cravat's Introduction
Cancer-Related Analysis of Variants Toolkit (CRAVAT - http://cravat.us) is an easy to use web-based tool for analysis of cancer variants (missense, nonsense, in-frame indel, frameshift indel, splice site, truncating). CRAVAT provides scores and a variety of annotations that assist in identification of important variants. Results are provided in an interactieve, highly graphical environment that assists with prioritization and investigation of study variants. In addition to the webservice, CRAVAT is also available for local or cloud- based installation as a docker container. See our introductory video: https://www.youtube.com/watch?v=xovmIy11Bcs
cravat's People
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cravat's Issues
Not able to rest password or contact your team through the interface
Hello, I have been trying to contact your team through the "contact" button http://www.cravat.us/CRAVAT/, but the message keeps failing and asks me to "try again"
I have an account with my email address [email protected] , and I am not able to reset the password. Please email me a reset password link . Thanks.
mysql process continually exiting
I am running cravat with the following command:
docker run --name cravatmupit -p 80:8080 -v /Users/my_path_to_local_dir/mysql:/var/lib/mysql -v /Users/my_path_to_local_dir/storage:/ext karchinlab/cravatmupit:5.0.2
Often (4 out of 5 times I run the container) mysql get's stuck in a continually exiting state:
2017-10-04 12:39:15,778 INFO exited: mysql (exit status 1; not expected)
2017-10-04 12:39:16,190 INFO spawned: 'mysql' with pid 92
2017-10-04 12:39:17,437 INFO success: mysql entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2017-10-04 12:39:18,173 INFO exited: mysql (exit status 1; not expected)
2017-10-04 12:39:19,176 INFO spawned: 'mysql' with pid 112
Here is the portion from /var/log/mysql/error.log on the running container that is repeating:
171003 18:46:42 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
171003 18:46:42 [Note] Plugin 'FEDERATED' is disabled.
171003 18:46:42 InnoDB: The InnoDB memory heap is disabled
171003 18:46:42 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171003 18:46:42 InnoDB: Compressed tables use zlib 1.2.8
171003 18:46:42 InnoDB: Using Linux native AIO
171003 18:46:42 InnoDB: Initializing buffer pool, size = 128.0M
171003 18:46:42 InnoDB: Completed initialization of buffer pool
171003 18:46:42 InnoDB: highest supported file format is Barracuda.
171003 18:46:42 InnoDB: Waiting for the background threads to start
171003 18:46:43 InnoDB: 5.5.57 started; log sequence number 1595675
ERROR: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'ALTER TABLE user ADD column Show_view_priv enum('N','Y') CHARACTER SET utf8 NOT ' at line 1
171003 18:46:43 [ERROR] Aborting
171003 18:46:43 InnoDB: Starting shutdown...
171003 18:46:44 InnoDB: Shutdown completed; log sequence number 1595675
171003 18:46:44 [Note] /usr/sbin/mysqld: Shutdown complete
171003 18:46:44 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
171003 18:46:44 [Note] Plugin 'FEDERATED' is disabled.
171003 18:46:44 InnoDB: The InnoDB memory heap is disabled
171003 18:46:44 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171003 18:46:44 InnoDB: Compressed tables use zlib 1.2.8
171003 18:46:44 InnoDB: Using Linux native AIO
171003 18:46:44 InnoDB: Initializing buffer pool, size = 128.0M
171003 18:46:44 InnoDB: Completed initialization of buffer pool
171003 18:46:44 InnoDB: highest supported file format is Barracuda.
171003 18:46:44 InnoDB: Waiting for the background threads to start
171003 18:46:45 InnoDB: 5.5.57 started; log sequence number 1595675
171003 18:46:45 InnoDB: Starting shutdown...
171003 18:46:46 InnoDB: Shutdown completed; log sequence number 1595675
171003 18:46:46 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
171003 18:46:46 [Note] Plugin 'FEDERATED' is disabled.
171003 18:46:46 InnoDB: The InnoDB memory heap is disabled
171003 18:46:46 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171003 18:46:46 InnoDB: Compressed tables use zlib 1.2.8
171003 18:46:46 InnoDB: Using Linux native AIO
171003 18:46:46 InnoDB: Initializing buffer pool, size = 128.0M
171003 18:46:46 InnoDB: Completed initialization of buffer pool
171003 18:46:46 InnoDB: highest supported file format is Barracuda.
171003 18:46:46 InnoDB: Waiting for the background threads to start
171003 18:46:47 InnoDB: 5.5.57 started; log sequence number 1595675
ERROR: 1050 Table 'plugin' already exists
171003 18:46:47 [ERROR] Aborting
171003 18:46:47 InnoDB: Starting shutdown...
171003 18:46:47 InnoDB: Shutdown completed; log sequence number 1595675
171003 18:46:47 [Note] /usr/sbin/mysqld: Shutdown complete
I have tried:
- Removing the image from my local machine and re-pulling
- Pulling and running different tags (
hybrid,latest,5.0.1)
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