myriad-buildscripts/ginkgo-install at master · UCL-BLIC/myriad-buildscripts · GitHub

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#!/usr/bin/bash -i

###############################################
# Installing ginkgo
#
# by Javier Herrero, 2019
#

APPNAME=${APPNAME:-ginkgo}
VERSION=${VERSION:-v082019}
COMMIT=${COMMIT:-364ef93d3bdabe8ad58f70bbc80f962c652e943e}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/depts/cancer/apps/$APPNAME/}
MD5=${MD5:-0269a81335f16427fbfe7545ea856aeb}
SHA1=${SHA1:-REPLACE}
SRC_ARCHIVE=${SRC_ARCHIVE:-https://github.com/UCL-BLIC/ginkgo/archive/${COMMIT}.zip}

set -e

module purge
module load r/recommended
module load compilers/intel/2019

export PATH=$INSTALL_PREFIX/bin:$PATH


mkdir -p $INSTALL_PREFIX

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

cd ${INSTALL_PREFIX}

wget -N $SRC_ARCHIVE

MD5SUM=`md5sum ${COMMIT}.zip | awk '{print $1}'`

if [ "$MD5SUM" != "$MD5" ]
then
    echo "Hash mismatch."
    echo "Expected: $MD5"
    echo "Got: $MD5SUM"
    exit
fi

# Uncompress the software
unzip -q ${COMMIT}.zip
rm ${COMMIT}.zip
mv ${APPNAME}-${COMMIT} ${VERSION}
cd ${VERSION}
make

# Include the genome files
mkdir -p ~/Scratch/${APPNAME}/genomes/hg19/original
ln -s /scratch/scratch/${USER}/${APPNAME}/genomes/hg19/ genomes/
cd ~/Scratch/${APPNAME}/genomes/hg19/original
wget -N http://qb.cshl.edu/ginkgo/uploads/hg19.original.tar.gz
tar -zxf hg19.original.tar.gz
rm hg19.original.tar.gz

# Install devtools and BiocManager (in HOME as can be used for many other projects) if required
mkdir -p ~/R
env R_LIBS=${HOME}/R R --vanilla <<'EOF'
if (!("devtools" %in% rownames(installed.packages()))) {
  install.packages("devtools", lib = "~/R", repos = "https://cran.ma.imperial.ac.uk/")
}

if (!("BiocManager" %in% rownames(installed.packages()))) {
  install.packages("BiocManager", lib = "~/R", repos = "https://cran.ma.imperial.ac.uk/")
}
EOF

# Add the R libraries for ginkgo
cd ${INSTALL_PREFIX}/${VERSION}
mkdir -p R

env R_LIBS=${INSTALL_PREFIX}/${VERSION}/R:${HOME}/R R --vanilla <<'EOF'
# amap is required by ctc and the default version is not compatible with the R version we are using here
install.packages("https://cran.r-project.org/src/contrib/Archive/amap/amap_0.8-14.tar.gz", lib = "R")

# Install ctc from bioconductor
BiocManager::install("ctc", lib = "R")

# Need to use a different version of gplots as the default one is very slow because of a bug (always calculates a HC of all rows)
library("devtools")
install_github("ChristophH/gplots", lib = "R")
EOF