diff --git a/dockerbuild/Dockerfile-base b/dockerbuild/Dockerfile-base index 2e9fb0a6..07f8b59d 100644 --- a/dockerbuild/Dockerfile-base +++ b/dockerbuild/Dockerfile-base @@ -100,5 +100,5 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86 COPY pasa_conf.txt /home/linuxbrew/PASApipeline/pasa_conf/conf.txt -RUN wget https://github.com/nextgenusfs/funannotate/archive/1.5.1.tar.gz && \ - tar -zxvf 1.5.1.tar.gz && rm 1.5.1.tar.gz && mv funannotate-1.5.1 funannotate +RUN wget https://github.com/nextgenusfs/funannotate/archive/1.5.2.tar.gz && \ + tar -zxvf 1.5.2.tar.gz && rm 1.5.2.tar.gz && mv funannotate-1.5.2 funannotate diff --git a/funannotate.py b/funannotate.py index 13761994..85943341 100755 --- a/funannotate.py +++ b/funannotate.py @@ -237,6 +237,7 @@ def fmtcols(mylist, cols): --rna_bam RNA-seq mapped to genome to train Augustus/GeneMark-ET --stringtie StringTie GTF result --augustus_species Augustus species config. Default: uses species name + --min_training_models Minimum number of models to train Augustus. Default: 200 --genemark_mode GeneMark mode. Default: ES [ES,ET] --genemark_mod GeneMark ini mod file --busco_seed_species Augustus pre-trained species to start BUSCO. Default: anidulans diff --git a/lib/library.py b/lib/library.py index 4aac9b04..c8595ec6 100644 --- a/lib/library.py +++ b/lib/library.py @@ -4180,6 +4180,7 @@ def RunGeneMarkET(command, input, ini, evidence, maxintron, softmask, cpus, tmpd with open(evidence, 'rU') as evid: for line in evid: if '\tintron\t' in line and '\tb2h\t' in line: + line[5] = 500 # for intron hint score to be 500 hints.write(line) log.info("Running GeneMark-ET on assembly") cmd = [command, '--ET', os.path.abspath(hintsfile), '--max_intron', str(maxintron), '--soft_mask', str(softmask), '--cores', str(cpus), '--sequence', contigs]