V20210413

Author: Antony Le Béchec

.env

@@ -103,13 +103,13 @@ DOCKER_HOWARD_SETUP_ANNOTATION="core,CLINVAR,COSMIC,snpeff"
 # All daabases can be downloaded independently, see ANNOVAR and snpEff doc
 
 # This simple command actually does not work for snpEff 5.0e (due to snpEff bug)
-#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
+#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=TSV --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
 
 # This command actually does not work for snpEff 5.0e (due to snpEff bug)
-#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then $JAVA -jar -Xmx4g -jar $SNPEFF download ${DOCKER_HOWARD_SETUP_ASSEMBLY}; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
+#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then $JAVA -jar -Xmx4g -jar $SNPEFF download ${DOCKER_HOWARD_SETUP_ASSEMBLY}; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=TSV --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
 
 # This command is more manual, but works (only for snpEff 5.0 and the indicated assembly)
-DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then wget --progress=bar -O ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip ; unzip ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=${DOCKER_HOWARD_SETUP_ANNOTATION} --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
+DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then wget --progress=bar -O ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip ; unzip -o ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/; mv ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/data/* ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=${DOCKER_HOWARD_SETUP_ANNOTATION} --calculation=BARCODE --prioritization=default --translation=TSV --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'