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Changed Ensembl_108 to 111 in workflows and scripts #64

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Changed Ensembl_108 to 111 in workflows and scripts #64

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475f49a
Changed Ensembl_108 to 111 in workflows and scripts
Nov 13, 2024
39f5a92
Change dependency in readme Ensembl_104 > 111
Nov 14, 2024
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6 changes: 3 additions & 3 deletions .github/disabled-workflows/on_gpml_change_auto_homology_conversion.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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10 changes: 5 additions & 5 deletions .github/disabled-workflows/on_gpml_change_meta_test.yml
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Expand Up @@ -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
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10 changes: 5 additions & 5 deletions .github/disabled-workflows/on_gpml_change_old_meta_data.yml
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Expand Up @@ -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
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10 changes: 5 additions & 5 deletions .github/workflows/on_gpml_change.yml
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Expand Up @@ -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
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10 changes: 5 additions & 5 deletions .github/workflows/scheduled_bridge_cache.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion scripts/homology-converter/README.md
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Expand Up @@ -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%.

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2 changes: 1 addition & 1 deletion scripts/homology-converter/properties/autorun.properties
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Expand Up @@ -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/
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4 changes: 2 additions & 2 deletions scripts/local-run/on-gpml-change_local.sh
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Expand Up @@ -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
Expand Down