diff --git a/docs/Software_installation_ultra2.md b/docs/Software_installation_ultra2.md index 19fe100bbb4e28a9d31df1f681fe35ec96ccbeb9..b5eb84a04ad7581371ae8b1aa3b3bb652a83bf90 100644 --- a/docs/Software_installation_ultra2.md +++ b/docs/Software_installation_ultra2.md @@ -1,4 +1,4 @@ -# Installation of software for trio whole exome project +# Ultra2 - Installation of software for trio whole exome project ## Aspera @@ -48,11 +48,20 @@ DATE=`date +%Y%m%d%H%M` /home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_logs/bcbio_install_datatarget_vep_${DATE}.log ``` -gnomAD 3.1.1 installation will take about 6 days (old ultra). Might be faster on ultra2. +We already had gnomAD 3.0 compiled and downloaded on the ultra2 bcbio installation, so this gets copied to `/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/variation`. + +``` +cd /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/variation +scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz ./ +scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz.csi ./ +scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz.tbi ./ +``` + +However, if needed, re-generate it like this. It took about 6 days on old ultra. ``` DATE=`date +%Y%m%d%H%M` -/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget gnomad &> bcbio_install_logs/bcbio_install_datatarget_gnomad_${DATE}.log +/home/u035/u035/shared/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget gnomad &> bcbio_install_datatarget_gnomad_${DATE}.log ``` Increase JVM memory for GATK in galaxy/bcbio_system.yaml