This page was last updated on Tuesday, 07-Mar-2017 13:54:43 CST

Installation notes for SSPACE-Standard version 3.0

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Prerequisites

Perl

getopts.pl, a Perl 4 core library no longer included in current Perl 5 distributions
Error message if this is missing is: Can't locate getopts.pl in @INC (@INC contains: …
$ sudo cpan Perl4::CoreLibs

SSPACE standard Installation

1. $ ver="3.0"
2. Program is obtained on request from BASECLEAR, SSPACE-STANDARD-3.0_linux-x86_64.tar.gz
3. $ cd /usr/local/bin
4. $ tar -zxvf /programinstallers/SSPACE-STANDARD-${ver}_linux-x86_64.tar.gz
5. Create a version-indipendent symlink
   $ ln -s SSPACE-STANDARD-${ver}_linux-x86_64 SSPACE
6. Add to default PATH
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/SSPACE"
   …
7. The executable is SSPACE_Standard_v3.0.pl

SSPACE longread Installation

1. $ ver="1-1"
2. Program is obtained on request from BASECLEAR, SSPACE-LongRead_v1-1.tar.gz
3. $ cd /usr/local/bin/SSPACE
4. $ tar -zxvf /programinstallers/SSPACE-LongRead_v$ver.tar.gz
   SSPACE-LongRead_v1-1/
   SSPACE-LongRead_v1-1/blasr
   SSPACE-LongRead_v1-1/SSPACE-LongRead.pl
5. Fix perl header
   $ sudo nano SSPACE-LongRead_v$ver/SSPACE-LongRead.pl
   Add as the first line
   #!/usr/bin/perl
6. $ sudo dos2unix SSPACE-LongRead_v$ver/SSPACE-LongRead.pl
7. $ sudo chmod +x SSPACE-LongRead_v$ver/SSPACE-LongRead.pl
8. Create a version-indipendent symlink
   $ sudo ln -s SSPACE-LongRead_v$ver/SSPACE-LongRead.pl
9. The executable is SSPACE-LongRead.pl