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bcl2fastq setup protocol
#!/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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