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DEPS_INSTALL.md

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abseqPy's external dependencies

This document describes the required dependencies to get abseqPy working. There is a handy installation script that automates this process, but this document serves as a backup if manual installation is required.

Mandatory dependencies

  • Clustal Omega v1.2.1 or higher
    • Download and extract the tarball or download and use the pre-compiled binaries
  • FastQC v0.11.5 or higher
    • Download and extract the binaries
  • leeHom latest GitHub version
    • Only one of leeHom, FLASH, PEAR is required.
    • This is the default merger used by AbSeq on non Windows machines. AbSeq switches to FLASH as the default merger if it detects Windows; Windows users might find it easier to just download the pre-built FLASH binary.
    • Follow the installation guide in their README , leeHom uses CMake and make as their build tool.
  • IgBLAST v1.7
    • Make sure to follow every step detailed in the guide
    • Important: The environment variable $IGDATA must be exported, as stated in the guide.
  • Ghostscript v9.22 or higher
    • Download and follow the instructions to install here

Optional dependencies

  • FLASH v1.2.11 or higher
    • Required if leeHom and PEAR is not installed
    • Download, extract, make or download the pre-built binary
  • PEAR any version
    • Required if FLASH and leeHom is not installed

IgBLAST configuration

A final note, if the installation script was not used, be sure to set the environment variable $IGBLASTDB to the path where the germline V, D, and J gene sequences are. (i.e. the directory where my_seq_file lives in the example in IgBLAST's how to setup).

If $IGBLASTDB is not set, abseqPy will require the -d or --database flag (see abseq -h) to be specified with the same directory as $IGBLASTDB would have had.

Regardless, the database files (my_seq_files) in $IGBLASTDB (or the files in -d / --database) must be named:

  1. imgt_human_ighv, imgt_human_ighd, imgt_human_ighj for Heavy chain VDJ (used when -c hv)
  2. imgt_human_igkv, imgt_human_igkj for Kappa chain VJ (used when -c kv)
  3. imgt_human_iglv, imgt_human_iglj for Lambda chain VJ (used when -c lv)
  4. imgt_human_igklv, imgt_human_igklj for Kappa and Lambda chains combined (used when -c klv)