diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 8db7563..a6b63da 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -14,8 +14,6 @@ jobs: steps: - name: 'Checkout git repo' uses: actions/checkout@v1 - - name: Install xz-utils - run: sudo apt-get update && sudo apt-get install -y xz-utils - name: Extract branch or tag name # The GITHUB_REF variable is like "refs/head/branch_name" or # "refs/tag/tag_name". If the tag is prefixed with v, this is a new @@ -38,8 +36,6 @@ jobs: steps: - name: 'Checkout git repo' uses: actions/checkout@v1 - - name: Install xz-utils - run: sudo apt-get update && sudo apt-get install -y xz-utils - name: Extract branch or tag name # The GITHUB_REF variable is like "refs/head/branch_name" # The format of image tag is e.g. v0.12_grch38_ensembl95 diff --git a/scripts/import_mongo.sh b/scripts/import_mongo.sh index 75f8e82..fc9b8ef 100755 --- a/scripts/import_mongo.sh +++ b/scripts/import_mongo.sh @@ -59,15 +59,11 @@ curl https://genome-nexus-static-data.s3.amazonaws.com/mutationassessor4_for_gen echo "Download completed." echo "Extracting Mutation assessor data" -apt install -y xz-utils -echo xz-utils version -exho $(xz --version) -xz -k ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.xz +gunzip ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.gz echo "Transforming Mutation assessor data" sed -i '' 's/uniprotId\tSV\thgvspShort\tF_score\tF_impact\tMSA\tMAV/uniprotId\tsv\thgvspShort\tf_score\tf_impact\tmsa\tmav/' ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv awk -F'\t' 'BEGIN{OFS="\t"} NR==1{print "_id",$0; next} {print $1","$3,$0}' ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv > processed_mutaiton_assessor_tsv_file.tsv -rm ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.xz rm ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv echo "Importing Mutation assessor data"