diff --git a/R/v4.0.5/base/Dockerfile b/R/v4.0.5/base/Dockerfile
index ed34473f4dbccd82b0f25eebd6d55ac8a294559a..5865d0ba8ca71ca96c77c4f9ca517c126104a7f2 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 f1233b71bf9b2a86361c1b0510e92c34987bdd5b..ffdeb4007c39a06f3ecaae06b148b9ad4c39032f 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 4d67f634f5cd7979ddef9bbc7b9085f1bcde37b6..a96650e3b7f2411a95b483acfaee9eecd07071d0 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 363ccb811a4f528726740de3d032875ba7ea2a02..f0fba5557b9c70ff3461a7f198425d603577b3b6 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 f2a3ca1bf597cdf405471914e02e011dc63471e1..f404855d7b12e313a9381d56f8c34ff8fe312672 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 cf31316536ae2521a139eee5282d9e804c8edd97..e7d31c86cd72b007e31a19fe378517c30cb6bc32 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 e190e216b4c3f052423197220c7b2bb9d602b6c3..b39bd9a1fb7474aa1f0ef1f2f00e9f454f16fba9 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 1f91edf998d25eed2501bb2ffc5ac457a4e769a3..f970f4390065e5d36d9eeed37c34c7c06635fe75 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 0000000000000000000000000000000000000000..6265e28315d2b6ea856dac922271626a0db06f22
--- /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 29a79f3bc67a6d86817b9a389257173d0199ffba..b5a7f5dc087dda614f64a420417730d1ae88b3fd 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 3805b041bbaee83cc71f57b2dfbae06797ee5362..2ea1fc23e29caa9f2219885ab396e2c94b80bcfe 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 3464157a59929eb17dbdb0dbee39eb6ce5f013ea..3f25f455fe86dd650439088b6e0e19e2585206a0 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