Tidy GTEx

Joshua Cook 2019-05-05

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This repository hold the Genotype-Tissue Expression (GTEx) project data in a tidy format for easy use with the R tidyverse.

“The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images.”

Data

Latest download: May 5, 2019

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Git Large File Storage

This repository uses git large file storage (“git-lfs”) in order to manage the large data files.

Installation

The instructions on installing git-lfs for Mac, Windows, and some linux distros are available on the git-lfs GitHub repo Wiki. Since I did this work remotely on the HMS Research Computing Cluster, I do not have root access and had to install from source.

1. Download the source code of the latest release from here.

wget https://github.com/git-lfs/git-lfs/releases/download/v2.7.2/git-lfs-v2.7.2.tar.gz

2. Build the binary using go build -o /path/to/dest/git-lfs, where /path/to/dest/git-lfs is the name of the directory you store your installed software in. This directory should be in your $PATH. For instance, I used ~/bin/git-lfs.

module load go
go build -o ~/bin/git-lfs

There should now be a file with the same path and name that you passed using the -o flag.

3. Set up git-lfs in your git repository.

cd /path/to/my/git/repo
git lfs install
#> Updated git hooks.
#> Git LFS initialized.

4. Declare which files to track.

git lfs track "*.bigfiles"
#> Tracking "really_big_file.bigfiles"
#> Tracking "so_big_such_wow.bigfiles"
#> Tracking "large_files_rock.bigfiles"

where "*.bigfiles" is the regular expression for large files in the repo.

5. Track “.gitattributes”.

git add .gitattributes
git commit .gitattributes -m "start git-lfs"

You should now be able to add, commit, and push files like normal. Steps 1 and 2 only need to be done once per machine. Steps 3-5 need to be completed once per repository.