Thank you for trying out the candidate releases, sharing your feedback, and trying out the fixes.
Based on your feedback we have fixed bugs affecting docker and sub-URI deployments, updated documentation for HPC-integration, and most importantly, we have created a path for migrating to NCBI’s newer V5 database format (see release notes below).
If you have 5 minutes, please help us by taking the following brief survey: https://forms.gle/yvDX9PTxSCgjZoqj7
# Release notes
1. Running 'sequenceserver -m' will now automatically detect older V4 databases, and those created without the '-parse_seqids' option of makeblastdb, and offer to rebuild them. This works even if you deleted the original FASTA files. Database titles are preserved when rebuilding, however, taxonomy information in the database is unfortunately not preserved.
2. If you do not wish to rebuild your databases yet, you can now run SequenceServer with BLAST+ 2.9.0 instead. The tradeoff is that you would have to manually download BLAST+ 2.9.0 and indicate its location in the configuration file. SequenceServer will only download 2.10 by default.
3. If building BLAST databases fails for some reason, the command that was tried and the resulting output is properly relayed to the user so that the problem can be diagnosed (#469). Thanks to mjcoynejr for testing the fix.
4. BLASTing a mix of older V4 and newer V5 databases causes error. SequenceServer now catches and informs the user of this error. Thanks to Massimiliano babbucci for reporting this issue.
5. On sub-URI deployments, clicking the back button would result in no databases to be displayed in the search form (#462). Fixed that. Thanks to Xiang Zhang for reporting the issue and testing the fix.
6. The list of databases in the search form should be alphabetically sorted. This behaviour was lost in the rewrite leading to version 2.0 and has now been fixed. Thanks to Loraine Guéguen for reporting the issue.
7. Docker-related optimisations: SequenceServer no longer prompts to join the mailing list when running under Docker (#468). Thanks to Matt for reporting the issue. Furthermore, we have updated the docker base image and reduced the image size by ~100 Mb.
8. Documentation for HPC integration was out of date with regard to how to invoke the wrapper script (#445). Thanks to Loraine Guéguen for reporting the issue, testing the fix.
Thanks to Niek Art, Matt Yoder, Massimiliano babbucci, Bjoernsen, and Eric Y for reporting database compatibility issues that prompted us to create a path for migrating to the new database format.
Upgrading is simple. If you have Ruby 2.3 or later, run:
gem install --pre sequenceserver
This does not remove your current sequenceserver installation. Instead, it changes
the default. If something breaks, you can rollback by running:
gem uninstall sequenceserver
# Issues / comments/ contributions
Please report any issues here: https://github.com/wurmlab/sequenceserver/issues.
You can also send us pull-requests. We welcome any help you may be able to provide in terms of improving test coverage and making code style checkers happy.
Priyam & Yannick
Evolutionary genomics @ Queen Mary U London