PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.

• Version: 3.41
• Added: January, 2022
• Link: https://github.com/BGI-shenzhen/PopLDdecay

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

Note 1: abricate only says that it requires BioPerl, but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl "use" statements.

Note 2: You can try without ''--force'' if you want, but many Perl modules "bail out" during installation because one out of a few hundred (or thousand) obscure or comprehensive tests fail.