Instructions for manual installation of gnomAD.

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