Merge pull request #53 from sii-companion/feature-braker3

Upgrade BRAKER to remove GM_KEY req

.github/workflows/docker-push-on-release.yml

@@ -4,9 +4,6 @@ on:
   release:
     types: [published]
 
-env:
-  GM_KEY: ${{ secrets.GM_KEY }}
-
 jobs:
   push_to_registry:
     name: Push Docker image to Docker Hub
@@ -34,5 +31,3 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-          build-args: |
-            GM_KEY="${{ env.GM_KEY }}"

Dockerfile

@@ -163,7 +163,7 @@ RUN cpanm File::Spec::Functions && \
     cpanm File::HomeDir && \
     cpanm threads
 RUN cd /opt && \
-    git clone https://github.com/Gaius-Augustus/BRAKER.git --branch v2.1.6 && \
+    git clone https://github.com/Gaius-Augustus/BRAKER.git --branch v3.06 && \
     cd BRAKER/scripts
 ADD http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz /opt/etp.for_braker.tar.gz
 RUN cd /opt && \
@@ -189,6 +189,8 @@ ADD https://genomethreader.org/distributions/gth-1.7.3-Linux_x86_64-64bit.tar.gz
 RUN cd /opt && \
     tar xzf gth-1.7.3-Linux_x86_64-64bit.tar.gz && \
     rm -f gth-1.7.3-Linux_x86_64-64bit.tar.gz
+RUN cd /opt && \
+    git clone https://github.com/Gaius-Augustus/TSEBRA
 
 #
 # install orthofinder
@@ -202,10 +204,6 @@ RUN cd /opt && \
     cd .. && \
     rm -f OrthoFinder_source.tar.gz
 
-## Make sure to build with 'docker build --build-arg GM_KEY=<GM_KEY> .' to populate this arg.
-ARG GM_KEY
-RUN echo ${GM_KEY} > ~/.gm_key
-
 #
 # install gffread
 #
@@ -228,3 +226,4 @@ ENV PROTHINT_PATH /opt/ProtHint/bin
 ENV BSSMDIR /opt/gth-1.7.3-Linux_x86_64-64bit/bin/bssm
 ENV GTHDATADIR /opt/gth-1.7.3-Linux_x86_64-64bit/bin/gthdata
 ENV ALIGNMENT_TOOL_PATH /opt/gth-1.7.3-Linux_x86_64-64bit/bin/
+ENV TSEBRA_PATH /opt/TSEBRA/bin

bin/run_braker.sh

@@ -21,7 +21,7 @@ if [ "$useExisting" == "true" ]
 then
     args+=(--species=augustus_species)
     args+=(--useexisting)
-    AUGUSTUS_CONFIG_PATH=$augustusModelPath; export AUGUSTUS_CONFIG_PATH 
+    AUGUSTUS_CONFIG_PATH=$augustusModelPath; export AUGUSTUS_CONFIG_PATH
 else
     args+=(--species=$spId)
 fi
@@ -34,4 +34,4 @@ then
 fi
 
 echo "${args[@]}"
-braker.pl --genome=$genome --prot_seq=$annProt --gff3 --cores $cores "${args[@]}"
+braker.pl --genome=$genome --prot_seq=$annProt --gff3 --threads $cores "${args[@]}"

loc_docker.config

@@ -12,6 +12,7 @@ params.CIRCOS_CONFIG_FILE = "/opt/data/circos/circos.debian.conf"
 params.CIRCOS_BIN_CONFIG_FILE = "/opt/data/circos/circos.bin.debian.conf"
 params.SPECFILE = "/opt/data/speck/output_check.lua"
 params.AUGUSTUS_EXTRINSIC_CFG = "/opt/data/augustus/extrinsic.MPE.cfg"
+params.NCRNA_MODELS = "/opt/data/cm/kinetoplastid_rnas.cm"
 
 process {
     container = 'uofgiii/companion:latest'