Database download simplified

Added cog2ko database
COG2KO now only written for KOs with more than 50 % for each COG

.github/workflows/main.yml

@@ -18,7 +18,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           context: .
-          file: ./Dockerfile
+          file: ./ci/Dockerfile
           tags: recognizer:latest
           outputs: type=docker,dest=/tmp/recognizer.tar
       - name: Upload artifact
@@ -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 --download-resources --quiet -sd -dbs COG,TIGRFAM"
+        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"
 
   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 --download-resources --quiet -sd"
+        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"
 
   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 --download-resources --quiet -sd -dbs resources_directory/db --custom-databases"
+        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"

meta.yaml

@@ -15,6 +15,12 @@ build:
   number: 0
   run_exports:
     - { { pin_subpackage(name, max_pin="x.x") } }
+  script: >
+    mkdir -p $PREFIX/bin && 
+    mkdir -p $PREFIX/share && 
+    cp recognizer.py resources/fun.tsv resources/cog2ko.tsv resources/cog2ec_recognizer.tsv $PREFIX/share &&
+    chmod +x $PREFIX/share/recognizer.py &&
+    ln -s $PREFIX/share/keggcharter.py $PREFIX/bin/keggcharter
 
 requirements:
   run: