
-
-Frédéric Lemoine, Hub-CBD, Institut Pasteur, Paris
-
-Bertrand Néron, Hub-CBD, Institut Pasteur, Paris
-
-Docker developers
-
-Gitlab developers
-
-Hub-CDB and Institut Pasteur
-
-
-
-<br /><br />
-## WHAT'S NEW IN
-
-### 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 />
-<br />
-Dockerfiles modified: <br />
-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
-
-
-### 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
-
-R\v4.0.5\base at date 20211001<br />
-R\v4.0.5\extended at date 20211001
-
-
-
-
+
+<br /><br />
+## TABLE OF CONTENTS
+
+ - [AIM](#aim)
+ - [VERSIONS](#versions)
+ - [LICENCE](#licence)
+ - [CITATION](#citation)
+ - [CREDITS](#credits)
+ - [ACKNOWLEDGEMENTS](#Acknowledgements)
+ - [WHAT'S NEW IN](#what's-new-in)
+
+
+
+<br /><br />
+## AIM
+
+Dockerfiles that generated the images in [dockerhub](https://hub.docker.com/u/gmillot).
+
+
+
+<br /><br />
+## VERSIONS
+
+The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/dockerfiles/-/tags)
+
+
+
+<br /><br />
+## 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.
+
+
+
+<br /><br />
+## CITATION
+
+None
+
+
+
+<br /><br />
+## CREDITS
+
+[Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, Paris, France
+
+
+
+<br /><br />
+## ACKNOWLEDGEMENTS
+
+Frédéric Lemoine, Hub-CBD, Institut Pasteur, Paris
+
+Bertrand Néron, Hub-CBD, Institut Pasteur, Paris
+
+Docker developers
+
+Gitlab developers
+
+Hub-CDB and Institut Pasteur
+
+
+
+<br /><br />
+## WHAT'S NEW IN
+
+### 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 />
+<br />
+Dockerfiles modified: <br />
+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
+
+
+### 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
+
+R\v4.0.5\base at date 20211001<br />
+R\v4.0.5\extended at date 20211001
+
+
+
+
diff --git a/ubuntu/v16.04/alien_trimmer/v0.4.0/AlienTrimmer.sh b/ubuntu/v16.04/alien_trimmer/v0.4.0/AlienTrimmer.sh
index 363ccb8..f0fba55 100644
--- a/ubuntu/v16.04/alien_trimmer/v0.4.0/AlienTrimmer.sh
+++ b/ubuntu/v16.04/alien_trimmer/v0.4.0/AlienTrimmer.sh
@@ -1,2 +1,2 @@
-#!/bin/sh
+#!/bin/sh
java -cp /usr/local/AlienTrimmer_0.4.0/src/ -Xmx2g AlienTrimmer ${1+"$@"}
\ No newline at end of file
diff --git a/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile b/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
index f2a3ca1..f404855 100644
--- a/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
+++ b/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
@@ -1,37 +1,37 @@
-# Alien Trimmer
-# ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
-# v0.4.0
-
-FROM gmillot/bash-extended_v1.0:gitlab_v1.0
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-COPY AlienTrimmer.sh /usr/local/bin/AlienTrimmer
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget openjdk-8-jre openjdk-8-jdk \
-# end install the required dependencies
-
-# alientrimmer install
-&& cd /usr/local/ \
-&& wget ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz \
-&& tar -xzvf AlienTrimmer_0.4.0.tar.gz \
-&& rm -rf AlienTrimmer_0.4.0.tar.gz \
-&& cd AlienTrimmer_0.4.0/src \
-&& javac AlienTrimmer.java \
-&& chmod +x /usr/local/bin/AlienTrimmer \
-# end alientrimmer install
-
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get remove -y wget openjdk-8-jdk \
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# Alien Trimmer
+# ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
+# v0.4.0
+
+FROM gmillot/bash-extended_v1.0:gitlab_v1.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+COPY AlienTrimmer.sh /usr/local/bin/AlienTrimmer
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget openjdk-8-jre openjdk-8-jdk \
+# end install the required dependencies
+
+# alientrimmer install
+&& cd /usr/local/ \
+&& wget ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz \
+&& tar -xzvf AlienTrimmer_0.4.0.tar.gz \
+&& rm -rf AlienTrimmer_0.4.0.tar.gz \
+&& cd AlienTrimmer_0.4.0/src \
+&& javac AlienTrimmer.java \
+&& chmod +x /usr/local/bin/AlienTrimmer \
+# end alientrimmer install
+
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get remove -y wget openjdk-8-jdk \
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/usr/local/bin/AlienTrimmer"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bash-extended/v1.0/Dockerfile b/ubuntu/v16.04/bash-extended/v1.0/Dockerfile
index cf31316..e7d31c8 100644
--- a/ubuntu/v16.04/bash-extended/v1.0/Dockerfile
+++ b/ubuntu/v16.04/bash-extended/v1.0/Dockerfile
@@ -1,60 +1,60 @@
-# Coreutils - GNU core utilities
-# https://www.gnu.org/software/coreutils/
-# v8.30
-
-# 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
-
-# base image: ubuntu:16.04
-FROM gmillot/coreutils_v8.30:gitlab_v1.0
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 libc6 ed texinfo \
-# end install the required dependencies
-
-# gawk install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
-&& tar -xf gawk-5.1.0.tar.gz \
-&& cd gawk-5.1.0 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf gawk-5.1.0 \
-# end gawk install
-
-# bc install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
-&& tar -xf bc-1.07.tar.gz \
-&& cd bc-1.07 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf bc-1.07 \
-# end bc install
-
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# Coreutils - GNU core utilities
+# https://www.gnu.org/software/coreutils/
+# v8.30
+
+# 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
+
+# base image: ubuntu:16.04
+FROM gmillot/coreutils_v8.30:gitlab_v1.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 libc6 ed texinfo \
+# end install the required dependencies
+
+# gawk install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
+&& tar -xf gawk-5.1.0.tar.gz \
+&& cd gawk-5.1.0 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf gawk-5.1.0 \
+# end gawk install
+
+# bc install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
+&& tar -xf bc-1.07.tar.gz \
+&& cd bc-1.07 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf bc-1.07 \
+# end bc install
+
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bash-extended/v2.0/Dockerfile b/ubuntu/v16.04/bash-extended/v2.0/Dockerfile
index e190e21..b39bd9a 100644
--- a/ubuntu/v16.04/bash-extended/v2.0/Dockerfile
+++ b/ubuntu/v16.04/bash-extended/v2.0/Dockerfile
@@ -1,81 +1,81 @@
-# Coreutils - GNU core utilities
-# https://www.gnu.org/software/coreutils/
-# v8.30
-
-# 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
-
-# git - github
-# https://github.com/git/git/archive/refs/tags/
-# v2.33.1
-
-# base image: ubuntu:16.04 + coreutils v8.30
-FROM gmillot/coreutils_v8.30:gitlab_v1.0
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 libc6 ed texinfo \
-# end install the required dependencies
-
-# gawk install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
-&& tar -xf gawk-5.1.0.tar.gz \
-&& cd gawk-5.1.0 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf gawk-5.1.0 \
-# end gawk install
-
-# bc install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
-&& tar -xf bc-1.07.tar.gz \
-&& cd bc-1.07 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf bc-1.07 \
-# end bc install
-
-# git install
-# install the required dependencies
-&& apt-get install -y wget dh-autoreconf libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev asciidoc xmlto docbook2x \
-# end install the required dependencies
-&& cd /usr/local/ \
-&& wget https://github.com/git/git/archive/refs/tags/v2.33.1.tar.gz \
-&& tar -xf v2.33.1.tar.gz \
-&& cd git-2.33.1 \
-&& make configure \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf git-2.33.1 \
-# end git install
-
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# Coreutils - GNU core utilities
+# https://www.gnu.org/software/coreutils/
+# v8.30
+
+# 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
+
+# git - github
+# https://github.com/git/git/archive/refs/tags/
+# v2.33.1
+
+# base image: ubuntu:16.04 + coreutils v8.30
+FROM gmillot/coreutils_v8.30:gitlab_v1.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 libc6 ed texinfo \
+# end install the required dependencies
+
+# gawk install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
+&& tar -xf gawk-5.1.0.tar.gz \
+&& cd gawk-5.1.0 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf gawk-5.1.0 \
+# end gawk install
+
+# bc install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
+&& tar -xf bc-1.07.tar.gz \
+&& cd bc-1.07 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf bc-1.07 \
+# end bc install
+
+# git install
+# install the required dependencies
+&& apt-get install -y wget dh-autoreconf libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev asciidoc xmlto docbook2x \
+# end install the required dependencies
+&& cd /usr/local/ \
+&& wget https://github.com/git/git/archive/refs/tags/v2.33.1.tar.gz \
+&& tar -xf v2.33.1.tar.gz \
+&& cd git-2.33.1 \
+&& make configure \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf git-2.33.1 \
+# end git install
+
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bc/v1.07/Dockerfile b/ubuntu/v16.04/bc/v1.07/Dockerfile
index 1f91edf..f970f43 100644
--- a/ubuntu/v16.04/bc/v1.07/Dockerfile
+++ b/ubuntu/v16.04/bc/v1.07/Dockerfile
@@ -1,37 +1,37 @@
-# bc - GNU core utilities
-# https://www.gnu.org/software/bc/
-# v1.07
-
-# base image: ubuntu:16.04
-FROM ubuntu:16.04
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar xz-utils make gcc dpkg libreadline6 libc6 ed texinfo \
-# end install the required dependencies
-# bc install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
-&& tar -xf bc-1.07.tar.gz \
-&& cd bc-1.07 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf bc-1.07 \
-# end bc install
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# bc - GNU core utilities
+# https://www.gnu.org/software/bc/
+# v1.07
+
+# base image: ubuntu:16.04
+FROM ubuntu:16.04
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar xz-utils make gcc dpkg libreadline6 libc6 ed texinfo \
+# end install the required dependencies
+# bc install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/bc/bc-1.07.tar.gz \
+&& tar -xf bc-1.07.tar.gz \
+&& cd bc-1.07 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf bc-1.07 \
+# end bc install
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bcftools/v1.14/Dockerfile b/ubuntu/v16.04/bcftools/v1.14/Dockerfile
new file mode 100644
index 0000000..6265e28
--- /dev/null
+++ b/ubuntu/v16.04/bcftools/v1.14/Dockerfile
@@ -0,0 +1,37 @@
+# bcftools
+# https://github.com/samtools/bcftools/releases/tag/1.14
+
+# v1.14
+
+# base image: ubuntu:16.04 + coreutils v8.30 + gawk v5.1.0 + bc v1.07 + git v2.33.1
+FROM gmillot/bash-extended_v2.0:gitlab_v3.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+ENV BCFTOOLS_VERSION=1.14
+ENV HTS_VERSION=1.14
+
+RUN apt-get update --fix-missing \
+ && apt-get install -y wget gcc make git libbz2-dev zlib1g zlib1g-dev liblzma5 liblzma-dev libncurses5 libncurses5-dev bzip2 libcurl4-openssl-dev libssl-dev libgetopt-complete-perl \
+ && cd /usr/local/ \
+ && git clone https://github.com/samtools/htslib.git \
+ && cd htslib && git checkout ${HTS_VERSION} \
+ && cd .. \
+ && git clone https://github.com/samtools/bcftools.git \
+ && cd bcftools \
+ && git checkout ${BCFTOOLS_VERSION} \
+ && make \
+ && make install \
+ && rm -rf /usr/local/bcftools \
+ && rm -rf /usr/local/htslib \
+# end coreutils install
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
+ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/coreutils/v8.30/Dockerfile b/ubuntu/v16.04/coreutils/v8.30/Dockerfile
index 29a79f3..b5a7f5d 100644
--- a/ubuntu/v16.04/coreutils/v8.30/Dockerfile
+++ b/ubuntu/v16.04/coreutils/v8.30/Dockerfile
@@ -1,38 +1,38 @@
-# coreutils - GNU core utilities
-# https://www.gnu.org/software/coreutils/
-# v8.30
-
-# base image: ubuntu:16.04
-FROM ubuntu:16.04
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 \
-# end install the required dependencies
-# coreutils install
-&& cd /usr/local/ \
-&& wget http://ftp.gnu.org/gnu/coreutils/coreutils-8.30.tar.xz \
-&& tar -xf coreutils-8.30.tar.xz \
-&& cd coreutils-8.30 \
-&& chmod u=rwx configure \
-&& export FORCE_UNSAFE_CONFIGURE=1 \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf coreutils-8.30 \
-# end coreutils install
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# coreutils - GNU core utilities
+# https://www.gnu.org/software/coreutils/
+# v8.30
+
+# base image: ubuntu:16.04
+FROM ubuntu:16.04
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 \
+# end install the required dependencies
+# coreutils install
+&& cd /usr/local/ \
+&& wget http://ftp.gnu.org/gnu/coreutils/coreutils-8.30.tar.xz \
+&& tar -xf coreutils-8.30.tar.xz \
+&& cd coreutils-8.30 \
+&& chmod u=rwx configure \
+&& export FORCE_UNSAFE_CONFIGURE=1 \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf coreutils-8.30 \
+# end coreutils install
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/gawk/v5.1.0/Dockerfile b/ubuntu/v16.04/gawk/v5.1.0/Dockerfile
index 3805b04..2ea1fc2 100644
--- a/ubuntu/v16.04/gawk/v5.1.0/Dockerfile
+++ b/ubuntu/v16.04/gawk/v5.1.0/Dockerfile
@@ -1,37 +1,37 @@
-# gawk - GNU core utilities
-# https://www.gnu.org/software/gawk/
-# v5.1.0
-
-# base image: ubuntu:16.04
-FROM ubuntu:16.04
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 \
-# end install the required dependencies
-# gawk install
-&& cd /usr/local/ \
-&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
-&& tar -xf gawk-5.1.0.tar.gz \
-&& cd gawk-5.1.0 \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf gawk-5.1.0 \
-# end gawk install
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# gawk - GNU core utilities
+# https://www.gnu.org/software/gawk/
+# v5.1.0
+
+# base image: ubuntu:16.04
+FROM ubuntu:16.04
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar xz-utils make gcc dpkg libblkid1 libreadline6 \
+# end install the required dependencies
+# gawk install
+&& cd /usr/local/ \
+&& wget https://ftp.gnu.org/gnu/gawk/gawk-5.1.0.tar.gz \
+&& tar -xf gawk-5.1.0.tar.gz \
+&& cd gawk-5.1.0 \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf gawk-5.1.0 \
+# end gawk install
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/git/v2.33.1/Dockerfile b/ubuntu/v16.04/git/v2.33.1/Dockerfile
index 3464157..3f25f45 100644
--- a/ubuntu/v16.04/git/v2.33.1/Dockerfile
+++ b/ubuntu/v16.04/git/v2.33.1/Dockerfile
@@ -1,38 +1,38 @@
-# gawk - GNU core utilities
-# https://www.gnu.org/software/gawk/
-# v5.1.0
-
-# base image: ubuntu:16.04
-FROM ubuntu:16.04
-# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
-
-LABEL Gael.Millot=gael.millot@pasteur.fr
-LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
-
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget tar dh-autoreconf libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev asciidoc xmlto docbook2x \
-# end install the required dependencies
-# git install
-&& cd /usr/local/ \
-&& wget https://github.com/git/git/archive/refs/tags/v2.33.1.tar.gz \
-&& tar -xf v2.33.1.tar.gz \
-&& cd git-2.33.1 \
-&& make configure \
-&& chmod u=rwx configure \
-&& ./configure \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf git-2.33.1 \
-# end git install
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
-
+# gawk - GNU core utilities
+# https://www.gnu.org/software/gawk/
+# v5.1.0
+
+# base image: ubuntu:16.04
+FROM ubuntu:16.04
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+RUN apt-get update --fix-missing \
+# update apt-get
+&& apt-get upgrade \
+# end update apt-get
+# install the required dependencies
+&& apt-get install -y wget tar dh-autoreconf libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev asciidoc xmlto docbook2x \
+# end install the required dependencies
+# git install
+&& cd /usr/local/ \
+&& wget https://github.com/git/git/archive/refs/tags/v2.33.1.tar.gz \
+&& tar -xf v2.33.1.tar.gz \
+&& cd git-2.33.1 \
+&& make configure \
+&& chmod u=rwx configure \
+&& ./configure \
+&& make \
+&& make install \
+&& cd /usr/local/ \
+&& rm -rf git-2.33.1 \
+# end git install
+# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
+# important to remove the dependencies after installation to save space in the image that will be built
+&& apt-get autoremove -y \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
+
ENTRYPOINT ["/bin/bash"]
\ No newline at end of file
--
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