Commit 94a38ef8 authored by Mikaël Salson's avatar Mikaël Salson

server.md: First instructions for using a CloneDB

See vdj#755
parent dba8ee31
Pipeline #48429 passed with stages
in 6 minutes and 34 seconds
......@@ -970,3 +970,23 @@ optional arguments:
--dry-run With a dry run, the data will not be saved to the database
--config CONFIG Select the config mapping file
```
# Using CloneDB [Under development]
The [CloneDB](https://gitlab.inria.fr/vidjil/clonedb) has to be installed
independently of the Vidjil platform.
Then one can easily extract data to be used with CloneDB. A script is provided
(`server/web2py/applications/vidjil/scripts/create_clone_db.py`) which
produces a FASTA file to be indexed with CloneDB. This script takes as
parameter the FASTA output file and one (or many) group IDs, which correspond
to the groups having access to the datasets. Note that for the moment the Vidjil platform only allow a per group access to the CloneDB.
The FASTA output filename must follow the format `clonedb_XXX.fa` where `XXX`
is replaced with the group ID.
Make sure that the `DIR_CLONEDB` variable is set in `defs.py` and points to
the CloneDB server directory. Make sure that in this directory the
`clonedb_defs.py` has been filled correctly.
Then index the created FASTA file with the CloneDB index (follow the
instructions from CloneDB).
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