Merge pull request #62 from unipept/feature/add-version-file

Automatically generate ".version" with current UniProt-version
unipept · Aug 13, 2024 · 3a44b71 · 3a44b71
2 parents 4f7aaa2 + ad038ad
commit 3a44b71
Show file tree

Hide file tree

Showing 7 changed files with 34 additions and 368 deletions.
diff --git a/.github/workflows/database.yml b/.github/workflows/database.yml
@@ -28,15 +28,15 @@ jobs:
       - name: Install required utilities
         run: |
           sudo apt-get update
-          sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel
+          sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel libxml2-utils
       - name: Prepare temporary directories
         run: sudo mkdir -p "index" "unipept-temp"
       - name: Generate tsv.gz files
         shell: bash
         run: sudo ./scripts/build_database.sh -i "index" -d "unipept-temp" -m "256M" "${{ matrix.type }}" "swissprot" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" "output"
       - name: Zip all tsv.gz files
         shell: bash
-        run: cd output && zip -r "../${{ matrix.type }}.zip" *
+        run: cd output && zip -r "../${{ matrix.type }}.zip" * && zip -u "../${{ matrix.type }}.zip" ".version"
       - name: Upload or Update Release
         id: upload_or_update_release
         uses: softprops/action-gh-release@v1

diff --git a/.github/workflows/static_database.yml b/.github/workflows/static_database.yml
@@ -25,7 +25,7 @@ jobs:
       - name: Install required utilities
         run: |
           sudo apt-get update
-          sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel
+          sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel libxml2-utils
       - name: Download Taxdmp file
         shell: bash
         run: wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip

diff --git a/schemas/headers.md b/schemas/headers.md
diff --git a/schemas/load_compress.sh b/schemas/load_compress.sh
diff --git a/schemas/user_data.sql b/schemas/user_data.sql
diff --git a/schemas_suffix_array/headers.md b/schemas_suffix_array/headers.md