Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Download NCBI Taxdmp file in CI #41

Merged
merged 9 commits into from
Mar 14, 2024
Merged

Download NCBI Taxdmp file in CI #41

Changes from 8 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
da911a8
Download taxdmp
stijndcl Feb 26, 2024
a007a50
Make id unique
stijndcl Feb 26, 2024
d2cf812
Use wget
stijndcl Feb 26, 2024
f2c4d38
Correctly name action
stijndcl Feb 26, 2024
bc6b305
Create separate job
stijndcl Feb 26, 2024
006087f
Name correctly
stijndcl Feb 26, 2024
950ce73
Ending newline
stijndcl Feb 26, 2024
3c3a5a5
Undo separation
stijndcl Feb 26, 2024
898182f
Update Taxdmp URL, use self-hosted if available
stijndcl Mar 8, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 16 additions & 3 deletions .github/workflows/static_database.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,10 @@ jobs:
- name: Install required utilities
run: |
sudo apt-get update
sudo apt-get -y install git maven curl unzip gawk sqlite3 libsqlite3-dev pv nodejs
sudo apt-get -y install git maven curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget
- name: Download Taxdmp file
shell: bash
run: wget https://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
- name: Generate tsv.gz files
shell: bash
run: ./scripts/build_database.sh static-database "swissprot,trembl" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz,https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.xml.gz" "output"
Expand Down Expand Up @@ -60,8 +63,8 @@ jobs:
release_name: Static database ${{ steps.date.outputs.date }}
draft: false
prerelease: false
- name: Upload Release Asset
id: upload-release-asset
- name: Upload Static Database Release Asset
id: upload-database-release-asset
uses: actions/upload-release-asset@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
Expand All @@ -70,3 +73,13 @@ jobs:
asset_path: ./output.zip
asset_name: unipept-static-db-${{ steps.date.outputs.date }}.zip
asset_content_type: application/zip
- name: Upload NCBI Taxdmp Release Asset
id: upload-taxdmp-release-asset
uses: actions/upload-release-asset@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ steps.create_release.outputs.upload_url }}
asset_path: ./taxdmp.zip
asset_name: ncbi-taxdmp.zip
asset_content_type: application/zip
Loading