Bootstrapping in and out:
user@biotite ~ $ cd work/railsapps/ggkbase/
1- Start redis:
user@biotite ~/work/railsapps/ggkbase $ ./redis_init.sh start Starting redis-server: all set
2- Check that redis is up:
user@biotite ~/work/railsapps/ggkbase $ ps -ef | grep klane user@biotite ~/work/railsapps/ggkbase $ psgg user 67702 1 0 10:10 ? 00:00:00 /opt/bin/bio/redis-server 127.0.0.1:0 user@biotite ~/work/railsapps/ggkbase $ tail -f log/redis.log
3- Start Sidekiq:
user@biotite ~/work/railsapps/ggkbase $ rprails sidekiq:start Starting Sidekiq…
4- Check that Sidekiq is up:
user@biotite ~/work/railsapps/ggkbase $ ps -ef | grep klane
user@biotite ~/work/railsapps/ggkbase $ psgg
user 52388 1 0 15:48 ? 00:00:26 /opt/bin/bio/redis-server 127.0.0.1:0
user 59270 1 2 15:49 ? 00:02:07 sidekiq 5.0.4 ggkbase [0 of 35 busy]
user@biotite ~/work/railsapps/ggkbase $ tail -f log/sidekiq.log
2017-08-14T17:20:27.710Z 45513 TID-gnrzvgst0 INFO: Running in ruby 2.3.1p112 (2016-04-26 revision 54768) [x86_64-linux]
2017-08-14T17:20:27.711Z 45513 TID-gnrzvgst0 INFO: Sidekiq Pro 3.5.1, commercially licensed. Thanks for your support!
2017-08-14T17:20:27.711Z 45513 TID-gnrzvgst0 INFO: Booting Sidekiq 5.0.4 with redis options {:id=>"Sidekiq-server-PID-45513", :url=>"unix:///home/user/work/railsapps/ggkbase/tmp/sockets/redis.sock"
5- Leaving:
user@biotite ~/work/railsapps/ggkbase $ rprails sidekiq:stop Stopping Sidekiq… user@biotite ~/work/railsapps/ggkbase $ ./redhttp://ggkbase-help.berkeley.edu/wp-admin/post-new.php#is_init.sh stop
(and check with tail-f log file and psgg as in steps 2 and 4)
Note that log files are continually appended. Run log:clear once in a while to empty them.
Possible Commands:
user@biotite ~/work/railsapps/ggkbase $ bin/rake -T user@biotite ~/work/railsapps/ggkbase $ bin/thor -T
Importing a Project:
Need: project, path to files
Example:
klane@biotite ~/work/railsapps/ggkbase $ time ./bin/thor importer:bin /data7/ThiocyanateBioreactor/assembly/06142017 _2/s11/ -f BioR1_s11_temp_20_scaffold_min1000 -p kate_test blablabla Import everything? y or n ##can choose to jump to any point in import.
Did it work?
rprails c p = Project.find "kate_test" p.is_complete # this should return true
Add organisms to a project:
Need: project name, tab delimited file containing <bin, sample>
### If tsv was made in excel, remove carriage returns.
Example:
time ./bin/thor batch_project:add_organisms -f ~/some.tsv -p project_name
Pull down the latest code updates from github:
user@biotite ~/work/railsapps/ggkbase $ git pull
Perhaps something went awry:
Clear the redis queue:
redis-cli -h
redis-cli -s tmp/sockits/redis.sock
FLUSHALL
OK
quit
Destroy project:
rprails c p = Project.last or p = Project.find ”klane_test” p.safe_destroy(false) p.contigs.count #should return 0