Commit 4c2b5506 authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/user.org: processing samples, #configs, details

parent 6ad80580
......@@ -219,14 +219,18 @@ probably contains both a part of the V and the J genes.
** Processing samples, configs
:PROPERTIES:
:CUSTOM_ID: configs
:END:
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
software lauched, the options set in the config, the size of the sample and the server load.
The base configurations are « TRG », « IGH », « multi » (=-g germline=), « multi+inc » (=-g germline -i=), « multi+inc+xxx » (=-g germline -i -2=, default advised configuration).
The base human configurations with the Vidjil built-in algorithm 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.
There are also configuration for other species and for other RepSeq algorithms, such as « MiXCR ».
The server mainteners can add new configurations tailored to specific needs, contact us if you have other 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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