diff --git a/.github/workflows/createrelease.yml b/.github/workflows/createrelease.yml new file mode 100644 index 000000000..54e86ece4 --- /dev/null +++ b/.github/workflows/createrelease.yml @@ -0,0 +1,38 @@ +name: Create Release + +on: + push: + branches: + - 'main' + tags: + - v* + +permissions: + contents: write + +jobs: + release: + name: Release pushed tag + runs-on: ubuntu-22.04 + steps: + - name: Create release + id: create_release + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + tag: ${{ github.ref_name }} + run: | + gh release create "$tag" \ + --repo="$GITHUB_REPOSITORY" \ + --title="${GITHUB_REPOSITORY#*/} ${tag#v}" \ + --generate-notes + - name: build artifacts + run: tar --exclude="test" --exclude=".git" --exclude=".github" --exclude=".snakemake" -zcvf harpy.${{tag#v}}.tar.gz . + - name: upload tarball + uses: actions/upload-release-asset@v1 + env: + GITHUB_TOKEN: ${{ github.token }} + with: + upload_url: ${{ steps.create_release.outputs.upload_url }} + asset_path: ./harpy.${{tag#v}}.tar.gz + asset_name: harpy.${{tag#v}}.tar.gz + asset_content_type: application/gzip \ No newline at end of file diff --git a/.github/workflows/impute.yml b/.github/workflows/impute.yml index ec2b5e28e..14ccc58ca 100644 --- a/.github/workflows/impute.yml +++ b/.github/workflows/impute.yml @@ -65,11 +65,11 @@ jobs: - name: impute shell: micromamba-shell {0} - run: harpy impute --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -q -s "--show-failed-logs" + run: harpy impute --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs" - name: impute from vcf shell: micromamba-shell {0} if: always() run: | rm -rf Impute - harpy impute --vcf-samples --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -q -s "--show-failed-logs" \ No newline at end of file + harpy impute --vcf-samples --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs" \ No newline at end of file diff --git a/resources/build.sh b/resources/build.sh index 21d616f10..5f2a99b47 100755 --- a/resources/build.sh +++ b/resources/build.sh @@ -3,13 +3,13 @@ mkdir -p ${PREFIX}/bin # install harpy proper -${PREFIX}/bin/python -m pip install . --no-deps -vv +${PYTHON} -m pip install . --no-deps -vvv # rules cp workflow/rules/*.smk ${PREFIX}/bin/ # associated scripts -chmod +x workdflow/scripts/* +chmod +x workflow/scripts/* cp workflow/scripts/* ${PREFIX}/bin/ # reports diff --git a/resources/meta.yaml b/resources/meta.yaml index f8744221a..b0b800d47 100644 --- a/resources/meta.yaml +++ b/resources/meta.yaml @@ -35,8 +35,17 @@ test: - "harpy --version" about: home: "https://github.com/pdimens/harpy/" - license: MIT + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: "Process raw haplotagging data, from raw sequences to phased haplotypes." + description: | + Harpy is a command-line tool to easily process haplotag or 10x linked-read data. It uses + Snakemake under the hood to execute different workflows (quality control, trimming, + alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed + to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, + and reproducibility, Harpy aims to quickly handle data processing so that you can focus more + on analyzing your data. doc_url: https://pdimens.github.io/harpy/ dev_url: https://github.com/pdimens/harpy @@ -46,4 +55,4 @@ extra: recipe-maintainers: - pdimens # skip-lints: -# - should_be_noarch_generic +# - should_be_noarch_generic \ No newline at end of file diff --git a/workflow/envs/harpy.yaml b/workflow/envs/harpy.yaml index 76a2ac327..bd9d21993 100644 --- a/workflow/envs/harpy.yaml +++ b/workflow/envs/harpy.yaml @@ -6,10 +6,11 @@ dependencies: - bcftools =1.19 - mamba - multiqc + - pandas - pysam =0.22 - python - rich-click - - snakemake + - snakemake-minimal - samtools - seqtk - tabix \ No newline at end of file