sangerpathogens/interproscan repository overview

⁠Bio-InterProScanWrapper

Wrapper around InterProScan

⁠Contents

• Introduction⁠
  • Features⁠
• Installation⁠
  • Required dependencies⁠
  • Using ⁠cpanm⁠
  • From Source⁠
  • Running the tests⁠
• Usage⁠
• License⁠
• Feedback/Issues⁠
• Further Information⁠

⁠Introduction

This is a wrapper around InterProScan. It takes in a FASTA file of proteins, splits them up into smaller chunks, processes them with individual instances of iprscan and then sticks it all back together again. It can run in parallelised mode on a single host or over LSF.

⁠Features

• Annotates using InterProScan 5.
• Intermediate files cleaned up as soon as they are finished with.
• Creates a GFF3 file with the input sequences at the end.

⁠Installation

Bio-InterProScanWrapper has the following dependencies:

⁠Required dependencies

• IPRscan 5⁠

Details for installing Bio-InterProScanWrapper are provided below. If you encounter an issue when installing Bio-InterProScanWrapper please contact your local system administrator. If you encounter a bug please log it here⁠ or email us at [email protected]⁠.

⁠Using cpanm

First install cpanm⁠, then install Bio-InterProScanWrapper:

cpanm Bio::InterProScanWrapper

⁠From Source

Clone the latest version of this repository and cd into it. Then:

dzil authordeps | cpanm
dzil listdeps | cpanm
dzil build

⁠Running the tests

The test can be run with dzil from the top level directory:

dzil test

⁠Usage

Usage: farm_interproscan [options]
Run InterProScan on the farm. It is limited to using 400 CPUs at once on the farm.

# Run InterProScan using LSF
farm_interproscan -a proteins.faa

# Provide an output file name
farm_interproscan -a proteins.faa -o output.gff

# Create 200 jobs at a time, writing out intermediate results to a file
farm_interproscan -a proteins.faa -p 200

# Run on a single host (no LSF). '-p x' needs x*2 CPUs and x*2GB of RAM to be available
farm_interproscan -a proteins.faa --no_lsf -p 10

# Run InterProScan using LSF with GFF input (standard genetic code for translation)
farm_interproscan -a annotation.gff -g

# Run InterProScan using LSF with GFF input (bacterial code for translation)
farm_interproscan -a annotation.gff -g -c 11

# This help message
farm_interproscan -h

⁠License

Bio-InterProScanWrapper is free software, licensed under GPLv3⁠.

⁠Feedback/Issues

Please report any issues to the issues page⁠ or email [email protected]⁠.

⁠Further Information

Sanger Institute staff should refer to the wiki⁠ for further information.