Ignore genome incompatibility (#30)

* fix: Ignore genome incompatibility * build: fix image registry
stjude · Jun 2, 2023 · fd52875 · fd52875
1 parent 4b4530b
commit fd52875
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diff --git a/.github/workflows/docker_branch.yml b/.github/workflows/docker_branch.yml
@@ -19,7 +19,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v3
         with:
-          images:  ${{ env.REPO_LOWER }}
+          images:  ghcr.io/${{ env.REPO_LOWER }}
           tags: |
             type=ref,event=branch,prefix=branch-
             type=ref,event=pr

diff --git a/Dockerfile b/Dockerfile
@@ -45,7 +45,7 @@ RUN apk add --no-cache bash
 RUN cpan App:cpanminus
 RUN cpanm --no-wget Data::Compare && chown -R root:root /root/.cpanm
 RUN cpanm --no-wget DB_File XML::Parser::PerlSAX XML::Twig XML::DOM
-RUN cpanm --no-wget Bio::Tools::CodonTable
+RUN cpanm --no-wget --force Bio::Tools::CodonTable
 RUN cpanm --no-wget DBI
 RUN cpanm --no-wget Set::IntSpan
 

diff --git a/src/main/docker/RNApeg.sh b/src/main/docker/RNApeg.sh
@@ -86,4 +86,4 @@ if [[ -n "$OUTPUT_DIR" ]]; then
     mkdir -p $OUTPUT_DIR
     output_arg="-o $OUTPUT_DIR"
 fi
-    junction_extraction_wrapper.pl -no-config -bam $BAMFILE -fasta $FASTA -refflat $REFFLAT -refgene $REFGENE -now ${output_arg}
+    junction_extraction_wrapper.pl -no-config -ignore-incompatible -bam $BAMFILE -fasta $FASTA -refflat $REFFLAT -refgene $REFGENE -now ${output_arg}