From a86e744886988a4b86d0aeddf324a8de25637e01 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 19 Aug 2020 10:29:16 +0100
Subject: [PATCH] Initial commit with Aspera, VASE, bcbio.

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 docs/Software_installation.md | 33 +++++++++++++++++++++++++++++++++
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+# 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].
-- 
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