Fixed tests, not moving cdd.tar.gz now

iquasere · Dec 27, 2023 · b60a4a6 · b60a4a6
1 parent 0603652
commit b60a4a6
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -41,7 +41,7 @@ jobs:
           docker load --input /tmp/recognizer.tar
           docker image ls -a
       - name: Default annotation
-        run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs COG,TIGRFAM --test-run"
+        run: docker run recognizer /bin/bash -c "recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs COG,TIGRFAM --test-run"
 
   taxonomy-based-annotation:
     runs-on: ubuntu-latest
@@ -57,7 +57,7 @@ jobs:
           docker load --input /tmp/recognizer.tar
           docker image ls -a
       - name: Taxonomy-based annotation
-        run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --tax-file reCOGnizer/ci/UPIMAPI_results.tsv --tax-col 'Taxonomic lineage IDs (SPECIES)' --protein-id-col qseqid --species-taxids --quiet --test-run"
+        run: docker run recognizer /bin/bash -c "recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --tax-file reCOGnizer/ci/UPIMAPI_results.tsv --tax-col 'Taxonomic lineage IDs (SPECIES)' --protein-id-col qseqid --species-taxids --quiet --test-run"
 
   custom-database-annotation:
     runs-on: ubuntu-latest
@@ -73,4 +73,4 @@ jobs:
           docker load --input /tmp/recognizer.tar
           docker image ls -a
       - name: Custom database annotation
-        run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; tar -xzf resources_directory/cdd.tar.gz -C resources_directory; makeprofiledb -in reCOGnizer/ci/ci.pn -out resources_directory/db; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs resources_directory/db --custom-databases --test-run"
+        run: docker run recognizer /bin/bash -c "tar -xzf reCOGnizer/ci/cdd.tar.gz -C resources_directory; makeprofiledb -in reCOGnizer/ci/ci.pn -out resources_directory/db; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs resources_directory/db --custom-databases --test-run"