diff --git a/.github/disabled-workflows/on_gpml_change_auto_homology_conversion.yml b/.github/disabled-workflows/on_gpml_change_auto_homology_conversion.yml index d583aa94e5..cfd1208097 100644 --- a/.github/disabled-workflows/on_gpml_change_auto_homology_conversion.yml +++ b/.github/disabled-workflows/on_gpml_change_auto_homology_conversion.yml @@ -83,15 +83,15 @@ jobs: id: cache with: path: ~/ - key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108.bridge + key: ${{ runner.os }}-java-Hs_Derby_Ensembl_111.bridge restore-keys: | ${{ runner.os }}-java- - if: steps.cache.outputs.cache-hit != 'true' name: Install deps run: | - if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1 + if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1 fi - name: Perform homology conversion diff --git a/.github/disabled-workflows/on_gpml_change_meta_test.yml b/.github/disabled-workflows/on_gpml_change_meta_test.yml index 77cdab1468..981477f6a3 100644 --- a/.github/disabled-workflows/on_gpml_change_meta_test.yml +++ b/.github/disabled-workflows/on_gpml_change_meta_test.yml @@ -323,17 +323,17 @@ jobs: uses: actions/cache@v3 id: cache with: - path: ./Hs_Derby_Ensembl_108.bridge - key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + path: ./Hs_Derby_Ensembl_111.bridge + key: ${{ runner.os }}-java-Hs_Derby_Ensembl_111 restore-keys: | - ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + ${{ runner.os }}-java-Hs_Derby_Ensembl_111 ${{ runner.os }}-java- - if: steps.cache.outputs.cache-hit != 'true' name: Install deps run: | - if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1 + if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1 fi - name: Perform homology conversion diff --git a/.github/disabled-workflows/on_gpml_change_old_meta_data.yml b/.github/disabled-workflows/on_gpml_change_old_meta_data.yml index fc58992322..f085e47663 100644 --- a/.github/disabled-workflows/on_gpml_change_old_meta_data.yml +++ b/.github/disabled-workflows/on_gpml_change_old_meta_data.yml @@ -262,17 +262,17 @@ jobs: uses: actions/cache@v3 id: cache with: - path: ./Hs_Derby_Ensembl_108.bridge - key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + path: ./Hs_Derby_Ensembl_111.bridge + key: ${{ runner.os }}-java-Hs_Derby_Ensembl_111 restore-keys: | - ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + ${{ runner.os }}-java-Hs_Derby_Ensembl_111 ${{ runner.os }}-java- - if: steps.cache.outputs.cache-hit != 'true' name: Install deps run: | - if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1 + if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1 fi - name: Perform homology conversion diff --git a/.github/workflows/on_gpml_change.yml b/.github/workflows/on_gpml_change.yml index cc712498fa..62a82287e8 100644 --- a/.github/workflows/on_gpml_change.yml +++ b/.github/workflows/on_gpml_change.yml @@ -416,18 +416,18 @@ jobs: uses: actions/cache@v4 id: cache with: - path: ${{ github.workspace }}/wikipathways-database/Hs_Derby_Ensembl_108.bridge - key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + path: ${{ github.workspace }}/wikipathways-database/Hs_Derby_Ensembl_111.bridge + key: ${{ runner.os }}-java-Hs_Derby_Ensembl_111 restore-keys: | - ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + ${{ runner.os }}-java-Hs_Derby_Ensembl_111 ${{ runner.os }}-java-Hs_Derby_Ensembl_ - if: steps.cache.outputs.cache-hit != 'true' name: Install deps run: | cd "${{ github.workspace }}/wikipathways-database" - if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1 + if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1 fi - name: Perform homology conversion diff --git a/.github/workflows/scheduled_bridge_cache.yml b/.github/workflows/scheduled_bridge_cache.yml index 3d680a0a04..ffd5215c89 100644 --- a/.github/workflows/scheduled_bridge_cache.yml +++ b/.github/workflows/scheduled_bridge_cache.yml @@ -50,18 +50,18 @@ jobs: uses: actions/cache@v4 id: cache with: - path: ${{ github.workspace }}/wikipathways-database/Hs_Derby_Ensembl_108.bridge - key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + path: ${{ github.workspace }}/wikipathways-database/Hs_Derby_Ensembl_111.bridge + key: ${{ runner.os }}-java-Hs_Derby_Ensembl_111 restore-keys: | - ${{ runner.os }}-java-Hs_Derby_Ensembl_108 + ${{ runner.os }}-java-Hs_Derby_Ensembl_111 ${{ runner.os }}-java-Hs_Derby_Ensembl_ - if: steps.cache.outputs.cache-hit != 'true' name: Install deps run: | cd "${{ github.workspace }}/wikipathways-database" - if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1 + if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1 fi - name: Generate gdb.config, fileNames.config, and fileDownloads.config diff --git a/scripts/homology-converter/README.md b/scripts/homology-converter/README.md index 7daaf5a4af..a8f06ace21 100644 --- a/scripts/homology-converter/README.md +++ b/scripts/homology-converter/README.md @@ -4,7 +4,7 @@ This repository is a prototype to test using GitHub Actions to trigger the autom When a new pathway is added to the /pathways folder, or an existing pathway is modified, the on_gpml_change_auto_homology_conversion.yml file triggers a workflow run. -The workflow run installs the necessary dependency; Hs_Derby_Ensembl_104.bridge from https://bridgedb.github.io/data/gene_database/ using a wget statement. +The workflow run installs the necessary dependency; Hs_Derby_Ensembl_111.bridge from https://bridgedb.github.io/data/gene_database/ using a wget statement. The line java -jar HomologyMapperAuto-WithDependencies.jar properties/autorun.properties $wpid runs the automated Local Homology Converter (https://github.com/hbasaric/homology.mapper.automated/). The converted pathway will only be committed if the conversion rate is greater than 80%. diff --git a/scripts/homology-converter/properties/autorun.properties b/scripts/homology-converter/properties/autorun.properties index 0dcdc2ab5c..17665dfc07 100644 --- a/scripts/homology-converter/properties/autorun.properties +++ b/scripts/homology-converter/properties/autorun.properties @@ -3,7 +3,7 @@ target.organisms=Bos taurus,Canis familiaris,Danio rerio,Equus caballus,Gallus g output.dir=scripts/homology-converter/outputs/ output.folders=Bt,Cf,Dr,Qc,Gg,Mm,Pt,Rn,Ss input.dir=pathways -source.gene.mapping.db=Hs_Derby_Ensembl_108.bridge +source.gene.mapping.db=Hs_Derby_Ensembl_111.bridge mapping.file.directory=scripts/homology-converter/homology/ mapping.files=hsa-bt.txt,hsa-cf.txt,hsa-dr.txt,hsa-qc.txt,hsa-gg.txt,hsa-mmu.txt,hsa-pt.txt,hsa-rn.txt,hsa-ss.txt new.gene.names.directory=scripts/homology-converter/genes/ diff --git a/scripts/local-run/on-gpml-change_local.sh b/scripts/local-run/on-gpml-change_local.sh index 4d25aca46c..5be6600f14 100755 --- a/scripts/local-run/on-gpml-change_local.sh +++ b/scripts/local-run/on-gpml-change_local.sh @@ -199,8 +199,8 @@ done ############################## echo "6. ACTION: homologyConversion" # NOTE: requires Java 8 -if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then - wget -O Hs_Derby_Ensembl_108.bridge "https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1" +if [ ! -e ./Hs_Derby_Ensembl_111.bridge ]; then + wget -O Hs_Derby_Ensembl_111.bridge "https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_111.bridge?download=1" fi for f in ${changed_gpmls[@]}; do