diff --git a/LICENSE b/LICENSE index 133587d..5322bc3 100644 --- a/LICENSE +++ b/LICENSE @@ -1,27 +1,43 @@ -Copyright (c) 2014, MarBL -All rights reserved. +PURPOSE + +Harvest is a suite of core-genome alignment and visualization tools +for quickly analyzing intraspecific microbial genomes. + +COPYRIGHT LICENSE + +Copyright © 2014, Battelle National Biodefense Institute (BNBI); +all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +Adam Phillippy + +This Software was prepared for the Department of Homeland Security +(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +part of contract HSHQDC-07-C-00020 to manage and operate the National +Biodefense Analysis and Countermeasures Center (NBACC), a Federally +Funded Research and Development Center. Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -* Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -* Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -* Neither the name of the {organization} nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +modification, are permitted provided that the following conditions are +met: + +1. Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst index 5b775fe..cbf4925 100644 --- a/docs/content/parsnp/quickstart.rst +++ b/docs/content/parsnp/quickstart.rst @@ -1,6 +1,8 @@ Quickstart ========== +Note: If you are currently using a Parsnp version prior to **v1.2** or Harvest version prior to **v1.1.2**, you should update to use the latest release before proceeding. The latest release includes a critical fix for FastTree2; see http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html for further details. + Before you run --------------- @@ -25,14 +27,14 @@ Parsnp is distributed as a precompiled binary that should be devoid of external On OSX: """"""" - 1. wget https://github.com/marbl/parsnp/releases/download/v1.1/parsnp-OSX64-v1.1.tar.gz - 2. tar -xvf parsnp-OSX64-v1.1.tar.gz + 1. wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-OSX64-v1.2.tar.gz + 2. tar -xvf parsnp-OSX64-v1.2.tar.gz On Linux: """"""""" - 1. wget https://github.com/marbl/parsnp/releases/download/v1.1/parsnp-Linux64-v1.1.tar.gz - 2. tar -xvf parsnp-Linux64-v1.1.tar.gz + 1. wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-Linux64-v1.2.tar.gz + 2. tar -xvf parsnp-Linux64-v1.2.tar.gz Basic usage: """""""""""" @@ -97,10 +99,9 @@ LCB alignment:: -n = : alignment program (default: libMUSCLE) -u = : output unaligned regions? .unaligned (default: NO) -SNP filters:: +Recombination filtration:: - -R = : enable (R)epeat filtering? - -x = : enable recombination filtering? (default: NO) + -x = : enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO) Misc:: diff --git a/docs/index.rst b/docs/index.rst index 87483b7..e42a848 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -30,10 +30,10 @@ detection, and phylogenetic trees. Genome Biology, 15 (11), 1-15 [`PDF `_] -**Download (v1.1.1, 20-Mar-2015)** +**Download (v1.1.2, 24-Mar-2015)** -* `Harvest-OSX64-v1.1.1.tar.gz `_ -* `Harvest-Linux64-v1.1.1.tar.gz `_ +* `Harvest-OSX64-v1.1.2.tar.gz `_ +* `Harvest-Linux64-v1.1.2.tar.gz `_ .. toctree:: :hidden: