The GORpipe analysis tool is developed and released by WuXi NextCODE Genomics. It originates from the pioneers of population based genomic analysis, deCODE genetics, headquartered in Reykjavik, Iceland.
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using a declarative query language, in a parallel execution engine. It is very efficient in a wide range of use-cases, including genome wide batch analysis, range-queries, genomic table joins of variants and segments, filtering, aggregation etc. The query language combines ideas from SQL and Unix shell pipe syntax, supporting seek-able nested queries, materialized views, and a rich set of commands and functions. For more information see the paper in Bioinformatics (https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtw199).
Before setting up GORpipe you need to have Java set up on your computer:
- 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/)
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
To get started with GORpipe, compile the code:
make build
Now gor queries can been run against test data. For example:
./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
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))
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.
Documentation for GORpipe can be found at: http://docs.gorpipe.org/. Additionally, help can be found while using GORpipe
by executing gorpipe help or just help within the GOR shell.
If you make use of GORpipe in your research, we would appreciate a citation to 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>