diff --git a/Dockerfile b/Dockerfile index 983fdc4..390d46d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -167,6 +167,16 @@ RUN cd /usr/share/augustus/scripts && \ wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/createAugustusJoblist.pl && \ chmod a+x optimize_augustus.pl aa2nonred.pl gff2gbSmallDNA.pl new_species.pl filterGenesIn_mRNAname.pl filterGenes.pl filterGenesIn.pl join_mult_hints.pl randomSplit.pl join_aug_pred.pl getAnnoFastaFromJoingenes.py gtf2gff.pl splitMfasta.pl createAugustusJoblist.pl +RUN cd /usr/share/augustus/config && \ + mkdir parameters && \ + cd parameters && \ + wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/AUG_CMDLN_PARAMETERS.md && \ + wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/aug_cmdln_parameters.json && \ + chmod a+r AUG_CMDLN_PARAMETERS.md aug_cmdln_parameters.json && \ + cd .. && \ + chmod a+r parameters && \ + chmod a+x parameters + # bamtools (ETP+) RUN apt update && \ @@ -188,9 +198,8 @@ USER root # braker including RNAseq test file RUN cd /opt && \ - git clone https://github.com/Gaius-Augustus/BRAKER.git && \ + git clone --depth=1 https://github.com/Gaius-Augustus/BRAKER.git && \ cd BRAKER && \ - git checkout braker3 && \ cd example && \ wget http://bioinf.uni-greifswald.de/augustus/datasets/RNAseq.bam @@ -204,7 +213,7 @@ RUN cd /opt && \ chmod a+x /opt/ETP/bin/*py /opt/ETP/bin/*pl /opt/ETP/tools/* ENV GENEMARK_PATH=/opt/ETP/bin -ENV PATH=${PATH}:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin +ENV PATH=${PATH}:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin:/opt/ETP/bin/gmes USER ${NB_UID}