cytofpipe-v1.3-install

#!/usr/bin/bash -i

###############################################
# Installing cytofpipe
#
# by Javier Herrero, 2017
#

APPNAME=${APPNAME:-cytofpipe}
VERSION=${VERSION:-v1.3}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/depts/cancer/apps/$APPNAME/}
MD5=${MD5:-REPLACE}
SHA1=${SHA1:-REPLACE}
SRC_ARCHIVE=${SRC_ARCHIVE:-NA}

set -e

module purge
module load r/recommended

export PATH=$INSTALL_PREFIX/bin:$PATH

mkdir -p $INSTALL_PREFIX

rm -rf ${INSTALL_PREFIX}/${VERSION}
mkdir -p ${INSTALL_PREFIX}/${VERSION}

cp -r cytofpipe/${VERSION}/* $INSTALL_PREFIX/${VERSION}

mkdir -p ${INSTALL_PREFIX}/${VERSION}/Rlibs

export R_LIBS=${INSTALL_PREFIX}/${VERSION}/Rlibs:${R_LIBS}

## If this fails, check that Bioconductor is not out of date. Uncomment the
## biocUpgrade line below if that is the case.
R --vanilla <<EOF
install.packages("ini", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
install.packages("hash", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
install.packages("rmarkdown", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")

#- cytofkit/openCyto
source("https://bioconductor.org/biocLite.R")
biocLite("biocUpgrade", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
biocLite("flowCore", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
biocLite("cytofkit", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
biocLite("openCyto", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")

#- scaffold
install.packages("devtools", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
library(devtools)
install_github("nolanlab/scaffold", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")

#- citrus
install.packages("glmnet", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/") 
install.packages("pamr", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/") 
install.packages("ggplot2", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
install.packages("survival", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
biocLite("impute", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
install.packages("samr", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs", repos = "https://cran.ma.imperial.ac.uk/")
install_github("nolanlab/Rclusterpp", lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
install_github('nolanlab/citrus', lib = "${INSTALL_PREFIX}/${VERSION}/Rlibs")
EOF