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gad-public
singularity
Commits
0e816f1d
Commit
0e816f1d
authored
Aug 19, 2022
by
Yannis Duffourd
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Adding R packages installation script
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bionano_solve_3.7.def
bionano_solve_3.7.def
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bionano_solve_3.7.def
View file @
0e816f1d
...
@@ -108,92 +108,96 @@ make altinstall
...
@@ -108,92 +108,96 @@ make altinstall
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/lohdetection
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/lohdetection
# R packages
# R packages
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=digest&version=0.6.13", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=digest&version=0.6.13", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=magrittr&version=1.5", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=magrittr&version=1.5", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=assertthat&version=0.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=assertthat&version=0.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=prettyunits&version=1.0.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=prettyunits&version=1.0.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bit&version=1.1-13", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bit&version=1.1-13", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=DBI&version=0.8", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=DBI&version=0.8", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=memoise&version=1.1.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=memoise&version=1.1.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pkgconfig&version=2.0.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pkgconfig&version=2.0.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Rcpp&version=1.0.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Rcpp&version=1.0.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=BH&version=1.66.0-1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=BH&version=1.66.0-1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plogr&version=0.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plogr&version=0.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=crayon&version=1.3.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=crayon&version=1.3.4", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=cli&version=1.0.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=cli&version=1.0.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=praise&version=1.0.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=praise&version=1.0.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R6&version=2.3.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R6&version=2.3.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=rlang&version=0.1.6", repos=NULL, type="source")'
#############################
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=withr&version=2.1.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=rlang&version=0.1.6", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=testthat&version=2.0.0", repos=NULL, type="source")'
#############################
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.methodsS3&version=1.7.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=withr&version=2.1.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.oo&version=1.22.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=testthat&version=2.0.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.utils&version=2.8.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.methodsS3&version=1.7.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=data.table&version=1.12.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.oo&version=1.22.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=outliers&version=0.14", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.utils&version=2.8.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=diptest&version=0.75-7", repos=NULL, type="source")'
###########
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=intervals&version=0.15.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=data.table&version=1.12.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=fansi&version=0.3.0", repos=NULL, type="source")'
############
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=utf8&version=1.1.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=outliers&version=0.14", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pillar&version=1.0.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=diptest&version=0.75-7", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=colorspace&version=1.3-2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=intervals&version=0.15.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=labeling&version=0.3", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=fansi&version=0.3.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=munsell&version=0.5.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=utf8&version=1.1.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RColorBrewer&version=1.0-5", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pillar&version=1.0.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=viridisLite&version=0.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=colorspace&version=1.3-2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=glue&version=1.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=labeling&version=0.3", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringi&version=1.1.6", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=munsell&version=0.5.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plyr&version=1.8.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RColorBrewer&version=1.0-5", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringr&version=1.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=viridisLite&version=0.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lattice&version=0.20-35", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=glue&version=1.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=nlme&version=3.1-131", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringi&version=1.1.6", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Matrix&version=1.2-15", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plyr&version=1.8.4", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=gtable&version=0.2.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringr&version=1.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lazyeval&version=0.2.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lattice&version=0.20-35", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=MASS&version=7.3-29", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=nlme&version=3.1-131", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=mgcv&version=1.7-28", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Matrix&version=1.2-15", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=reshape2&version=1.4.3", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=gtable&version=0.2.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dichromat&version=2.0-0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lazyeval&version=0.2.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=scales&version=0.5.0", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=MASS&version=7.3-29", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tibble&version=1.4.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=mgcv&version=1.7-28", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=ggplot2&version=2.2.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=reshape2&version=1.4.3", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=purrr&version=0.2.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dichromat&version=2.0-0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tidyselect&version=0.2.3", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=scales&version=0.5.0", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindr&version=0.1.1", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tibble&version=1.4.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindrcpp&version=0.2.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=ggplot2&version=2.2.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dplyr&version=0.7.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=purrr&version=0.2.4", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RSQLite&version=0.11.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tidyselect&version=0.2.3", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=XML&version=3.98-1.2", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindr&version=0.1.1", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tiff&version=0.1-5", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindrcpp&version=0.2.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=inline&version=0.3.13", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dplyr&version=0.7.4", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=igraph&version=1.2.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RSQLite&version=0.11.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=wbs&version=1.3", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=XML&version=3.98-1.2", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=argparser&version=0.4", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tiff&version=0.1-5", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=htmltools&version=0.3.6", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=inline&version=0.3.13", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=jsonlite&version=1.6", repos=NULL, type="source")'
/usr/local/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=igraph&version=1.2.4", repos=NULL, type="source", lib="/work/gad/shared/bin/bionano/private_env/Rlib")'
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Maintainer Yannis Duffourd
Maintainer Yannis Duffourd
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