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bcl2fastq setup protocol
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#!/bin/sh | |
# Protocol for setting up an environemnt for bcl2fastq 1.8.4 | |
# See: http://seqanswers.com/forums/showpost.php?p=141026&postcount=29 | |
# lior.galanti@nyu.edu | |
# for bcl2fastq2 see http://backwardincompatible.com/post/169360794395/compiling-illumina-bcl2fastq-220-on-ubuntu-with | |
# On Ubuntu | |
sudo apt-get install \ | |
libexpat1-dev \ | |
libexpat1 \ | |
expat \ | |
alien \ | |
build-essential \ | |
xsltproc \ | |
imagemagick \ | |
gnuplot | |
# On RedHat | |
yum install \ | |
expat-devel \ | |
expat \ | |
libxslt-devel \ | |
libxslt \ | |
ImageMagick \ | |
gnuplot | |
curl -O ftp://webdata:webdata@ussd-ftp.illumina.com//Downloads/Software/bcl2fastq/bcl2fastq-1.8.4-Linux-x86_64.rpm | |
sudo alien -iv bcl2fastq-1.8.4-Linux-x86_64.rpm | |
curl -kL http://install.perlbrew.pl | bash | |
echo >> ~/.bash_profile "source ~/perl5/perlbrew/etc/bashrc" | |
source ~/.bash_profile | |
perlbrew install perl-5.14.4 | |
perlbrew switch perl-5.14.4 | |
perlbrew install-cpanm | |
cpanm XML/Simple.pm |
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