Commit ddb95672 authored by Marc Duez's avatar Marc Duez
parents cba1bcd2 4f6dbc1c
...@@ -22,16 +22,14 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -22,16 +22,14 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
The vidjil browser displays =.vidjil= files that summarize the V(D)J The vidjil browser displays =.vidjil= files that summarize the V(D)J
rearrangements and the sequences found in a run. rearrangements and the sequences found in a run.
If you have an access to the patient database, you are able to upload, The easiest way to get these files is to [[http://rbx.vidjil.org/browser][request an account]] on the Vidjil server.
manage, process your runs (=.fasta=, =.fastq= or =.clntab= files) directly on the browser You will then be able to upload,
manage, process your runs (=.fasta=, =.fastq=, =.gz= or =.clntab= files) directly on the browser
(see below 'patient database'), and the server behind the patient (see below 'patient database'), and the server behind the patient
database computes these .vidjil files. database computes these .vidjil files.
Otherwise, such .vidjil files can be obtained: Otherwise, such .vidjil files can be obtained:
- by sending us your .fasta/.fastq files, either through
http://www.vidjil.org/submit.html or using any other method
(e.g. your own FTP)
- from the command-line version of Vidjil (starting from - from the command-line version of Vidjil (starting from
=.fasta= or =.fastq= files, see [[http://git.vidjil.org/blob/master/doc/algo.org][algo.org]]) =.fasta= or =.fastq= files, see [[http://git.vidjil.org/blob/master/doc/algo.org][algo.org]]).
To gather several .vidjil files, you have to use the [[http://git.vidjil.org/blob/master/server/fuse.py][fuse.py]] script To gather several .vidjil files, you have to use the [[http://git.vidjil.org/blob/master/server/fuse.py][fuse.py]] script
- or by post-processing of other V(D)J analysis pipelines (contact us - or by post-processing of other V(D)J analysis pipelines (contact us
if you are interested) if you are interested)
...@@ -118,14 +116,15 @@ Otherwise, such .vidjil files can be obtained: ...@@ -118,14 +116,15 @@ Otherwise, such .vidjil files can be obtained:
- You can unselect all sequences by clicking on the background of the scatterplot. - You can unselect all sequences by clicking on the background of the scatterplot.
** The patient database (experimental) ** The patient database and the server
This part is experimental, we have provided an access to some labs to this feature. If a server with a patient database is configured with your
The release is expected to be at Q1 2015. installation of Vidjil (as on http://rbx.vidjil.org/browser), the
'patient' menu gives you access to the server.
A server links the browser and the algorithmic part. You can upload, With authentication, you can add patients, then add either
manage, process your runs (.fasta/.fastq or .clntab files) directly on =.fasta=/=.fastq=/=.gz= files or =.clntab= files, then process your
the browser. runs and save the results of your analysis.
*** Patients *** Patients
...@@ -139,7 +138,7 @@ If you have an admin access, you can grant access to other users ('p'). ...@@ -139,7 +138,7 @@ If you have an admin access, you can grant access to other users ('p').
*** Samples *** Samples
Clicking on a patient give acccess the "samples" page. Each sample is Clicking on a patient give acccess the "samples" page. Each sample is
a .fasta/.fastq file that will be processed by one or several a =.fasta=/=.fastq=/=.gz=/=.clntab= file that will be processed by one or several
pipelines. pipelines.
You can see which samples have been processed with the selected You can see which samples have been processed with the selected
config, and download the sequence files if they are available ("dl"). config, and download the sequence files if they are available ("dl").
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...@@ -25,8 +25,7 @@ demo login: <i>demo@vidjil.org</i> ...@@ -25,8 +25,7 @@ demo login: <i>demo@vidjil.org</i>
</p> </p>
<p> <p>
Please <a href="mailto:contact@vidjil.org?subject=Vidjil">contact us</a> You can <a href="mailto:contact@vidjil.org?Subject=%5BVidjil%5D%20Account%20on%20rbx.vidjil.org&Body=%0ADear%20Vidjil%20Team%2C%0A%0AI%20would%20like%20to%20have%20an%20account%20on%20the%20Vidjil%20server.%0A%0A">request an account</a> on this server to test your data.
if you would like to test your data and have a full account on this server.
</p> </p>
{{pass}} {{pass}}
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