diff --git a/genomeFiles/package.json b/genomeFiles/package.json index 4b12a27..2253c43 100644 --- a/genomeFiles/package.json +++ b/genomeFiles/package.json @@ -1,6 +1,6 @@ { "name": "@platforma-open/milaboratories.star-read-mapping.genome-asset", - "version": "1.0.3", + "version": "1.0.4", "description": "STAR indexed genome references", "scripts": { "build-skip": "echo 'This is fake build script for CI optimization'", diff --git a/genomeFiles/run_star_index.sh b/genomeFiles/run_star_index.sh index 41f7f2d..f494dda 100755 --- a/genomeFiles/run_star_index.sh +++ b/genomeFiles/run_star_index.sh @@ -15,6 +15,8 @@ SPECIES="${1}" PARAMS_JSON_FILE="${2}" OUTPUT_FOLDER="${3}" +echo "Running $SPECIES $PARAMS_JSON_FILE $OUTPUT_FOLDER " + # Automatically download STAR on Linux and Mac OS X if ! command -v "${STAR_CMD}" >/dev/null; then _os="$(uname)" @@ -88,21 +90,9 @@ echo "Generating genome index with sjdbOverhang=${SJDB_OVERHANG} and genomeSAind "${STAR_CMD}" --runThreadN ${NUM_THREADS} --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles genome.fa \ --sjdbGTFfile ${GTF_FILENAME} --sjdbOverhang ${SJDB_OVERHANG} --genomeSAindexNbases ${GENOME_SA_INDEX_NBASES} -# Compress the genome index into a tar file -TAR_FILENAME="${SPECIES}_${ASSEMBLY_VERSION}_genome_index.tar.gz" -echo "Compressing genome index into ${TAR_FILENAME}..." -tar -czvf ${TAR_FILENAME} Genome SA SAindex chrLength.txt chrName.txt chrNameLength.txt chrStart.txt \ - exonGeTrInfo.tab exonInfo.tab geneInfo.tab genomeParameters.txt sjdbInfo.txt sjdbList.fromGTF.out.tab \ - sjdbList.out.tab transcriptInfo.tab - -# Compress the GTF file after indexing -echo "Compressing the GTF file: ${GTF_FILENAME}..." -gzip ${GTF_FILENAME} - # Cleanup: Remove intermediate files rm genome.fa -rm -rf SA SAindex Genome chrLength.txt chrName.txt chrNameLength.txt chrStart.txt exonGeTrInfo.tab exonInfo.tab \ - geneInfo.tab genomeParameters.txt sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tab _STARtmp/ +rm -rf _STARtmp/ -echo "Output files: ${GTF_FILENAME} and ${TAR_FILENAME}" +# echo "Output files: ${GTF_FILENAME} and ${TAR_FILENAME}" echo "Genome index generation and packaging complete."