PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.
See which versions of poplddecay are available:
$ module avail poplddecay
Load one version into your environment and run it:
$ module load poplddecay/3.41 $ PopLDdecay $ Plot_OnePop.pl $ plink2genotype.pl
Notes from the sysadmin during installation:
$ cd /tmp
$ git clone https://github.com/tseemann/abricate.git -b v1.0.1
$ cd abricate
$ grep -rh -oE "use Bio::.*$" bin/* | sort -u | awk '{print $2}'
Bio::Seq;
Bio::SeqIO;
$ mkdir perl5lib
$ cpanm -l perl5lib LWP::Simple Bio::Seq Bio::SeqIO JSON Path::Tiny --force
$ module load any2fasta/0.4.2
$ module load blast/2.7.1+
$ export PERL5LIB=perl5lib/lib/perl5
$ ./bin/abricate --check
$ ./bin/abricate --setupdb
$ ./bin/abricate test/assembly.fa
$ sudo mkdir -p /export/apps/abricate/1.0.1
$ sudo cp -r * /export/apps/abricate/1.0.1