Good morning,
I’m trying to integrate multiple SequenceServer instances to multiple JBrowse as I’m working on multiple genotypes. I was able to linkout SequenceServer to show the target hit on the correct genome browser, now I’d like to do the opposite, sending sequences from JBrowse to SequenceServer blast. Is there any way to pass the FASTA sequence through SequenceServer URL to populate the Query Sequence field automatically so the user can that just select the db to blast against?
Thanks in advance
Andrea
Hi Andrea,
This is not directly possible at the moment. However, we do plan to incorporate this feature as it has been requested before as well. In the proposed implementation, you will be able to include one or more sequence ids in the URL. SequenceServer will fetch sequences corresponding to the given ids and populate the query field automatically. The sequences will be fetched (using blastdbcmd) from the BLAST databases listed in the search form.
I plan to include this feature in the next beta release of SequenceServer 1.1.0 which should be this week (or second week of October if I fail this week).
Priyam
Hi Andrea,
I have implemented this feature and opened a pull-request to solicit feedback from users interested in the feature. Are you able to try and let me know if it works for you?
https://github.com/wurmlab/sequenceserver/pull/382
Priyam
Hi Priyam,
I’ll try to patch the code of the edited files and give a try (I’m running multiple instances through passport so I guess that’s fastest way to test it)
Andrea
I patched the changed files but the app broke.
This is the log in Apache error file
`
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/database.rb:193: warning: #Class:SequenceServer::Database#sys at /home/aminio/.rbenv/versions/2.5.1/lib/ruby/2.5.0/forwardable.rb:157 forwarding to private method Module#sys
App 45868 output: Error: The application encountered the following error: uninitialized constant #Class:SequenceServer::Database::CommandFailed (NameError)
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/database.rb:197:in rescue in blastdbcmd' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/database.rb:190:in blastdbcmd’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/database.rb:202:in scan_databases_dir' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver.rb:132:in init_database’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver.rb:40:in init' App 45868 output: config.ru:3:in block in ’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rack-1.5.0/lib/rack/builder.rb:55:in instance_eval' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rack-1.5.0/lib/rack/builder.rb:55:in initialize’
App 45868 output: config.ru:1:in new' App 45868 output: config.ru:1:in ’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:101:in eval' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:101:in preload_app’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:189:in block in <module:App>' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/ruby_supportlib/phusion_passenger/loader_shared_helpers.rb:380:in run_block_and_record_step_progress’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:188:in <module:App>' App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:30:in module:PhusionPassenger’
App 45868 output: /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/passenger-5.3.4/src/helper-scripts/rack-preloader.rb:29:in `’
[ E 2018-10-12 10:31:42.2541 45680/T1m age/Cor/App/Implementation.cpp:221 ]: Could not spawn process for application /home/aminio/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sequenceserver-1.0.11-CabSauv: The application encountered the following error: uninitialized constant #Class:SequenceServer::Database::CommandFailed (NameError)
`
Hi Andrea,
I am sorry about that. The patch would be applied to beta release of SequenceServer 1.1.0. I think you are running version 1.0.x, and that is causing this error.
Please see this thread to learn more about upcoming release of SequenceServer: https://groups.google.com/d/msg/sequenceserver/2G4_jdAr4-k/2yxQKixVBQAJ
Priyam
Hi Priyam,
I tried to update the system (I use passenger to have multiple instances working). I was using blast 2.7.1 but I had to downgrade it because of the version checking, not a big deal, but now none of the blast servers works properly.
The main blast is completely unreachable (passenger does not create a the subfolder seems), the others give no error but shows just the header and the footer of sequenceserver and nothing else (and it is the best case). Any clue?
Ok, I were able to recover the unseen tool, but the result was the same with the others.
Is there any way, while I test the beta tool to keep the other 3 sequence servers active with the older version? (I need them to be up while I’m installing and debugging this new version)
Hi Andrea,
I am really sorry for the slow response.
The simplest way to try the new version is using the built-in web server. That is, without passenger.
Get sequenceserver source code
git clone https://github.com/wurmlab/sequenceserver
Install dependencies
cd sequenceserver
gem install bundler
bundle install --without=development
Run with default configuration file (~/.sequenceserver.conf)
bundle exec bin/sequenceserver
Run with a different configuration file
bundle exec bin/sequenceserver --config_file /path/to/custom_config_file
Priyam