diff --git a/README.md b/README.md index ef02dd6..a7e55c4 100644 --- a/README.md +++ b/README.md @@ -1,66 +1,10 @@ -Harvest -======= +## Harvest + +![](https://raw.githubusercontent.com/marbl/gingr/master/html/img/harvest.png) Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific -microbial genomes. Harvest includes: Parsnp, a fast core-genome -multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools. - -##Release status - -Pending: `v1.1` - -##Harvest suite download: - -* OSX (10.7 or newer): - * https://github.com/marbl/harvest/releases/download/v1.1/harvest-OSX64-v1.1.tar.gz - * MD5 sum: 86df3afe4ea61f5799bd4dfdf18087e9 -* Linux/*nix: - * https://github.com/marbl/harvest/releases/download/v1.1/harvest-Linux64-v1.1.tar.gz - * MD5 sum: a6227d26b5c94a9904039c3e67a160cf - -##Harvest suite documentation (in prep): - -* http://harvest.readthedocs.org/en/latest/ - -##Individual Harvest components: - -1. **Parsnp** - * Description: core genome aligner - * Project url: http://github.com/marbl/parsnp - * Language: C, C++, Python - * OSX prebuilt binary: - * https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-OSX64-v1.0.tar.gz - * MD5 sum: 08c19b4d12e8199b2ce098550b4100e6 - * Linux prebuilt binary: - * https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-Linux64-v1.0.tar.gz - * MD5 sum: f82b6b9dae456fe9263ee6214b2633af - -2. **Gingr** - * Description: GUI, interactive visualization of multiple alignments, phylogenies and variants (SNPs etc) - * Gingr is able to display: - * Newick formatted trees - * XMFA formatted multi-alignments (with synteny view) - * VCF formatted variants - * Harvest tools GGR format - * Project url: http://github.com/marbl/gingr - * Language: C++ - * OSX prebuilt binary: - * https://github.com/marbl/gingr/releases/download/v1.1/gingr-OSX64-v1.1.zip - * MD5 sum: 455ebd0b68e064b1fd5b18decfc49905 - * Linux prebuilt binary: - * https://github.com/marbl/gingr/releases/download/v1.1/gingr-Linux64-v1.1.tar.gz - * MD5 sum: 386dee47f6be86367e7ab92ad1334ef1 - -3. **Harvest tools** - * Description: binary format and conversion utilities - * Project url: http://github.com/marbl/harvest-tools - * Language: C++, Python - * OSX prebuilt binary: - * https://github.com/marbl/harvest-tools/releases/download/v1.1/harvesttools-OSX64-v1.1.tar.gz - * MD5 sum: bbc75536d40b02e597589e55df189235 - * Linux prebuilt binary: - * https://github.com/marbl/harvest-tools/releases/download/v1.1/harvesttools-Linux64-v1.1.tar.gz - * MD5 sum: 48386692d434bbc947ea0058e95b2f15 +microbial genomes. +For more information, see harvest.readthedocs.org diff --git a/docs/content/harvest-tools.rst b/docs/content/harvest-tools.rst index 67ea1bf..2eddaa5 100644 --- a/docs/content/harvest-tools.rst +++ b/docs/content/harvest-tools.rst @@ -28,6 +28,8 @@ generic conversion between standard bioinformatics file formats. harvest/source harvest/license +**Resources** + `All releases`_ ~ `Source code`_ ~ `Report an issue`_ .. _All releases: https://github.com/marbl/harvest-tools/releases diff --git a/docs/content/parsnp/installation.rst b/docs/content/parsnp/installation.rst index fc279ca..c231c4c 100644 --- a/docs/content/parsnp/installation.rst +++ b/docs/content/parsnp/installation.rst @@ -27,7 +27,7 @@ Before you start, if running OSX Mavericks, OpenMP is not supported via Clang, s * Install Macports, then: - sudo port install gcc49 - - sudo port gcc-select mp-gcc49 + - sudo port select gcc mp-gcc49 * (or) Install Homebrew, then: @@ -48,7 +48,7 @@ Once OpenMP support is added, the first (required!) step is to build libMUSCLE:: cd muscle ./autogen.sh - ./configure --prefix=`pwd` + ./configure --prefix=`pwd` CXXFLAGS=’-fopenmp’ make install Then, build Parsnp::