Commit 3b190688 authored by Bayo Lau's avatar Bayo Lau
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start tracking of discovar denovo 52488

http://www.broadinstitute.org/software/discovar/blog/
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DISCOVAR de novo installation
=============================
Requirements
------------
64 bit x86_64 based linux distribution
GCC 4.7 or above
jemalloc 3.6.0 or above
samtools (required if using bam files)
Building
--------
Ensure that GCC and jemalloc are built and installed on your system.
Download the latest version of DISCOVAR de novo from the FTP site.
Extract the contents of the downloaded file:
tar xzf discovardenovo-NNNNN.tar.gz
Move into the unpacked directory:
cd discovardenovo-NNNNN
Execute the configuration script:
./configure
This assumes that you can copy executables to /usr/local/bin. If you cannot, you should instead execute:
./configure --prefix=<install-root-dir>
For example:
./configure --prefix=/usr/local
Build the software:
make all
Install the software:
make install
The executables will be in /usr/local/bin, or in the location you provided with the prefix option. We recommend you add the executables directory to your path.
Troubleshooting
---------------
The 'configure' script supports numerous options that allow control of which functionality is enabled. To see these options use:
./configure --help
DISCOVAR de novo requires jemalloc to be built and installed. The configuration script will try to find the appropriate library, but if it fails you can specify the location using:
./configure --with-jemalloc=<jemalloc-lib-dir>
e.g.
./configure --with-jemalloc=/usr/local/jemalloc/lib
Copyright (c) 2015 Broad Institute
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
AUTOMAKE_OPTIONS = foreign
SUBDIRS = src
ACLOCAL_AMFLAGS = -I m4
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DISCOVAR de novo
================
DISCOVAR de novo is a short read genome assembly developed by the Broad Institute. It can generate high quality assemblies from the latest 250 base Illumina paired-end PCR-free fragment reads.
DISCOVAR is undergoing continuous development. There is no 'official' release, instead please download the latest source code from our nightly builds. Check back often for updates.
The LICENSE file contains copyright and licensing information.
The INSTALL file contains information on how to configure, build, and install DISCOVAR de novo.
The docs directory contains documentation on DISCOVAR de novo and its associated tools:
DiscovarDeNovo - DISCOVAR de novo manaul
NhoodInfo - NhoodInfo manual
CrossOut - CrossOut manual
For more information, visit the DISCOVAR blog:
http://www.broadinstitute.org/software/discovar/blog/
The above link includes directions on using the tool, along with other documentation.
-Computational R&D, The Broad Institute, Cambridge, MA
http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development
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