Commit 13fe84fe authored by Mikaël Salson's avatar Mikaël Salson

Merge branch 'doc/4143-reorganize-nav' into 'dev'

mkdocs.yml: reorganize doc

Closes #4143

See merge request !583
parents 31b608e8 56c64e9e
Pipeline #119418 passed with stages
in 53 minutes and 8 seconds
......@@ -95,7 +95,7 @@ http://dx.doi.org/10.3324/haematol.2017.177444
Yann Ferret et al.,
*Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis*,
British Journal of Haematology, 2016, 173, 413–420
http://dx.doi.org/10.1111/bjh.13981
https://hal.archives-ouvertes.fr/hal-01279160
Henrike J. Fischer et al.,
*Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion*
......
Here are aggregated notes forming the developer documentation of vidjil-algo.
This documentation is a work-in-progress, it is far from being as polished as the user documentation.
Help can also be found in the source code and in the commit messages.
Here are aggregated notes forming a part of the developer documentation on vidjil-algo.
These notes are a work-in-progress, they are not as polished as the user documentation.
Developers should also have a look at the [documentation for bioinformaticians and server administrators](/),
at the [issues](http://gitlab.vidjil.org), at the commit messages, and at the source code.
# Algorithm
# Development notes -- Vidjil-algo
## Code organisation
......
Here are aggregated notes forming the developer documentation on the Vidjil web client.
This documentation is a work-in-progress, it is far from being as polished as the user documentation.
Help can also be found in the source code and in the commit messages.
Here are aggregated notes forming a part of the developer documentation on the Vidjil web client.
These notes are a work-in-progress, they are not as polished as the user documentation.
Developers should also have a look at the [documentation for bioinformaticians and server administrators](/),
at the [issues](http://gitlab.vidjil.org), at the commit messages, and at the source code.
# Client
# Development notes -- Client
## Installation
......@@ -388,7 +388,7 @@ webpage.
The Firefox version used can be set with an environment variable (see
below). By default, the tests only work with Firefox ≤ 45. But this can be
modified with an environment variable. All Firefox releases are [available here](https://download-installer.cdn.mozilla.net/pub/firefox/releases/%20).
modified with an environment variable. All Firefox releases are [available here](https://download-installer.cdn.mozilla.net/pub/firefox/releases/).
One can instead choose to launch functional tests using chrome. You should
install `chromium-browser` as well as `chromium-chromedriver`. On old Chrome
......
<link rel="stylesheet" type="text/css" href="org-mode.css" />
Here are aggregated notes forming the developer documentation on the Vidjil server,
Here are aggregated notes forming a part of the developer documentation on the Vidjil server,
on client-server interaction as well as on packaging.
This documentation is a work-in-progress, it is far from being as polished as the user or maintainer documentation.
Help can also be found in the source code and in the commit messages.
These notes are a work-in-progress, they are not as polished as the user documentation.
Developers should also have a look at the [documentation for bioinformaticians and server administrators](/),
at the [issues](http://gitlab.vidjil.org), at the commit messages, and at the source code.
# Server
# Development notes -- Server
## Notifications
......
......@@ -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
......
......@@ -150,7 +150,7 @@ The paper \[1\] includes an evaluation of the V(D)J designation of 125 clones.
1. Yann Ferret, A. Caillault et al.,
*Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis*,
British Journal of Haematology, 2016, 173, 413–420,
<http://dx.doi.org/10.1111/bjh.13981>
<https://hal.archives-ouvertes.fr/hal-01279160>
2. Mikaël Salson et al., A dataset of sequences with manually curated V(D)J designations
RepSeq 2015,
......
......@@ -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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