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Troubleshooting and FAQs
Nalini Ganapati edited this page Aug 3, 2018
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The checklist below describes the common pitfalls that most people get trapped into
-
[TileDB] Verify that the workspace and all its sub-directories have read and execute permission for the user running the uwsgi app.
- Run
chmod -R ga+rx <path to TileDB workspace>
- Run
-
[Library] Run
ldd libquery.so
and verify that all dependencies are mapped correctly. If any of them do not look right, compile the search_library and dependencies:make BUILD=release GENOMICSD_DB=/path/to/GenomicsSampleAPI/search_library/dependencies/GenomicsDB
-
libquery.so
can be found underGenomicsSampleAPIs/search_library/lib
folder
-
-
[GA4GH] Verify that the
GenomicsSampleAPIs/web/<array_name>_ga4gh.conf
file has the right absolute paths.-
WORKSPACE
is the path to where the Database was setup (fromcreate_tiledb_workspace
), and not to the GenomicsDB/TileDB github repo. - Most of the time when a new DB array is created, folks forget to update the
ARRAYNAME
-
-
[NGINX] SELinux will sometimes prevent nginx from accessing the uwsgi socket.
- nginx isn't allowed to access the socket, so give it permissions:
sudo semanage fcontext -a -t httpd_sys_rw_content_t 'ga4gh.sock' sudo restorecon -v 'ga4gh.sock'
- set a policy to allow nginx to access sockets:
sudo grep nginx /var/log/audit/audit.log | audit2allow -M mypol sudo semodule -i mypol.pp
- How do I remove the array that is already created in Tile DB?
- In the directory corresponding to the TileDB workspace, you will find a directory <array_name> which contains all the data corresponding to the array. Delete the directory <array_name>.
- Variant Store
- Python API
- Utils
- MAF to TileDB Import
- VCF to TileDB Import
- Additional Info