THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE

Nextflow Conversion of Iprscan5Task.pm

Iprscan5

flowchart TD
    p0((Channel.fromPath))
    p1([splitFasta])
    p2[iprscan5:Iprscan]
    p3([collectFile])
    p4(( ))
    p0 --> p1
    p1 -->|seqs| p2
    p2 --> p3
    p3 --> p4

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Get Started

• Install Nextflow

  curl https://get.nextflow.io | bash

• Run the script

  nextflow run VEuPathDB/Iprscan5 -with-trace -c <config_file> -r main

Decription of nextflow configuration parameters:

param	value type	description
seqFile	string	Path to input file
outputDir	string	Path to where you would like output files stored
outputFile	string	How you would like the outputFile to be named
appls	string	Comma separated list of analyses (options are PANTHER, SMART, TIGRFAM, Gene3D, PIRSF, CDD, Pfam, SUPERFAMILY, ProSiteProfiles, MobiDBLite, PRINTS, Coils, ProSitePatterns), if none are specified, all will be run.

Notes

In order to run this workflow, you will need to download the needed data files and the RpsbProc software and map them into the docker container. These can be downloaded like so

wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.51-85.0/alt/interproscan-data-5.51-85.0.tar.gz

wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.51-85.0/alt/interproscan-data-5.51-85.0.tar.gz.md5

wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/rpsbproc/RpsbProc-x64-linux.tar.gz

md5sum -c interproscan-data-5.51-85.0.tar.gz.md5

tar -pxzf interproscan-data-5.51-85.0.tar.gz

tar -pxzf RpsbProc-x64-linux.tar.gz

These can then be mapped into the container in the docker runOptions in the nextflow config like so

docker { enabled = true runOptions = "-v /pathtodata/interproscan-5.51-85.0/data:/opt/interproscan/data -v /pathtoRpsbProc/RpsbProc-x64-linux/*:/opt/interproscan/RpsbProc-x64-linux/" }

You may run into the error

Error: File format problem in trying to open HMM file /opt/interproscan/data/gene3d/4.3.0/gene3d_main.hmm. Opened /opt/interproscan/data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

Here is how I solved this problem. I pulled and ran veupathdb/iprscan5. I then copied the interproscan data dir into the container at /opt/interproscan/data. You can then run the following commands.

/opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/pirsf/3.18/sf_hmm_all /opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/gene3d/4.3.0/gene3d_main.hmm /opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/hamap/2020_05/hamap.hmm.lib /opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/panther/15.0/panther.hmm /opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/pfam/33.1/pfam_a.hmm /opt/interproscan/bin/hmmer/hmmer3/3.1b1/hmmpress -f data/sfld/4/sfld.hmm /opt/interproscan/bin/hmmer/hmmer3/3.1b1/hmmpress -f data/superfamily/1.75/hmmlib_1.75 /opt/interproscan/bin/hmmer/hmmer3/3.3/hmmpress -f data/tigrfam/15.0/TIGRFAMs_HMM.LIB

Once this is done, you should not run into any errors.