ATLAS-ADNA_install

#!/usr/bin/env bash

###############################################
# Installing ATLAS Ancient DNA Analysis
#
# by Brian Alston April 2021
# Updated with a bug fix suggested by the developers August 2021.


set -e

for i in ${includes_dir:=$(dirname $0 2>/dev/null)/includes}/{module_maker,require}_inc.sh; do . $i; done

require gcc-libs/10.2.0
require compilers/gnu/10.2.0
require openblas/0.3.13-native-threads/gnu-10.2.0
require arpack-ng/3.8.0-threaded/gnu-10.2.0
require superlu/5.2.1/gnu-10.2.0
require armadillo/10.4.0/gnu-10.2.0

APPNAME=${APPNAME:-ATLAS-ADNA}
TODAY=${TODAY:-`date +%F`}
VERSION=${VERSION:-0.9_${TODAY}}
COMPILER_TAG=${COMPILER_TAG:-gnu-10.2.0}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/$APPNAME/$VERSION/$COMPILER_TAG}
SRC_ARCHIVE=${SRC_ARCHIVE:-https://bitbucket.org/WegmannLab/atlas.git}

mkdir -p /dev/shm/$APPNAME
temp_dir=`mktemp -d -p /dev/shm/$APPNAME`

cd $temp_dir

git clone --depth 1 $SRC_ARCHIVE
cd atlas

# Implement bug fix suggested by developers.
sed -i.bak '1520s/alignmentParser.bamHeader.ReadGroups.Add(readGroupTruncated)/alignmentParser.readGroups.addTruncatedOrMergedRG(alignmentParser.bamHeader, vec[0], readGroupTruncated)/' TGenome.cpp

make

# No make install so:
mkdir -p $INSTALL_PREFIX/bin
cp atlas $INSTALL_PREFIX/bin/

# I'm not sure if any support files are needed from the git clone so stopping at this point.