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¶
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/
Create and place the needed module file. Create a file with the following content:
#%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>