This page was last updated on Sunday, 13-Nov-2016 20:07:46 CST

Installation notes for Trans-ABySS version 1.5.5 (Aug 02, 2016)

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Prerequisites

• Perl modules
  $ sudo cpan Config::General IO::Uncompress::Gunzip
• Blat
• Pysam
  $ sudo apt-get install python-pysam
• BioPython
  $ sudo apt-get install python-biopython
• python-igraph 0.7.0+
  $ sudo pip install python-igraph
• Samtools
• Bowtie
• BWA

Installation

1. $ ver="1.5.5"
2. $ cd /programinstallers/
3. $ http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/$ver/transabyss-$ver.zip
4. $ cd /usr/local/bin
5. $ unzip /programinstallers/transabyss-$ver.zip
6. $ rm trans-ABySS ; ln -s transabyss-$ver trans-ABySS
7. Make additions to /etc/profile as described in the Trans-ABySS README file
   $ sudo nano /etc/profile
   ...
   #trans-ABySS
   export TRANSABYSS_PATH=/usr/local/bin/trans-ABySS
   export PYTHONPATH=.:$PYTHONPATH:$TRANSABYSS_PATH
   export PERL5LIB=.:$PERL5LIB:$TRANSABYSS_PATH/wrappers ...
8. Version 1.4.8 had a bug at line 27 of script check-prereqs.sh, an extra ` needs to be removed