Compiling Arks And Links¶
Author: | Brant C. Faircloth |
---|---|
Copyright: | This documentation is available under a Creative Commons (CC-BY) license. |
Steps¶
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
Download and compile a local copy of sparsehash
# in $HOME/project/shared/src cd sparsehash/ && ./configure && make && cd ../
Load the Boost and GCC 6 modules and set
CC
andCXX
andCPPFLAGS
module load boost/1.63.0/INTEL-18.0.0 module load gcc/6.4.0 export CC=`which gcc` export CXX=`which g++` export CPPFLAGS=-I$(readlink -f sparsehash/src)
Enter the arks directory and run
autogen.sh
andconfigure
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
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
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
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
Finally, create a conda environment that contains the remaning dependencies or arks:
conda create -n scaffolding tigmint bwa samtools bedtools