From eddf903a05a2eda80d6df09d6f552edf23fa6e37 Mon Sep 17 00:00:00 2001 From: ondovb Date: Wed, 24 Dec 2014 16:16:37 -0500 Subject: [PATCH 1/4] Streamlined README for simpler landing page MD5s have been moved to release pages. --- README.md | 84 ++++++++++++++++++++++++--------------------------------------- 1 file changed, 32 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index 112d6a8..17f3893 100644 --- a/README.md +++ b/README.md @@ -1,66 +1,46 @@ -Harvest -======= +## Harvest 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. +microbial genomes. -##Release status +#### Components -08/08/14: `v1.0.1` +* **Parsnp** - core-genome alignment and analysis +* **Gingr** - interactive visualization of alignments, trees and variants +* **Harvest tools** - archiving and postprocessing -##Harvest suite download: +#### Documentation -* OSX (10.7 or newer): - * https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-OSX64-v1.0.1.tar.gz - * MD5 sum: 86df3afe4ea61f5799bd4dfdf18087e9 -* Linux/*nix: - * https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-Linux64-v1.0.1.tar.gz - * MD5 sum: a6227d26b5c94a9904039c3e67a160cf +* [Harvest](http://harvest.readthedocs.org/en/latest/) + * [Parsnp](http://harvest.readthedocs.org/en/latest/content/parsnp.html) + * [Gingr](http://harvest.readthedocs.org/en/latest/content/gingr.html) + * [Harvest tools](http://harvest.readthedocs.org/en/latest/content/harvest-tools.html) -##Harvest suite documentation (in prep): +#### Downloads -* http://harvest.readthedocs.org/en/latest/ +OSX 10.7+ is required for Mac. Linux binaries work on most common disributions. Source for individual tools is available at release pages. -##Individual Harvest components: +* Harvest suite ([all releases](https://github.com/marbl/harvest/releases)) + * [harvest-OSX64-v1.0.1.tar.gz](https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-OSX64-v1.0.1.tar.gz) + * [harvest-Linux64-v1.0.1.tar.gz](https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-Linux64-v1.0.1.tar.gz) +* Individual tools + * Parsnp ([all releases](https://github.com/marbl/parsnp/releases)) + * [parsnp-OSX64-v1.0.tar.gz](https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-OSX64-v1.0.tar.gz) + * [parsnp-Linux64-v1.0.tar.gz](https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-Linux64-v1.0.tar.gz) + * Gingr ([all releases](https://github.com/marbl/gingr/releases)) + * [gingr-OSX64-v1.0.1.zip](https://github.com/marbl/gingr/releases/download/v1.0.1/gingr-OSX64-v1.0.1.zip) + * [gingr-Linux64-v1.0.1.tar.gz](https://github.com/marbl/gingr/releases/download/v1.0.1/gingr-Linux64-v1.0.1.tar.gz) + * Harvest tools ([all releases](https://github.com/marbl/harvest-tools/releases)) + * [harvesttools-OSX64-v1.0.1.tar.gz](https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-OSX64-v1.0.1.tar.gz) + * [harvesttools-Linux64-v1.0.1.tar.gz](https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-Linux64-v1.0.1.tar.gz) -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 +#### News +* 08/08/14 - Version [1.0.1](https://github.com/marbl/harvest/releases/tag/v1.0.1) is available -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/v1.0.1/gingr-OSX64-v1.0.1.zip - * MD5 sum: 455ebd0b68e064b1fd5b18decfc49905 - * Linux prebuilt binary: - * https://github.com/marbl/gingr/releases/download/v1.0.1/gingr-Linux64-v1.0.1.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/v1.0.1/harvesttools-OSX64-v1.0.1.tar.gz - * MD5 sum: bbc75536d40b02e597589e55df189235 - * Linux prebuilt binary: - * https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-Linux64-v1.0.1.tar.gz - * MD5 sum: 48386692d434bbc947ea0058e95b2f15 +#### Project pages +* [Parsnp](http://github.com/marbl/parsnp) +* [Gingr](http://github.com/marbl/gingr) +* [Harvest tools](http://github.com/marbl/harvest-tools) From d47621f8fe492e38ca74085dd91485fcc455c751 Mon Sep 17 00:00:00 2001 From: ondovb Date: Mon, 29 Dec 2014 18:02:21 -0500 Subject: [PATCH 2/4] added logos to Readme --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 17f3893..88fa6b0 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,16 @@ ## 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. #### Components -* **Parsnp** - core-genome alignment and analysis -* **Gingr** - interactive visualization of alignments, trees and variants +* ![Parsnp](https://raw.githubusercontent.com/marbl/gingr/master/html/img/res/parsnp_icon_small.png) **Parsnp** - core-genome alignment and analysis +* ![Gingr](https://raw.githubusercontent.com/marbl/gingr/master/html/img/res/gingr_icon_small.png) **Gingr** - interactive visualization of alignments, trees and variants * **Harvest tools** - archiving and postprocessing #### Documentation From ef428a262f81876a59a8fdb1c80eb83014100154 Mon Sep 17 00:00:00 2001 From: Todd J Treangen Date: Tue, 27 Jan 2015 05:12:18 -0500 Subject: [PATCH 3/4] update port select --- docs/content/parsnp/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/content/parsnp/installation.rst b/docs/content/parsnp/installation.rst index fc279ca..2296b6d 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: From addb07f18608cc91621eebac7979698ec59b6f27 Mon Sep 17 00:00:00 2001 From: Todd J Treangen Date: Tue, 27 Jan 2015 07:39:50 -0500 Subject: [PATCH 4/4] update fopenmp flag --- docs/content/parsnp/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/content/parsnp/installation.rst b/docs/content/parsnp/installation.rst index 2296b6d..c231c4c 100644 --- a/docs/content/parsnp/installation.rst +++ b/docs/content/parsnp/installation.rst @@ -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::