Installation

This page describes how to get started with GORpipe.

Prerequisites

Before setting up GORpipe the following need to be installed:

Setting up test data

Test data for GOR is obtained by cloning the GOR test data repository (https://github.com/gorpipe/gor-test-data) as a submodule into the tests/data folder:

git submodule update --init --recursive

Getting started with GORPipe

To get started with GORPipe, compile the code:

make build

Now gor queries can been run against test data. For example via:

./gortools/build/install/gor-scripts/bin/gorpipe "gor tests/data/gor/dbsnp_test.gor | top 10"

The results should be as follows:

Chrom   POS     reference       allele  differentrsIDs
chr1    10179   C       CC      rs367896724
chr1    10250   A       C       rs199706086
chr10   60803   T       G       rs536478188
chr10   61023   C       G       rs370414480
chr11   61248   G       A       rs367559610
chr11   66295   C       A       rs61869613
chr12   60162   C       G       rs544101329
chr12   60545   A       T       rs570991495
chr13   19020013        C       T       rs181615907
chr13   19020145        G       T       rs28970552

Setting up GOR shell

GORpipe can be invoked and used through an interactive shell session in a terminal - a sort of REPL for GOR, coined GORshell. Start a GORshell by executing:

tools/build/install/tools/bin/gorshell

This will start an interactive shell session where queries can be executed:

gor tests/data/gor/dbsnp_test.gor | top 10

For a list of GOR input sources, pipe commands and other details, simply type help within the GOR shell.

Running GOR without setting up the test data submodule can be done by generating GOR rows and then running GOR against that data. For example:

gor <(gorrows -p chr1:1000-20000 -segment 100 -step 50 | multimap -cartesian <(norrows 100 | group -lis -sc #1))

Setting environment variables

For convenience, GORpipe and GORshell can be added to path. For example on Mac by editing /etc/paths:

sudo vim /etc/paths

and add the following lines:

<PATH_TO_GOR_REPO>/gortools/build/install/gor-scripts/bin
<PATH_TO_GOR_REPO>/tools/build/install/tools/bin/gorshell

Then GORpipe and GORshell can be started via gorpipe and gorshell from any location.

Other

Citations

If you make use of GORpipe in your research, we would appreciate a citation of the following paper:

GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture Bioinformatics, Volume 32, Issue 20, 15 October 2016, Pages 3081–3088, https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtw199

License

GORpipe is free software: you can redistribute it and/or modify it under the terms of the AFFERO GNU General Public License as published by the Free Software Foundation.

GORpipe is distributed “AS-IS” AND WITHOUT ANY WARRANTY OF ANY KIND, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE. See the AFFERO GNU General Public License for the complete license terms.

You should have received a copy of the AFFERO GNU General Public License along with GORpipe. If not, see <http://www.gnu.org/licenses/agpl-3.0.html>