Commit 1a0779ef authored by Mathieu Giraud's avatar Mathieu Giraud

mkdocs.yml, doc/index.md: reorganize doc

Closes #4143
parent 400c513c
......@@ -12,33 +12,35 @@ high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html)
methods and software.
### Web application, user documentation
- Tutorial "Mastering the Vidjil web application": [english](./tutorial/mastering-vidjil.html) ([pdf](./tutorial/mastering-vidjil.pdf)), [français](./tutorial/mastering-vidjil-fr.html)
([pdf](./tutorial/mastering-vidjil-fr.pdf)). Start by this tutorial to have an overview of Vidjil.
- Web platform [user manual](user.md)
- [Demo access](http://app.vidjil.org/) to the patient, experiment and sample server
### Quality documentation and open data
- [Software Quality and Human Processes](quality.md)
- [Public datasets](http://www.vidjil.org/data/) supporting Vidjil publications
### Algorithm and server documentation
### Life scientist
- Tutorial "Mastering the Vidjil web application": [english](./tutorial/mastering-vidjil.html) ([pdf](./tutorial/mastering-vidjil.pdf)), [français](./tutorial/mastering-vidjil-fr.html) ([pdf](./tutorial/mastering-vidjil-fr.pdf)) 🔗. Start by this tutorial to have an overview of Vidjil.
- Web platform [user manual](user.md). This is the main user manual of the Vidjil platform.
- [Libraries and recombinations](locus.md), documentation on library preparation and sequencing as well on detected immune recombinations
- [Demo access](http://app.vidjil.org/) 🔗 to the patient, experiment and sample public test server
### Bioinformatician
- [Vidjil-algo documentation](vidjil-algo.md), usage from the command-line
- [Server administration](admin.md), configuration and administration features available from the web application
- [Docker/Server installation and maintenance](server.md), server installation, configuration and maintenance from the command line
- [fuse.py](tools.py), converting and merging immune repertoire data
- Specification of the [.vidjil format](vidjil-format.md) to encode immune repertoires with clones with V(D)J recombinations
- Specification of the [warnings](warnings.md), list of default [tags](tags.org)
- Specification of the [.should-vdj.fa tests](should-vdj.md) for encoding and testing curated V(D)J designations
### Server administrator
- [Server administration (web)](admin.md), configuration and administration features available from the web application
- [Server installation and maintenance (docker)](server.md), server installation, configuration and maintenance from the command line
### Developer documentation
### Quality, open data, roadmap, credits
- [Software and developement quality](quality.md), including software engineering methods and human and team processes
<!-- - [Roadmap](roadmap.md) -->
- [Public datasets](http://www.vidjil.org/data/) 🔗 supporting Vidjil publications
- [Credits, references](credits.md)
- [Encoding clones with V(D)J recombinations](vidjil-format.md), specification of the `.vidjil` file format
- Specification of the [.should-vdj](should-vdj.org) format for encoding curated V(D)J designations
- List of implemented [warnings](warnings.md), list of default [tags](tags.org)
- Developer documentation: [Vidjil-algo](dev-algo.md), web application: [client](dev-client.md), [server](dev-server.md)
### Further developer documentation
These documentations and additional developer and maintainer documentation
are available from the [doc/](http://gitlab.vidjil.org/tree/master/doc) directory in the source files.
are available from the [doc/](http://gitlab.vidjil.org/tree/master/doc) directory in the source files,
including development notes on Vidjil-algo (`dev-algo.md`)
and on the web application client (`dev-client.md`) and the server (`dev-server.md`).
### Further help
......
......@@ -7,16 +7,29 @@ plugins: []
repo_url: https://gitlab.inria.fr/vidjil/vidjil
repo_name: gitlab
pages:
nav:
- / : index.md
- user manual: user.md
- libraries, recombinations: locus.md
- vidjil-algo: vidjil-algo.md
- .vidjil format: vidjil-format.md
- admin: admin.md
- server: server.md
- quality: quality.md
- credits: credits.md
- Life scientist:
- Web application user manual: user.md
- Libraries and recombinations: locus.md
- Tutorial "Mastering the Vidjil web application" 🔗: http://www.vidjil.org/doc/tutorial/mastering-vidjil.html
- Demo access to app.vidjil.org 🔗: http://app.vidjil.org/
- Bioinformatician:
- vidjil-algo, command-line manual: vidjil-algo.md
- fuse.py, converting and merging immune repertoire data: tools.md
- Specification of the .vidjil format: vidjil-format.md
- Specification of the warnings: warnings.md
- Specification of the .should-vdj.fa tests: should-vdj.md
- Further developer documentation: /#further-developer-documentation
- Server administrator:
- Server administration (web): admin.md
- Server installation and maintenance (docker): server.md
- Further developer documentation: /#further-developer-documentation
- Quality, roadmap, credits:
- Software and development quality: quality.md
- Public datasets supporting Vidjil publications 🔗: http://www.vidjil.org/data
# - Roadmap: roadmap.md
- Credits, references: credits.md
extra_css:
- mkdocs-extra.css
......
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