Initial commit with Aspera, VASE, bcbio.

docs/Software_installation.md

+# Installation of software for trio whole exome project
+
+## Aspera
+
+Downloaded Aspera Connect version 3.7.4.147727 from [https://downloads.asperasoft.com] and extracted to /home/u035/project/software.
+
+## bcbio
+
+This will take a long time, and may require multiple runs if it fails on a step. It will resume if needed. Run on a screen session and log each attempt.
+
+```
+cd /home/u035/project/software/install
+wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
+
+python bcbio_nextgen_install.py /home/u035/project/software/bcbio \
+  --tooldir /home/u035/project/software/bcbio/bin \
+  --genomes hg38 --aligners bwa \
+  --datatarget variation --datatarget gnomad \
+  --datatarget vep --datatarget dbnsfp --cores 32 &> bcbio_install_YYYYMMDDhhmm.log
+```
+
+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
+
+```
+  gatk:
+    jvm_opts: ["-Xms500m", "-Xmx5g"]
+```
+
+## VASE
+
+VASE was installed following the instructions at [https://github.com/david-a-parry/vase].