This page describes how to get started with GORpipe.
Before setting up GORpipe the following need to be installed:
Java JDK or JRE version 8 or higher (https://www.oracle.com/java/technologies/javase-downloads.html)
Open JDK can also be used (https://openjdk.java.net/install/)
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:
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:
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:
Then GORpipe and GORshell can be started via gorpipe and gorshell from any location.
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
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>