Merge branch 'release/1.6.5'

Author: saramonzon

Dockerfile

@@ -13,7 +13,6 @@ ADD CHANGELOG.md /opt/plasmidID/
 ADD LICENSE /opt/plasmidID/
 
 RUN cd /opt/plasmidID
-RUN apt install -y libgd-dev
 RUN /opt/conda/bin/conda env create -f /opt/plasmidID/environment.yml && /opt/conda/bin/conda clean -a
 RUN /opt/conda/bin/conda env export --name plasmidID > plasmidID.yml
 ENV PATH /opt/conda/envs/plasmidID/bin:$PATH

bin/prokka_annotation.sh

@@ -212,7 +212,7 @@ prokka --force --outdir $output_dir \
 --usegenus \
 --centre BU-ISCIII \
 --locustag $prefix \
---compliant \
+--addgenes \
 --cpus $threads \
 $input_file #|| error ${LINENO} $(basename $0) "Prokka command failed. See $output_dir/logs for more information."
 

environment.yml

@@ -5,6 +5,7 @@ channels:
   - defaults
 dependencies:
   - python>=3.6
+  - bioconda::perl-gd>=2.71
   - bioconda::bowtie2
   - bioconda::bedtools
   - bioconda::samtools