From 336d45c4ab721e4057dc74815cc81631a1cf23ee Mon Sep 17 00:00:00 2001 From: Brian Ondov Date: Mon, 9 Feb 2015 15:54:11 -0500 Subject: [PATCH] HarvestTools update and sidebar cleanup --- docs/content/harvest-tools.rst | 27 +++++++++++++++++++++------ docs/content/parsnp.rst | 7 ++++--- docs/index.rst | 2 +- 3 files changed, 26 insertions(+), 10 deletions(-) diff --git a/docs/content/harvest-tools.rst b/docs/content/harvest-tools.rst index ead417b..67ea1bf 100644 --- a/docs/content/harvest-tools.rst +++ b/docs/content/harvest-tools.rst @@ -1,12 +1,20 @@ -================================================================= -harvest-tools: binary archive and format conversion tool -================================================================= +============ +HarvestTools +============ +**Archiving and postprocessing** -Project home page: https://github.com/marbl/harvest-tools +HarvestTools is a utility for creating and interfacing with Gingr files, which +are efficient archives that the Harvest Suite uses to store reference-compressed +multi-alignments, phylogenetic trees, filtered variants and annotations. Though +designed for use with Parsnp and Gingr, HarvestTools can also be used for +generic conversion between standard bioinformatics file formats. -harvest-tools primarily serves as a reference-based compression tool for large genomic datasets. In addition, it serves as a proxy between several alignment and variant & annotated feature formats. While it was designed for use with both Parsnp & Gingr, it can also be used as standalone tool to efficiently compress multiple alignments, variants, phylogenies and annotations to a single convenient binary archive. +**Download (v1.2)** -Contents: + * `harvesttools-OSX64-v1.2.zip `_ + * `harvesttools-Linux64-v1.2.tar.gz `_ + +**Documentation** .. toctree:: :maxdepth: 2 @@ -19,3 +27,10 @@ Contents: harvest/tutorial harvest/source harvest/license + +`All releases`_ ~ `Source code`_ ~ `Report an issue`_ + +.. _All releases: https://github.com/marbl/harvest-tools/releases +.. _Source code: https://github.com/marbl/harvest-tools +.. _Report an issue: https://github.com/marbl/harvest-tools/issues + diff --git a/docs/content/parsnp.rst b/docs/content/parsnp.rst index 6e15081..2363a82 100644 --- a/docs/content/parsnp.rst +++ b/docs/content/parsnp.rst @@ -1,6 +1,7 @@ -========================================= -Parsnp: rapid core genome multi-alignment -========================================= +====== +Parsnp +====== +**Rapid core genome multi-alignment** Project home page: https://github.com/marbl/parsnp diff --git a/docs/index.rst b/docs/index.rst index b52f5a0..6ac2dc4 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -38,7 +38,7 @@ detection, and phylogenetic trees. .. toctree:: :hidden: - content/gingr content/parsnp + content/gingr content/harvest-tools