ckandoth

#!/bin/bash

# GOAL: Set up a local instance of Ensembl's database and REST API

# If I don't already have sudo rights, then first login as root with `su`, and type `visudo` to
# edit `/etc/sudoers`, and uncomment this line in that file:
# %wheel ALL=(ALL) ALL
# This allows any user in group `wheel` to use `sudo`. Add myself to the `wheel` group using:
# usermod -a -G wheel kandoth
# Also set `SELINUX=disabled` in `/etc/selinux/config`, because its a PITFA.

ckandoth

# GOAL: Fetch VCFs generated by TCGA PancanAtlas MC3 unified variant calling effort and curate

##########
## DATA ##
##########

# Data from DNANexus/UCSC came in as 3 batches. Batches 1 and 2 had GATK cocleaned bams available,
# while batch 3 needed realignment. Batch 1 had RNA (to run radia), batch 2 didn't. Kyle Elrott
# is the point person for these batches. Available on GChat.
# Batches were later merged by Singer Ma at DNANexus, into a single folder called full_v1.

ckandoth

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

sudo yum install -y curl rsync tar make perl perl-core
## OR ##
sudo apt-get install -y curl rsync tar make perl perl-base

VEP requires Perl 5.10 or newer, but I'd strongly recommend at least 5.18. If your system Perl is outdated, then follow this gist to set up Perl 5.22. Once that's done, set temporary shell variables pointing to where Perl and its libraries live. Change this as needed for y

ckandoth

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

sudo yum install -y curl rsync tar make perl perl-core
## OR ##
sudo apt-get install -y curl rsync tar make perl perl-base

You'll also need samtools and tabix in your $PATH, which can be found at htslib.org

ckandoth

# GOAL: On a CentOS 6.7 minimal install, set up nginx as a reverse proxy to uWSGI Emperor with python 2.7.11 as a plugin to run Flask apps

# ::NOTE:: All instructions below are run as a sudoer, not as root. Talk to your sysadmins if you're not a sudoer.

# Install bare essentials:
sudo yum install -y epel-release
sudo yum groupinstall 'Development Tools'
sudo yum install -y vim openssl unzip nginx openssl-devel zlib-devel sqlite-devel bzip2-devel libffi-devel lapack-devel blas-devel libpng-devel freetype-devel

# Set SELINUX=disabled in the file below, and reboot, or this tutorial will get unnecessarily complicated: