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Commit 9b8406d6 authored by Gael MILLOT's avatar Gael MILLOT
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release v9.3:R/v4.1.2/extended/v3.0 and R/v4.1.2/ig_clustering/v1.0

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R/v4.1.2/contracted/v1.0/Dockerfile
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......@@ -77,9 +77,11 @@ RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n
value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)), \
warning = W \
) ; \
return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
return(if(is.null(output$warning)){NULL}else{as.character(output$warning)}) \
} ; \
message(paste0('\n\n\n\n================\n\nR PACKAGE REMOVAL ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
tempo <- paste0('\n\n\n\n================\n\nR PACKAGE REMOVAL ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n') ; \
message(tempo) ; \
print(tempo) ; \
remove.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library') \
" ; \
done \
......
R/v4.1.2/extended/v3.0/Dockerfile 0 → 100644
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#########################################################################
## ##
## Dockerfile ##
## R extended ##
## ##
## Gael A. Millot ##
## Bioinformatics and Biostatistics Hub ##
## Computational Biology Department ##
## Institut Pasteur Paris ##
## ##
#########################################################################
# to see the log of the building:
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
# cat building.log
# to export the log file of the image building from the container:
# sudo docker images
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
# exit
# sudo docker container ls -a # to get all the active containers
# sudo docker cp <containerNAMES>:/building.log </host/path/target>
# sudo docker cp <containerNAMES>:/installed_r_packages.csv </host/path/target>
# base image:
FROM gmillot/r-base_v4.1.2:gitlab_v8.2
# 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 APT_GET_LINUX_LIB="\
procps \
libfontconfig1-dev \
ghostscript \
lmodern \
pandoc \
pandoc-citeproc \
qpdf \
texinfo \
texlive-fonts-extra \
texlive-fonts-recommended \
texlive-latex-extra \
texlive-latex-recommended \
texlive-luatex \
texlive-plain-generic \
texlive-science \
texlive-xetex \
libpoppler-cpp-dev \
"
ENV APT_LINUX_LIB="\
build-essential \
libcurl4-gnutls-dev \
libxml2-dev \
libssl-dev \
libgit2-dev \
libcairo2-dev \
libxt-dev \
"
ENV CRANREPO="'https://cran.irsn.fr/'"
ENV BIOCONDUCTOR_REPO="'https://cloud.r-project.org'"
ENV RLIB="\
'BiocManager' \
'devtools' \
'Cairo' \
'dplyr' \
'data.table' \
'gridExtra' \
'mgcv' \
'InteractionSet' \
'GenomicRanges' \
'IRanges' \
'BiocParallel' \
'QDNAseq' \
'GenomeInfoDbData' \
'ggplot2' \
'HiCcompare' \
'lubridate' \
'parallel' \
'reshape2' \
'binb' \
'linl' \
'pinp' \
'tint' \
'pdftools' \
'qqman' \
"
# fun.warning.capture from fun_get_message() of the cute package.
# I used a first loop because I cannot use array in dockerfiles.
# Inactivate sink(file = tempo, append = TRUE, type = 'message') for debbuging.
RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > building.log \
&& add-apt-repository -y ppa:cran/poppler \
&& apt-get update \
| tee -a building.log ; echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \
&& apt-get install -y $APT_GET_LINUX_LIB \
| tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \
&& apt -y install $APT_LINUX_LIB \
| tee -a building.log \
&& RLIB_LENGTH=0 \
&& for i2 in $RLIB ; do RLIB_LENGTH=$((RLIB_LENGTH+1)) ; done \
&& COUNT=0 \
&& for i2 in $RLIB ; do \
COUNT=$((COUNT+1)) ; \
Rscript --vanilla -e " \
options(warn = 1, verbose = TRUE) ; \
tempo <- file('building.log', open = 'a+b') ; \
sink(file = tempo, append = TRUE, type = 'message') ; \
fun.warning.capture <- function(expr){ \
W <- NULL ; \
w.handler <- function(w){ \
W <<- w ; \
invokeRestart('muffleWarning') \
} ; \
output <- list( \
value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)), \
warning = W \
) ; \
return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
} ; \
message(paste0('\n\n\n\n================\n\nR PACKAGE INSTALLATION ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
if( ! ($i2 %in% c('ggplot2', 'SARTools'))){ \
tempo.warn <- fun.warning.capture(exp = install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO)) ; \
if(is.null(tempo.warn)){ \
tempo <- paste0('STANDARD INSTALLATION ATTEMPT FOR ', $i2) ; \
message(paste0('\n\n', tempo, '\n\n')) ; \
cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO) \
}else{ \
tempo <- paste0('BiocManager INSTALLATION ATTEMPT FOR ', $i2) ; \
message(paste0('\n\n', tempo, '\n\n')) ; \
cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
BiocManager::install(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, update = FALSE, site_repository = $BIOCONDUCTOR_REPO) \
} \
}else if($i2 == 'ggplot2'){ \
devtools::install_version(package = 'ggplot2', version = '3.3.3', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repos = $CRANREPO) \
}else if($i2 == 'SARTools'){ \
devtools::install_github('PF2-pasteur-fr/SARTools', build_opts='--no-resave-data', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, upgrade = "always") \
} \
" ; \
done \
&& Rscript --vanilla -e " \
options(warn = 1, verbose = TRUE) ; \
args <- commandArgs(trailingOnly = TRUE) ; \
if(any(is.na(args))){ \
stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE args OBJECT HAS NA\n\n================\n\n'), call. = FALSE) \
} ; \
tempo.arg.names <- c( \
'RLIB' \
) ; \
if(length(args) != length(tempo.arg.names)){ \
stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE NUMBER OF ELEMENTS IN args (', length(args),') IS DIFFERENT FROM THE NUMBER OF ELEMENTS IN tempo.arg.names (', length(tempo.arg.names),')\nargs:', paste0(args, collapse = ','), '\ntempo.arg.names:', paste0(tempo.arg.names, collapse = ','), '\n\n================\n\n'), call. = FALSE) \
} ; \
for(i1 in 1:length(tempo.arg.names)){ \
assign(tempo.arg.names[i1], args[i1]) \
} ; \
RLIB <- strsplit(RLIB, split = ',')[[1]] ; \
RLIB <- RLIB[RLIB != ''] ; \
if(file.exists('installed_r_packages.csv')){ \
file.remove('installed_r_packages.csv') \
} ; \
if(file.exists('not_installed_r_packages.txt')){ \
file.remove('not_installed_r_packages.txt') \
} ; \
tempo <- file('building.log', open = 'a+b') ; \
sink(file = tempo, append = TRUE, type = 'message') ; \
message(paste0('\n\n\n\n================\n\nR PACKAGES INSTALLED\n\n================\n\n\n\n')) ; \
message('SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
capture.output(as.data.frame(installed.packages())[1:4], file = tempo, append = TRUE, type = 'output') ; \
df <- as.data.frame(installed.packages()) ; \
for (i2 in 1:length(df)){ \
df[, i2] <- gsub(x = df[, i2], replacement = '', pattern = '\n', fixed = TRUE) \
} ; \
write.table(x = df, file = 'installed_r_packages.csv', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
message(paste0('\n\n\n\n================\n\nR PACKAGES NOT INSTALLED\n\n================\n\n\n\n')) ; \
df2 <- as.data.frame(RLIB[ ! RLIB %in% df[ , 'Package']]) ; \
if(nrow(df2) == 0){ \
message('ALL THE PACKAGES HAVE BEEN INSTALLED\n\n') \
}else{ \
message('SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
names(df2) <- 'Name' ; \
capture.output(df2, file = tempo, append = TRUE, type = 'output') ; \
write.table(x = df2, file = 'not_installed_r_packages.txt', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
} \
" $(echo "$RLIB" | sed 's/ \{1,\}/,/g' | sed "s/'//g") \
&& echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> building.log \
&& apt-get autoremove -y \
| tee -a building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> building.log \
&& apt-get clean \
| tee -a building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> building.log \
&& rm -rf /var/lib/apt/lists/* \
| tee -a building.log \
&& echo "\n\n\n\n================\n\nLINUX PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \
&& apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
>> /building.log
# dependencies=NA means c("Depends", "Imports", "LinkingTo"). Do no use TRUE -> install suggesting packages which inflates tremendously the image.
ENTRYPOINT ["/usr/bin/R"]
R/v4.1.2/extended/v3.0/building.log 0 → 100644
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R/v4.1.2/extended/v3.0/installed_r_packages.csv 0 → 100644
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R/v4.1.2/ig_clustering/v1.0/Dockerfile 0 → 100644
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#########################################################################
## ##
## Dockerfile ##
## R extended ##
## ##
## Gael A. Millot ##
## Bioinformatics and Biostatistics Hub ##
## Computational Biology Department ##
## Institut Pasteur Paris ##
## ##
#########################################################################
# to see the log of the building:
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
# cat building.log
# to export the log file of the image building from the container:
# sudo docker images
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
# exit
# sudo docker container ls -a # to get all the active containers
# sudo docker cp <containerNAMES>:/building.log </host/path/target>
# sudo docker cp <containerNAMES>:/installed_r_packages.csv </host/path/target>
# base image:
FROM gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3
# 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 APT_GET_LINUX_LIB=""
ENV APT_LINUX_LIB=""
ENV CRANREPO="'https://cran.irsn.fr/'"
ENV BIOCONDUCTOR_REPO="'https://cloud.r-project.org'"
ENV RLIB="\
'Rccp' \
'Biostrings' \
'GenomicAlignments' \
'IRanges' \
'igraph' \
'alakazam' \
'shazam' \
'tiger' \
'scoper' \
'dowser' \
"
# fun.warning.capture from fun_get_message() of the cute package.
# I used a first loop because I cannot use array in dockerfiles.
# Inactivate sink(file = tempo, append = TRUE, type = 'message') for debbuging.
RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > building.log \
&& add-apt-repository -y ppa:cran/poppler \
&& apt-get update \
| tee -a building.log ; echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \
&& apt-get install -y $APT_GET_LINUX_LIB \
| tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \
&& apt -y install $APT_LINUX_LIB \
| tee -a building.log \
&& RLIB_LENGTH=0 \
&& for i2 in $RLIB ; do RLIB_LENGTH=$((RLIB_LENGTH+1)) ; done \
&& COUNT=0 \
&& for i2 in $RLIB ; do \
COUNT=$((COUNT+1)) ; \
Rscript --vanilla -e " \
options(warn = 1, verbose = TRUE) ; \
tempo <- file('building.log', open = 'a+b') ; \
sink(file = tempo, append = TRUE, type = 'message') ; \
fun.warning.capture <- function(expr){ \
W <- NULL ; \
w.handler <- function(w){ \
W <<- w ; \
invokeRestart('muffleWarning') \
} ; \
output <- list( \
value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)), \
warning = W \
) ; \
return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
} ; \
message(paste0('\n\n\n\n================\n\nR PACKAGE INSTALLATION ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
if( ! ($i2 %in% c('ggplot2', 'SARTools'))){ \
tempo.warn <- fun.warning.capture(exp = install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO)) ; \
if(is.null(tempo.warn)){ \
tempo <- paste0('STANDARD INSTALLATION ATTEMPT FOR ', $i2) ; \
message(paste0('\n\n', tempo, '\n\n')) ; \
cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO) \
}else{ \
tempo <- paste0('BiocManager INSTALLATION ATTEMPT FOR ', $i2) ; \
message(paste0('\n\n', tempo, '\n\n')) ; \
cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
BiocManager::install(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, update = FALSE, site_repository = $BIOCONDUCTOR_REPO) \
} \
}else if($i2 == 'ggplot2'){ \
devtools::install_version(package = 'ggplot2', version = '3.3.3', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repos = $CRANREPO) \
}else if($i2 == 'SARTools'){ \
devtools::install_github('PF2-pasteur-fr/SARTools', build_opts='--no-resave-data', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, upgrade = "always") \
} \
" ; \
done \
&& Rscript --vanilla -e " \
options(warn = 1, verbose = TRUE) ; \
args <- commandArgs(trailingOnly = TRUE) ; \
if(any(is.na(args))){ \
stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE args OBJECT HAS NA\n\n================\n\n'), call. = FALSE) \
} ; \
tempo.arg.names <- c( \
'RLIB' \
) ; \
if(length(args) != length(tempo.arg.names)){ \
stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE NUMBER OF ELEMENTS IN args (', length(args),') IS DIFFERENT FROM THE NUMBER OF ELEMENTS IN tempo.arg.names (', length(tempo.arg.names),')\nargs:', paste0(args, collapse = ','), '\ntempo.arg.names:', paste0(tempo.arg.names, collapse = ','), '\n\n================\n\n'), call. = FALSE) \
} ; \
for(i1 in 1:length(tempo.arg.names)){ \
assign(tempo.arg.names[i1], args[i1]) \
} ; \
RLIB <- strsplit(RLIB, split = ',')[[1]] ; \
RLIB <- RLIB[RLIB != ''] ; \
if(file.exists('installed_r_packages.csv')){ \
file.remove('installed_r_packages.csv') \
} ; \
if(file.exists('not_installed_r_packages.txt')){ \
file.remove('not_installed_r_packages.txt') \
} ; \
tempo <- file('building.log', open = 'a+b') ; \
sink(file = tempo, append = TRUE, type = 'message') ; \
message(paste0('\n\n\n\n================\n\nR PACKAGES INSTALLED\n\n================\n\n\n\n')) ; \
message('SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
capture.output(as.data.frame(installed.packages())[1:4], file = tempo, append = TRUE, type = 'output') ; \
df <- as.data.frame(installed.packages()) ; \
for (i2 in 1:length(df)){ \
df[, i2] <- gsub(x = df[, i2], replacement = '', pattern = '\n', fixed = TRUE) \
} ; \
write.table(x = df, file = 'installed_r_packages.csv', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
message(paste0('\n\n\n\n================\n\nR PACKAGES NOT INSTALLED\n\n================\n\n\n\n')) ; \
df2 <- as.data.frame(RLIB[ ! RLIB %in% df[ , 'Package']]) ; \
if(nrow(df2) == 0){ \
message('ALL THE PACKAGES HAVE BEEN INSTALLED\n\n') \
}else{ \
message('SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
names(df2) <- 'Name' ; \
capture.output(df2, file = tempo, append = TRUE, type = 'output') ; \
write.table(x = df2, file = 'not_installed_r_packages.txt', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
} \
" $(echo "$RLIB" | sed 's/ \{1,\}/,/g' | sed "s/'//g") \
&& echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> building.log \
&& apt-get autoremove -y \
| tee -a building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> building.log \
&& apt-get clean \
| tee -a building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> building.log \
&& rm -rf /var/lib/apt/lists/* \
| tee -a building.log \
&& echo "\n\n\n\n================\n\nLINUX PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \
&& apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
>> /building.log
# dependencies=NA means c("Depends", "Imports", "LinkingTo"). Do no use TRUE -> install suggesting packages which inflates tremendously the image.
ENTRYPOINT ["/usr/bin/R"]
R/v4.1.2/ig_clustering/v1.0/building.log 0 → 100644
+ 1141
− 0
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R/v4.1.2/ig_clustering/v1.0/installed_r_packages.csv 0 → 100644
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README.md
+ 8
− 1
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......@@ -71,7 +71,14 @@ Hub-CDB Institut Pasteur & DSI Institut Pasteur
Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below
### 9.1
### 9.3
Dockerfiles added: <br />
R/v4.1.2/extended/v3.0 at date 20221108: from gmillot/r-base_v4.1.2:gitlab_v8.2 used as base for R/v4.1.2/ig_clustering
R/v4.1.2/ig_clustering/v1.0 at date 20221108: from gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3 <br />
### 9.2
Dockerfiles added: <br />
python/3.9.10/changeo_presto/v1.0 at date 20221007: from ubuntu:20.04 & python v3.9.10 <br />
......
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