This page was last updated on Tuesday, 13-Dec-2016 16:03:20 CST

Installation notes for Biopieces version 2282

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Prerequisites

• svn
  $ sudo apt-get install subversion
• Ruby
  1. $ sudo apt-get install ruby gem ruby-dev
• Ruby modules
  1. $ sudo gem install gnuplot
  2. $ sudo gem install narray
  3. $ sudo gem install RubyInline
  4. $ sudo gem install terminal-table
  Error encountered was Invalid gemspec in [/var/lib/gems/1.9.1/specifications/ZenTest-4.9.5.gemspec]: Illformed requirement ["< 3.0, >= 1.8"]
  See this page message # 6, for this solution:
  1. $ sudo gem uninstall ZenTest
  2. $ sudo rm /var/lib/gems/1.9.1/specifications/ZenTest-4.9.5.gemspec
  3. $ sudo gem install ZenTest -v 4.3.0
• Perl modules
  1. $ sudo cpan Inline::C JSON::XS SVG Bit::Vector

Installation

1. $ cd /usr/local/bin
2. $ svn checkout http://biopieces.googlecode.com/svn/trunk/ biopieces
   ...
   A biopieces/00README
   Checked out revision 2282.
3. $ cd biopieces
4. $ svn checkout http://biopieces.googlecode.com/svn/wiki bp_usage
   ...
   A bp_usage/assemble_tag_contigs.wiki Checked out revision 2282.
5. Every user will have to do this one time:
   $ mkdir ~/biopiecesdata ; mkdir ~/logs ; mkdir ~/logs/biopieceslog
6. Every user will need to add this to their ~/.bashrc
   

   # biopieces
   export BP_DIR="/usr/local/bin/biopieces"  # Directory where biopieces are installed
   export BP_DATA="$HOME/biopiecesdata"      # Contains genomic data etc.
   export BP_TMP="/tmp"                      # Required temporary directory.
   export BP_LOG="$HOME/logs/biopieceslog"   # Required log directory.
   if [ -f "$BP_DIR/bp_conf/bashrc" ]; then
       source "$BP_DIR/bp_conf/bashrc"
   fi

7. Test
   $ bp_test
   

   Testing Perl version ... OK
   Testing required Perl module - "Inline": OK
   Testing required Perl module - "JSON::XS": OK
   Testing required Perl module - "SVG": OK
   Testing required Perl module - "Bit::Vector": OK
   Testing required Perl module - "Time::HiRes": OK
   Testing Ruby version ... OK
   Testing required Ruby gem - "gnuplot": OK
   Testing required Ruby gem - "narray": OK
   Testing required Ruby gem - "RubyInline": OK
   Testing required Ruby gem - "terminal-table": OK
   Testing auxiliary program - "blastall": WARNING
   Testing auxiliary program - "blat": OK
   Testing auxiliary program - "bwa": OK
   Testing auxiliary program - "bowtie": WARNING
   Testing auxiliary program - "bowtie2": WARNING
   Testing auxiliary program - "formatdb": WARNING
   Testing auxiliary program - "hmmsearch": WARNING
   Testing auxiliary program - "gnuplot": OK
   Testing auxiliary program - "idba_hybrid": WARNING
   Testing auxiliary program - "muscle": OK
   Testing auxiliary program - "mummer": OK
   Testing auxiliary program - "mysql": OK
   Testing auxiliary program - "prodigal": WARNING
   Testing auxiliary program - "Ray": WARNING
   Testing auxiliary program - "scan_for_matches": WARNING
   Testing auxiliary program - "usearch": WARNING
   Testing auxiliary program - "velveth": WARNING
   Testing auxiliary program - "velvetg": WARNING
   Testing auxiliary program - "vmatch": WARNING

   ...