Compiling Arks And Links

Author:Brant C. Faircloth Copyright:This documentation is available under a Creative Commons (CC-BY) license.

Steps

1. Download and unpack arks

   wget -O arks-v1.0.4.tar.gz https://github.com/bcgsc/arks/archive/v1.0.4.tar.gz
   tar -xzvf arks-v1.0.4.tar.gz
   

2. Download and compile a local copy of sparsehash

   # in $HOME/project/shared/src
   cd sparsehash/ && ./configure && make && cd ../
   

3. Load the Boost and GCC 6 modules and set CC and CXX and CPPFLAGS

   module load boost/1.63.0/INTEL-18.0.0
   module load gcc/6.4.0
   
   export CC=`which gcc`
   export CXX=`which g++`
   export CPPFLAGS=-I$(readlink -f sparsehash/src)
   

4. Enter the arks directory and run autogen.sh and configure and, finally, make install

   cd arks-1.0.4/
   ./autogen.sh
   ./configure --with-boost=/usr/local/packages/boost/1.63.0/INTEL-18.0.0/lib --prefix=$HOME/project/shared
   make install
   

5. Apparently, one of the needed files does not get copies to bin, so:

   cd ~/project/shared/bin
   ln -s ../src/arks-1.0.4/Examples/makeTSVfile.py
   

6. Download links and unzip it

   wget https://github.com/bcgsc/LINKS/releases/download/v1.8.7/links_v1-8-7.tar.gz
   tar -xvf links_v1-8-7.tar.gz
   

7. We need to build the bloomfilter module for links. To compile with more modern versions of GCC (> v4), omit the -Dbool=char flag:

   module load perl/5.24.0/INTEL-18.0.0
   cd links_v1.8.7/lib
   rm -rf bloomfilter/
   git clone git://github.com/bcgsc/bloomfilter.git
   cd bloomfilter/swig
   swig -Wall -c++ -perl5 BloomFilter.i
   # omit the -Dbool=char flag in the following
   g++ -c BloomFilter_wrap.cxx -I/usr/local/packages/perl/5.24.0/INTEL-18.0.0/lib/5.24.0/x86_64-linux-thread-multi/CORE -fPIC -Dbool=char -O3
   g++ -Wall -shared BloomFilter_wrap.o -o BloomFilter.so -O3
   
   # test with
   perl test.pl
   

8. Finally, create a conda environment that contains the remaning dependencies or arks:

   conda create -n scaffolding tigmint bwa samtools bedtools