Upped mamba version in Dockerfile #34
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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: ./Dockerfile | |
tags: keggcharter:latest | |
outputs: type=docker,dest=/tmp/keggcharter.tar | |
- name: Upload artifact | |
uses: actions/upload-artifact@v2 | |
with: | |
name: keggcharter | |
path: /tmp/keggcharter.tar | |
use: | |
runs-on: ubuntu-latest | |
needs: build | |
steps: | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v1 | |
- name: Download artifact | |
uses: actions/download-artifact@v2 | |
with: | |
name: keggcharter | |
path: /tmp | |
- name: Load Docker image | |
run: | | |
docker load --input /tmp/keggcharter.tar | |
docker image ls -a | |
- name: Check base entrypoint | |
run: docker run keggcharter /bin/bash -c "ls" | |
- name: Run KEGGCharter | |
run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/ci/keggcharter_input.tsv -rd resources_directory -mm 00190,00680 -keggc 'Cross-reference (KEGG)' -gcol mg -tcol mt_0.01a,mt_1a,mt_100a,mt_0.01b,mt_1b,mt_100b,mt_0.01c,mt_1c,mt_100c -tc 'Taxonomic lineage (SPECIES)' -mm 00680" |