pegi3s/sapp
SAPP (http://sapp.gitlab.io/) docker image.
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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
)
This repository keeps three types of tags:
stable-[yyyy.mm.dd]
: images built with the stable jar files in http://download.systemsbiology.nl/sapp/.dev-[yyyy.mm.dd]
: images built with the development jar files in http://download.systemsbiology.nl/sapp/dev.latest
: an image that always points to the most recent dev-[yyyy.mm.dd]
image.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
To test the previous command, the datasets used are available as FlyBase_JCLNID.fasta and DMelanogaster.hdt.
docker pull pegi3s/sapp