brucemoran/Singularity:ucs_ucec_rnaseq.analysis
$ singularity pull shub://brucemoran/Singularity:ucs_ucec_rnaseq.analysis
Singularity Recipe
Bootstrap:shub
From:brucemoran/Singularity:centos7-r_3.5.1_jupyter
%post
R --slave -e 'library("devtools"); devtools::install_github(c("renozao/rngtools", "renozao/NMF"), build_vignettes = FALSE); library("BiocManager"); BiocManager::install(c("CellMix"), site_repository="http://web.cbio.uct.ac.za/~renaud/CRAN")'
#BiocManager to install packages
R --slave -e 'library("BiocManager"); BiocManager::install(c("rngtools", "NMF", "CAMERA", "DEFormats", "apeglm", "ggpubr", "roots", "viper", "mixtools", "bcellViper", "aracne.networks", "rgexf", "fgsea", "PoiClaClu", "GSVA"), dependencies=c("Depends", "Imports", "LinkingTo"), update=TRUE, ask=FALSE, build_vignettes=FALSE, clean=TRUE)'
cd /usr/local
yum install -y java-1.8.0-openjdk ant
git clone https://github.com/califano-lab/ARACNe-AP
cd ARACNe-AP
ant main
echo -e "#! /bin/bash\njavamem=""\nif [[ \$1 =~ "-Xmx" ]];then javamem=\$1; shift 1; fi\nexec java \$javamem -jar /usr/local/src/ARACNe-AP/dist/aracne.jar "\$@"" > /usr/local/bin/ARACNe-AP
Collection
- Name: brucemoran/Singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/brucemoran-Singularity-ucs_ucec_rnaseq.analysis |
collection name | brucemoran/Singularity |
branch | master |
tag | ucs_ucec_rnaseq.analysis |
commit | c574a3f18e7b1c408721d7a5d0d3bf4add0cc641 |
version (container hash) | 0fc1799f49674dddc5c26203f84de264 |
build date | 2019-06-21T13:53:24.552Z |
size (MB) | 3484 |
size (bytes) | 1427677215 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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