diff --git a/docs/Software_installation.md b/docs/Software_installation.md index c14bbd5602661cc797b8809e2b9aad7de27f6be4..39c7dc4a9889c37bfd08ab64803c8213bb9615af 100644 --- a/docs/Software_installation.md +++ b/docs/Software_installation.md @@ -21,6 +21,27 @@ python bcbio_nextgen_install.py /home/u035/project/software/bcbio \ --datatarget vep --datatarget dbnsfp --cores 32 &> bcbio_install_YYYYMMDDhhmm.log ``` +The bcbio gnomAD installation was failing because the software *vt* had problems. Solution: replace vt with version from bcbio-1.2.0. See https://github.com/bcbio/bcbio-nextgen/issues/3327 and https://github.com/bcbio/bcbio-nextgen/issues/3328. + +``` +cd /home/u035/project/software/bcbio/anaconda/bin +mv vt vt.bcbio-1.2.3 +scp ameyner2@eddie.ecdf.ed.ac.uk:/exports/igmm/software/pkg/el7/apps/bcbio/1.2.0/bin/vt ./ +chmod a+x vt + +cd ../../genomes/Hsapiens/hg38/txtmp/ +qsub /home/u035/project/scripts/bcbio_gnomad_install.sh +``` + +This will take a few days (4-6) to run. When complete: + +``` +cd ../../genomes/Hsapiens/hg38/txtmp/ +mv variation/gnomad* ../variation/ +``` + +Now restart the installation as above. + Put a fake file name for genotype2phenotype field in genomes/hg38/seq/hg38-resources.yaml Increase JVM memory for GATK in galaxy/bcbio_system.yaml