pegi3s/sapp

Sponsored OSS

By i3S

Updated 4 months ago

SAPP (http://sapp.gitlab.io/) docker image.

Image
Data Science
Machine Learning & AI

248

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of SAPP, a Semantic genome Annotation Platform with Provenance and designed on the basis of Semantic Web. The platform and corresponding modules allow the user to annotate genomes of various qualities linked to a full chain of data provenance. Resulting is an annotated genome in the RDF data model which the user can query and analyse using SPARQL. Various modules are available which allow users to compare, annotate and visualise genomes and export annotations to various standard genome annotation formats.

SAPP platform includes the following jar packages:

  • Aragorn.jar
  • BLAST.jar
  • CRT.jar
  • Conversion.jar
  • EnzDP.jar
  • GenomeInformation.jar
  • GenomeSync.jar
  • HDTQuery.jar
  • HMM.jar
  • InterProScan.jar
  • Loader.jar
  • RDFLoader.jar
  • TMHMM.jar
  • Transcriptomics.jar
  • WoLFPSort.jar
  • assembly.jar
  • genecaller.jar
  • pathwayAnalysis.jar
  • rnammer.jar
  • signalp.jar

To obtain the help of a package, you just need to run: docker run --rm pegi3s/sapp java -jar <package.jar> --help (e.g. docker run --rm pegi3s/sapp java -jar Conversion.jar --help)

SAPP versions and Docker tags

This repository keeps three types of tags:

Using the SAPP image in Linux

To run a package, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/sapp java -jar <package.jar> <options>

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input files you want to analyze.
  • <package.jar> to the name of the SAPP package you want to use.
  • <options> with the specific options of the SAPP package. These options will include the input/output files, which should be referenced under /data/.

For instance, to run the Conversion.jar package for an Eukaryotic Genome, you should run: docker run --rm -v /your/data/dir:/data pegi3s/sapp java -jar Conversion.jar -fasta2hdt -input /data/FlyBase_JCLNID.fasta -o /data/DMelanogaster.hdt -genome -chromosome -id DMelanogaster -org "Drosophila melanogaster" -codon 0

Now you can run Augustus, for gene prediction, with the following command: docker run --rm -v /your/data/dir:/data pegi3s/sapp java -jar genecaller.jar -augustus -i /data/DMelanogaster.hdt -o /data/DMelanogaster_augustus.hdt -s fly

Test data

To test the previous command, the datasets used are available as FlyBase_JCLNID.fasta and DMelanogaster.hdt.

Docker Pull Command

docker pull pegi3s/sapp