Remove taxonomy.rdf #77
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name: CI | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches: [ master ] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v2 | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v1 | |
- name: Build and push | |
uses: docker/build-push-action@v2 | |
with: | |
context: . | |
file: ./ci/Dockerfile | |
tags: recognizer:latest | |
outputs: type=docker,dest=/tmp/recognizer.tar | |
- name: Upload artifact | |
uses: actions/upload-artifact@v2 | |
with: | |
name: recognizer | |
path: /tmp/recognizer.tar | |
vanilla-annotation: | |
runs-on: ubuntu-latest | |
needs: build | |
steps: | |
- name: Download artifact | |
uses: actions/download-artifact@v2 | |
with: | |
name: recognizer | |
path: /tmp | |
- name: Load Docker image | |
run: | | |
docker load --input /tmp/recognizer.tar | |
docker image ls -a | |
- name: Default annotation | |
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 | |
needs: build | |
steps: | |
- name: Download artifact | |
uses: actions/download-artifact@v2 | |
with: | |
name: recognizer | |
path: /tmp | |
- name: Load Docker image | |
run: | | |
docker load --input /tmp/recognizer.tar | |
docker image ls -a | |
- name: Taxonomy-based annotation | |
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 | |
needs: build | |
steps: | |
- name: Download artifact | |
uses: actions/download-artifact@v2 | |
with: | |
name: recognizer | |
path: /tmp | |
- name: Load Docker image | |
run: | | |
docker load --input /tmp/recognizer.tar | |
docker image ls -a | |
- name: Custom database annotation | |
run: docker run recognizer /bin/bash -c "mkdir resources_directory; 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" |