diff --git a/README.md b/README.md index ebd9f86..6aa03ce 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ [![Build Status](https://travis-ci.org/chungongyu/siga.svg?branch=master)](https://travis-ci.org/chungongyu/siga) ![GitHub release](https://img.shields.io/github/release/chungongyu/siga.svg) +[![Conventional Commits](https://img.shields.io/badge/Conventional%20Commits-1.0.0-yellow.svg)](https://conventionalcommits.org) [![GitHub license](https://img.shields.io/github/license/chungongyu/siga.svg)](https://github.com/chungongyu/siga) [![GitHub issues](https://img.shields.io/github/issues/chungongyu/siga.svg)](https://github.com/chungongyu/siga/issues) diff --git a/docs/_config.yml b/docs/_config.yml index bbd95a1..56f440a 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -16,7 +16,10 @@ title: SIGA description: An open-source de novo assembly toolkit containing various assembly pipelines. baseurl: "/siga" # the subpath of your site, e.g. /blog +url: "http://bioinfo.ict.ac.cn" show_downloads: true +google_analytics: "UA-131018484-1" +favicon: "favicon.png" #github: [metadata] github: repository_url: https://github.com/chungongyu/siga diff --git a/docs/_layouts/default.html b/docs/_layouts/default.html new file mode 100644 index 0000000..9e5d943 --- /dev/null +++ b/docs/_layouts/default.html @@ -0,0 +1,64 @@ + + + + + + + + {% if site.favicon %} + + {% endif %} + + + {{ site.title | default: site.github.repository_name }} | {{ site.description | default: site.github.project_tagline }} +{% seo title=false %} + + + + + +
+
+ View on GitHub + +

{{ site.title | default: site.github.repository_name }}

+

{{ site.description | default: site.github.project_tagline }}

+ + {% if site.show_downloads %} +
+ Download this project as a .zip file + Download this project as a tar.gz file +
+ {% endif %} +
+
+ + +
+
+ {{ content }} +
+
+ + + + + {% if site.google_analytics %} + + {% endif %} + + diff --git a/docs/favicon.png b/docs/favicon.png new file mode 100644 index 0000000..e8e1175 Binary files /dev/null and b/docs/favicon.png differ diff --git a/docs/index.md b/docs/index.md index 9f750f0..5192ab9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,4 @@ -Home +Contents ==== [![Build Status](https://travis-ci.org/chungongyu/siga.svg?branch=master)](https://travis-ci.org/chungongyu/siga) @@ -14,7 +14,7 @@ Home * [Running SIGA](#running-siga) * [Benchmarks](#benchmarks) * [Citation](#citation) -* [Related Publications](#related-publications) +* [Publications](#publications) * [FAQ](#faq) * [Support](#support) * [Authors](#authors) @@ -22,7 +22,7 @@ Home Overview ======== -SIGA is an open-source _de novo_ assembly toolkit containing various assembly pipelines which are totally compatible with [SGA](https://github.com/jts/sga) file format. Similar to [SGA](https://github.com/jts/sga), it is designed as a [modular set of programs](#running-siga), which are used to form an assembly pipeline. +SIGA is an open-source _de_ novo assembly toolkit containing various assembly pipelines which are totally compatible with [SGA](https://github.com/jts/sga) file format. Similar to [SGA](https://github.com/jts/sga), it is designed as a [modular set of programs](#running-siga), together which form an assembly pipeline. Quick Start =========== @@ -37,6 +37,8 @@ Quick Start * [rapidjson](https://github.com/Tencent/rapidjson) * [gperftools](https://github.com/gperftools/gperftools) (optional but suggested) +Dependencies may be installed using the package manager [Homebrew](https://homebrew.sh) on macOS and [Linxubrew](http://linuxbrew.sh) on Linux and Windows, using [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/). + ### Compiling SIGA If you cloned the repository from github, run `autogen.sh` from the root directory @@ -134,30 +136,36 @@ siga index --help Benchmarks ======== -Comming soon... +Comming soon ... Citation ======== ## [SIGA](https://github.com/chungongyu/siga) -Chungong Yu, Yu Lin, Guozheng Wei, Bing Wang, Yanbo Li and Dongbo Bu. **SIGA** : A Sensitive and Intelligent *de* novo Genome Assembler. +Chungong Yu, Yu Lin, Guozheng Wei, Bing Wang, Yanbo Li and Dongbo Bu. **SIGA** : An open-source Sensitive and Intelligent *de* novo Genome Assembler. -Related Publications -==================== +Publications +============ -None yet! ^_~ +None yet! ^_~ FAQ ==== 1. **Where can I get further help or advice?** - See [Support](#support) or the [siga wiki](https://github.com/chungongyu/siga/wiki). + See [Support](#support) or the [siga wiki](https://github.com/chungongyu/siga/wiki). + +2. **What parameters should I tune to improve my assembly?** + + See [here](https://github.com/chungongyu/siga/wiki/SIGA-parameter-tuning) Support ======= +[Create a new issue](https://github.com/chungongyu/siga/issues) on GitHub. + Contact [siga@ict.ac.cn](mailto:siga@ict.ac.cn) Authors