UMI Scripts - Install

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Standard installation

This package can by installed using the standard Perl Module::Build incantation.

perl ./Build.PL
./Build
./Build installdeps   # if necessary
./Build install

Otherwise, a Perl package manager may be used, such as CPAN or CPAN Minus. If you have downloaded this package from GitHub, use one of the following inside the package directory.

cpan  .
cpanm .
cpanp .

This installation will allow the scripts to work with Fastq files. However, to use the scripts with bam files, specifically bam_umi_dedup.pl, follow the Advanced installation, below.

Advanced installation

The bam_umi_dedup application requires the installation of the Bio::DB::HTS Perl adapter, which in turn requires the external HTSlib library to be installed.

While Bio::DB::HTS may be installed from CPAN, there are two prerequisites which should be installed first. These are listed below.

• Install htslib

  This may already be available on your system, or available either through your OS package manager or an alternative package manager like Homebrew. It is also included with Samtools, although it is not installed by default.

  Follow the directions within for installation. Version 1.9 is officially recommended by the Bio::DB::HTS authors; however, later versions appear to work just fine and should probably be preferred. Version 1.19 have been used successfully by this author. By default, it installs into /usr/local, or it may be set to another directory ($HOME for example) by adding --prefix=$HOME option to the configure step.

• Install BioPerl

  The BioPerl package is a prerequiste of Bio::DB::HTS. It is a large bundle consisting of hundreds of modules and bundled scripts, the vast majority of which is not needed. Unless users have other requirements or explicit needs for BioPerl, it is strongly recommended to install an unofficial, custom, simplified minimal version generated by the author. This is considerably faster to install and has a footprint one-third the size of the full distribution; use this file to install.

  As a Perl module, it can be installed as described above.

Once these two prerequisites are installed, the remaining Perl modules can be installed. These are listed as recommendations in Build.PL and are not installed automatically as dependencies. Most Perl package managers, such as CPANMinus, CPANPlus, or CPAN can be used here. Use one of the following, as appropriate:

cpan  -i Bio::DB::HTS Parallel::ForkManager List::MoreUtils
cpanm -i Bio::DB::HTS Parallel::ForkManager List::MoreUtils
cpanp -i Bio::DB::HTS Parallel::ForkManager List::MoreUtils

If you are installing from the downloaded package directory and using CPANMinus, you could alternatively invoke the following

cpanm --installdeps --with-recommends .

If htslib is in a non-standard location, you may have to specify this manually or run the installer interactively. The Build.PL script in Bio::DB::HTS accepts the --htslib <PATH> option to specify the location. If you’re using cpanm, you could pass the path directly with the option --configure-args="--htslib <PATH>".