Commit aefe5ab0 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.org: details, updated wording

parent c442c679
......@@ -73,13 +73,13 @@ to learn the essential features of Vidjil.
* The elements of the Vidjil web application
** The info panel (upper left panel)
- patient information :: user can put some informations in this case to retain about the patient.
- patient/run information :: user can put some informations in this case to retain about the patient or the run.
- locus :: germline used for analyzing the data. In case of multi-locus
data, you can select what locus should be displayed (see [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]])
- analysis :: name (without extension) of the loaded file used for displaying the data
- sample :: name of the current sample point. You can also change the current point by clicking directly on his name in the graph panel (when available).
#The name can be edited (“edit”).
- date :: indicate the date of the run of the current sample point (edit with the database, on the patient tab).
- date :: indicate the date of the run of the current sample point (edit with the database, on the patient/run tab).
You can change the point viewed by clickong on the =←= and =→= buttons. A cycling view is available by the fix button.
- analyzed reads :: number of reads where Vidjil found a CDR3, for that sample point
See [[Number of analyzed reads]] below.
......@@ -154,9 +154,9 @@ If a server with a patient/experiment database is configured with your
installation of Vidjil (as on http://app.vidjil.org/), the
'patient' menu gives you access to the server.
With authentication, you can add patients, then add either
=.fasta=, =.fastq=, =.gz= or =.clntab= files, then process your
runs and save the results of your analysis.
With authentication, you can add patients or runs,
then add "samples" (=.fasta=, =.fastq=, =.gz= or =.clntab= files), possibly pre-processed,
then process your data and save the results of your analysis.
** The different elements
......@@ -228,6 +228,7 @@ software lauched, the options set in the config, the size of the sample and the
The base configurations are « TRG », « IGH », « multi » (=-g germline=), « multi+inc » (=-g germline -i=), « multi+inc+xxx » (=-g germline -i -2=, default advised configuration).
See https://github.com/vidjil/vidjil/blob/master/doc/locus.org for information on these configurations.
The server mainteners can add new configurations tailored to specific needs.
The « reload » button (bottom left) updates the status of the task, that should do =QUEUED= → =ASSIGNED= → =RUNNING= → =COMPLETED=.
It is possible to launch several process at the same time (some will wait in the =QUEUED= / =ASSIGNED= states), and also to launch process while you
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