Commit eca7b0ac authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'doc/2526-productivity' into 'dev'

doc/vidjil-algo.md: productivity discordance + server

See merge request !475
parents 5f449d1a aad0c6a2
Pipeline #79519 passed with stages
in 6 minutes and 11 seconds
......@@ -25,7 +25,7 @@ methods and software.
- [Docker/Server installation and maintenance](server.md)
These documentations and additional developer and maintainer documentation
are availaible 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.
### Further help
......
This is the preliminary help of the Vidjil server on Ubuntu server 14.04.
This is the help of the Vidjil server.
This help is intended for server administrators.
Users should consult the web application manual.
Other documentation can also be found in [dev.org](http://git.vidjil.org/blob/dev/doc/dev.org).
Users should consult the [web application manual](http://www.vidjil.org/doc/user/)
Other documentation can also be found in [doc/](http://www.vidjil.org/doc/).
Finally, developer documentation
# Plain installation or Docker containers
# Docker containers or Plain installation
There are two ways to install and run a Vidjil server:
- We are developping and deploying in 2018 **Docker containers** to ease the installation and the maintenance.
These Docker containers are now used in some partner hospitals.
- We are developping and deploying since 2018 **Docker containers** to ease the installation and the maintenance.
These Docker containers are used on the public server (<https://app.vidjil.org>) as well as in some partner hospitals.
We recommend this installation for new instances of Vidjil.
We also provide support and remote maintenance
of such in-hospital servers through
the [VidjilNet consortium](http://www.vidjil.net/index.en.html).
- The **plain installation of the server** should run on any Linux/Unix server with Nginx (recommanded) or Apache.
We provide below detailed instructions for Ubuntu 14.04 LTS.
We use this installation on the public server (<https://app.vidjil.org>) since October 2014.
We used this installation on the public server between 2014 and 2018.
# Requirements
......@@ -371,8 +374,10 @@ docker-compose up -d nginx
# Plain server installation
This installation is not supported anymore.
We rather advise to use the Docker containers (see above).
## Requirements
## Requirements (for Ubuntu 16.04)
``` bash
apt-get install git
......
......@@ -473,8 +473,12 @@ with gapped V and J sequences, as for instance, for V genes, IMGT/GENE-DB sequen
as provided by `make germline`.
The CDR3/JUNCTION detection won't work with custom non-gapped V/J repertoires.
CDR3 are reported as productive when they come from an in-frame recombination
and when the sequence does not contain any in-frame stop codons.
CDR3 are reported as *productive* when they come from an in-frame recombination
and when the full sequence does not contain any in-frame stop codons.
Note that some other software only consider stop codons in the CDR3,
and may thus under-estimate non-productivity. Vidjil-algo looks for in-frame stop codons
on all the available sequence (and may sometimes over-estimate non-productivity when
the sequence contains intronic regions).
The advanced `--analysis-cost` option sets the parameters used in the comparisons between
the clone sequence and the V(D)J germline genes. The default values should work.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment