Commit 43ff7f41 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by HERBERT Ryan
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doc

parent f7c816af
......@@ -140,7 +140,8 @@ The aligner display nucleotide sequences from selected clones.
- You can further analyze the sequences with IMGT/V-QUEST and IgBlast on the selected sequences. This opens another window/tab.
- You can unselect all sequences by clicking on the background of the grid.
** The patient database and the server
* The patient database and the server
If a server with a patient/experiment database is configured with your
installation of Vidjil (as on http://app.vidjil.org/), the
......@@ -150,16 +151,20 @@ 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.
** The different elements
*** Patients
Once you are authentified, this page show the patient list. Here you
Once you are authenticated, this page show the patient list. Here you
can see your patients and patients whose permission has been given to you.
New patients can be added ('add patient'), edited ('e') or deleted ('X').
By default, you are the only one who can see and update this new patient.
If you have an admin access, you can grant access to other users ('p').
*** Samples
*** Runs
*** Adding a sample
Clicking on a patient give acccess the "samples" page. Each sample is
a =.fasta=, =.fastq=, =.gz= or =.clntab= file that will be processed by one or several
......@@ -175,7 +180,7 @@ Depending on your granted access, you can add a new sample to the list (=add fil
download sequence files when they are available (=dl=) or delete sequence files (=X=).
Note that sequence file may be deleted (in particular to save server disk space) while still keeping the results.
*** Processing samples
*** Processing samples, configs
Depending on your granted accesses, you can schedule a processing for a sequence file (select a config and =run=).
The processing can take a few seconds to a few hours, depending on the
......@@ -187,6 +192,8 @@ are uploading data. Finally, you can safely close the window with the patient da
The only thing you should not do is to close completely the browser while sequences are uploading.
*** Groups
* Can I see all the clones ?
......
#+TITLE: Vidjil -- Server Manual
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/org-mode.css" />
This is the preliminary help of the upcomping Vidjil server.
This help is intended for server administrators.
......
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