bioconda_miniconda-3-install

#!/usr/bin/bash -i

###############################################
# Installing miniconda and bioconda packages
#
# by LC, 2018 
#


################################################
####               !UNTESTED!               ####
################################################


APPNAME=${APPNAME:-miniconda}
VERSION=${VERSION:-3}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/depts/cancer/apps/$APPNAME/}
MD5=${MD5:-REPLACE}
SHA1=${SHA1:-REPLACE}

SRC_ARCHIVE=${SRC_ARCHIVE:-https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh}

set -e

export PATH=$INSTALL_PREFIX:$PATH

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


wget -N $SRC_ARCHIVE
bash Miniconda3-latest-Linux-x86_64.sh


##- deeptools
#conda install -c bioconda deeptools

##- multiQC (install 1.6, 0.9 crashes on nextflow_chipseq)
##- config conda to download 1.6, normal installation would install 0.9 as described here (https://github.com/ewels/MultiQC/issues/729)
#conda config --add channels defaults
#conda config --add channels conda-forge
#conda config --add channels bioconda
#conda install -c bioconda multiqc multiqc=1.6

##- UCSC bedGraphToBigWig, bigWigToWig, wigToBigWig
#conda config --add channels defaults
#conda config --add channels conda-forge
#conda config --add channels bioconda
#conda install -c bioconda ucsc-bedgraphtobigwig
#conda install -c bioconda ucsc-bigwigtowig
#conda install -c bioconda ucsc-wigtobigwig