LINKS 1.8.7

Basic information

• Deploy date: 22 October 2019

• Official Website: https://github.com/bcgsc/abyss

• License: GNU GPL v3

• Installed on: Apolo II

• Dependencies:

  • GCC

  • Perl

Installation

1. Make sure you have GCC and Perl installed, then run:

   $ git clone https://github.com/bcgsc/LINKS.git
   $ cd LINKS/releases/links_v1.8.7
   $ tar xvf lib.tar.gz
   $ cd lib/
   $ rm -rf bloomfilter
   $ git clone git://github.com/bcgsc/bloomfilter.git
   $ cd bloomfilter/swig
   $ module load gcc/5.4.0
   $ module load perl/5.26.1_gcc-4.4.7
   $ swig -Wall -c++ -perl5 BloomFilter.i
   $ g++ -std=c++11 -c BloomFilter_wrap.cxx -I/share/apps/perl/5.26.1_gcc-4.4.7/lib/5.26.1/x86_64-linux-thread-multi-ld/CORE -fPIC -Dbool=char -O3 -mavx2
   $ g++ -std=c++11 -Wall -shared BloomFilter_wrap.o -o BloomFilter.so -O3 -mavx2
   $ ./test.pl
   

   Make sure the tests run correctly. Then install it:

   # Go back to the links 1.8.7 root directory
   $ cd ../../../
   $ rm lib.tar.gz
   
   $ mkdir -p /share/apps/links/1.8.7/gcc/5.4.0
   
   # There is no installation script, so install it manually
   $ cp -r ./* /share/apps/links/1.8.7/gcc/5.4.0/
   

2. Create and place the needed module file. Create a file with the following content:

   1.8.7_gcc-5.4.0_perl-5.26.1

   #%Module1.0####################################################################
   ##
   ## module load links/1.8.7
   ##
   ## /share/apps/links/1.8.7/gcc/5.4.0
   ## Written by Vincent A. Arcila L and Hamilton Tobon Mosquera.
   ##
   
   proc ModulesHelp {} {
            global version modroot
            puts stderr "Sets the environment for using links 1.8.7\
            \nin the shared directory /share/apps/links/1.8.7/gcc/5.4.0\
            \nbuilt with GCC 5.4.0.
   }
   
   module-whatis "(Name________) links"
   module-whatis "(Version_____) 1.8.7"
   module-whatis "(Compilers___) gcc-5.4.0"
   module-whatis "(System______) x86_64-redhat-linux"
   module-whatis "(Libraries___) "
   
   # for Tcl script use only
   set         topdir        /share/apps/links/1.8.7/gcc/5.4.0
   set         version       1.8.7
   set         sys           x86_64-redhat-linux
   
   conflict links
   module load perl/5.26.1_gcc-4.4.7
   
   prepend-path   PATH            $topdir
   prepend-path   PATH            $topdir/test
   prepend-path   PATH            $topdir/tools
   

   Create the needed folder and place it:

   $ sudo mkdir /share/apps/modules/links
   $ sudo mv 1.8.7_gcc-5.4.0_perl-5.26.1 /share/apps/modules/links/
   

Troubleshooting

There is a problem compiling with GCC 7.4.0, it seems like a problem with some instructions that are not supported by the C++ standard that GCC 7.4.0 implements. So, try using GCC 5.4.0.

Authors

• Hamilton Tobon-Mosquera <htobonm@eafit.edu.co>