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Update bash scripts format following ShellCheck #135

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Aug 23, 2021
Merged

Update bash scripts format following ShellCheck #135

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6 changes: 3 additions & 3 deletions .github/release-drafter.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name-template: 'v$NEXT_PATCH_VERSION'
tag-template: 'v$NEXT_PATCH_VERSION'
name-template: 'v$NEXT_MINOR_VERSION'
tag-template: 'v$NEXT_MINOR_VERSION'
categories:
- title: '🧬 Features'
labels:
Expand Down Expand Up @@ -31,4 +31,4 @@ template: |
## Changes
$CHANGES
## 🕵️‍♀️ Full commit logs
- https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION
- https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_MINOR_VERSION
38 changes: 19 additions & 19 deletions .github/workflows/compare-study-annotation.yml
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Expand Up @@ -36,40 +36,40 @@ jobs:
git checkout -b compare

STUDY=msk_impact_2017
DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/$STUDY
DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/"$STUDY"

MUTATION_DATA_NAME=data_mutations_extended.txt
CLINICAL_DATA_NAME=data_clinical_sample.txt
FUSION_DATA_NAME=data_fusions.txt
CNA_DATA_NAME=data_CNA.txt

cd data
curl -s $DATAHUB_URL/$MUTATION_DATA_NAME -O
curl -s $DATAHUB_URL/$CLINICAL_DATA_NAME -O
curl -s $DATAHUB_URL/$FUSION_DATA_NAME -O
curl -s $DATAHUB_URL/$CNA_DATA_NAME -O
cd data || exit
curl -s "$DATAHUB_URL"/"$MUTATION_DATA_NAME" -O
curl -s "$DATAHUB_URL"/"$CLINICAL_DATA_NAME" -O
curl -s "$DATAHUB_URL"/"$FUSION_DATA_NAME" -O
curl -s "$DATAHUB_URL"/"$CNA_DATA_NAME" -O
cd ..

# create compare folder to add all annotated files
mkdir compare

PREFIX=oncokb
IMAF=data/$MUTATION_DATA_NAME
OMAF=compare/"$PREFIX"_$MUTATION_DATA_NAME
IMAF=data/"$MUTATION_DATA_NAME"
OMAF=compare/"$PREFIX"_"$MUTATION_DATA_NAME"

IC=data/$CLINICAL_DATA_NAME
OC=compare/"$PREFIX"_$CLINICAL_DATA_NAME
IC=data/"$CLINICAL_DATA_NAME"
OC=compare/"$PREFIX"_"$CLINICAL_DATA_NAME"

IF=data/$FUSION_DATA_NAME
OF=compare/"$PREFIX"_$FUSION_DATA_NAME
IF=data/"$FUSION_DATA_NAME"
OF=compare/"$PREFIX"_"$FUSION_DATA_NAME"

ICNA=data/$CNA_DATA_NAME
OCNA=compare/"$PREFIX"_$CNA_DATA_NAME
ICNA=data/"$CNA_DATA_NAME"
OCNA=compare/"$PREFIX"_"$CNA_DATA_NAME"

python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $ONCOKB_API_TOKEN
python FusionAnnotator.py -i $IF -o $OF -c $IC -b $ONCOKB_API_TOKEN
python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $ONCOKB_API_TOKEN
python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OCNA,$OF
python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$ONCOKB_API_TOKEN"
python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$ONCOKB_API_TOKEN"
python CnaAnnotator.py -i "$ICNA" -o "$OCNA" -c "$IC" -b "$ONCOKB_API_TOKEN"
python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OCNA,$OF"

git config user.name oncokb-bot
git config user.email dev.oncokb@gmail.com
Expand All @@ -89,7 +89,7 @@ jobs:
# remove everything under compare folder and replace wiht the ones from oncokb-data
rm -f compare/*.txt

cd compare
cd compare || exit
curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/$STUDY | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do
if [[ "$name" == "$FIEL_NAME_PREFIX"* ]]; then
curl -s "$downloadurl" -o $name
Expand Down
32 changes: 20 additions & 12 deletions example.sh
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Original file line number Diff line number Diff line change
@@ -1,36 +1,44 @@
#!/usr/bin/env bash
IMAF="data/example_maf.txt"
OMAF="data/example_maf.oncokb.txt"

IMAF38="data/example_maf_grch38.txt"
OMAF38="data/example_maf_grch38.oncokb.txt"

OMAFHGVSPSHORT="data/example_maf_hgsp_short.oncokb.txt"
OMAFHGVSP="data/example_maf_hgsp.oncokb.txt"
OMAFHGVSG="data/example_maf_hgsg.oncokb.txt"
OMAFGC="data/example_maf_genomic_change.oncokb.txt"

IATYPICALALT="data/example_atypical_alterations.txt"
OATYPICALALT="data/example_atypical_alterations.oncokb.txt"

IF="data/example_fusions.txt"
OF="data/example_fusions.oncokb.txt"

ICNA="data/example_cna.txt"
OCNA="data/example_cna.oncokb.txt"

IC="data/example_clinical.txt"
OC="data/example_clinical.oncokb.txt"

OCPDF="data/example_clinical.oncokb.pdf"

TOKEN="" #OncoKB API Token
README="data/example_README.txt"

python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $TOKEN
python MafAnnotator.py -i $IMAF -o $OMAFHGVSPSHORT -c $IC -b $TOKEN -q hgvsp_short
python MafAnnotator.py -i $IMAF -o $OMAFHGVSP -c $IC -b $TOKEN -q hgvsp
python MafAnnotator.py -i $IMAF -o $OMAFHGVSG -c $IC -b $TOKEN -q hgvsg
python MafAnnotator.py -i $IMAF -o $OMAFGC -c $IC -b $TOKEN -q genomic_change
python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$TOKEN"
python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSPSHORT" -c "$IC" -b "$TOKEN" -q hgvsp_short
python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSP" -c "$IC" -b "$TOKEN" -q hgvsp
python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSG" -c "$IC" -b "$TOKEN" -q hgvsg
python MafAnnotator.py -i "$IMAF" -o "$OMAFGC" -c "$IC" -b "$TOKEN" -q genomic_change

python MafAnnotator.py -i $IMAF38 -o $OMAF38 -c $IC -b $TOKEN
python MafAnnotator.py -i "$IMAF38" -o "$OMAF38" -c "$IC" -b "$TOKEN"

python MafAnnotator.py -i $IATYPICALALT -o $OATYPICALALT -c $IC -b $TOKEN
python MafAnnotator.py -i "$IATYPICALALT" -o "$OATYPICALALT" -c "$IC" -b "$TOKEN"

python FusionAnnotator.py -i $IF -o $OF -c $IC -b $TOKEN
python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $TOKEN
python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OATYPICALALT,$OCNA,$OF
python OncoKBPlots.py -i $OC -o $OCPDF -c ONCOTREE_CODE #-n 10
python GenerateReadMe.py -o $README
python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$TOKEN"
python CnaAnnotator.py -i "$ICNA" -o "$OCNA" -c "$IC" -b "$TOKEN"
python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OATYPICALALT,$OCNA,$OF"
python OncoKBPlots.py -i "$OC" -o "$OCPDF" -c ONCOTREE_CODE #-n 10
python GenerateReadMe.py -o "$README"