1.2.8-alpha

A DEVELOPMENT RELEASE. Use at your own risk.
This is for me to test the pipeline in numerous environments so that I can track down the SignalP issue described in #92, and #93.

What's Changed

We've removed Pfamscan as Pfam seems to be undergoing some changes and the old pfamscan script doesn't always work.
I have plans to enable integration of interproscan results shortly.

Fixes a bug causing only a subset of PHI-base searches to be run.

Updated the installation and links in documentation for Phobius as the source has moved (thanks to @markusHaferkamp for reporting this).
Updated installer to use SignalP 6.0h.

Improved error reporting for SignalP 3 and 4. These programs sometimes fail silently, causing cryptic errors down the road about Dmatrix types in xgboost.
I still haven't been able to reproduce the segfaults observed by some people, so i can't find the cause.
But this will at least be clearer as to what's going on.

Related to signalp3. The Dmatrix datatypes are now explicitly set, so even if SignalP3 doesn't give any results you'll be able to get some ranked outputs.

Full Changelog: 1.2.7...1.2.8-alpha

1.2.7

What's Changed

• Copy result files to results folder instead of linking by @IdoBar in #85
• Updates deepredeff implementation to use plain python. Avoids issue using R and reticulate inside conda environment.
• New version of predector utils adds tool to map protein results onto genome coordinates for visualisation.

Full Changelog: 1.2.6...1.2.7

1.2.7-alpha

What's Changed

• Copy result files to results folder instead of linking by @IdoBar in #85

Full Changelog: 1.2.6...1.2.7-alpha

1.2.6

What's Changed

• Remove pinning of python to v3.6 by @IdoBar in #80
• New release by @darcyabjones in #83
• Fixes bug causing protein names to be "." in individual results tables.

New Contributors

• @IdoBar made their first contribution in #80

Full Changelog: 1.2.5...1.2.6

1.2.6-alpha

What's Changed

• 1.2.5 tag by @darcyabjones in #76
• Remove pinning of python to v3.6 by @IdoBar in #80
• Pinned to python 3.9
• Updated dependencies.
• Fixed bug causing names to be absent from some results tables.

New Contributors

• @IdoBar made their first contribution in #80

Full Changelog: 1.2.5...1.2.6-alpha

Release with Signalp6 G

1.2.5-alpha

Bump version: 1.2.4 → 1.2.5-alpha

1.2.5

What's Changed

• Update to work with SignalP 6.0g
• Fixes issue with installer calling chmod -R . failing

NOTE. SignalP 6.0g was distributed with the GPU model, this installer not backwards compatible.

Full Changelog: 1.2.4...1.2.5

1.2.4

Incorporates new version of SignalP 6, other bug-fixes, and new options for skipping analyses.

• SignalP 6.0e support now added, with the suggested patch in fteufel/signalp-6.0#3. There are still known issues with 6.0e so I was waiting for the update, but it's probably worth having this now.
• Fixed a bug in decode_seqs that could cause error if only one file goes into it. (in which case it will be symlinked as just the extension, so the file looks like a dotfile and isn't captured by the glob.
• Added support to not install signalp6 in the environment. In this case the pipeline will automatically detect that it isn't installed and skip the analysis.
• Added flags to not do perform the analyses: signalp 6, pfamscan, dbcan searches, effectordb searches, phibase searches.
• Added flag to control the batch size for signalp6 to control memory usage.

Full Changelog: 1.2.3...1.2.4

1.2.3

Adds support for SignalP 6.0c.

This is functionally identical to 6.0b.
I filed a bug report, and they fixed it really quickly.
The results are the same, the installer is the same.
6.0c just handles a really niche case if you happen to have something that looks like a bacterial SP.

Full Changelog: 1.2.2...1.2.3

1.2.2

Adds support for SignalP 6.0b.
Update broke previous installers, and they don't keep the old versions around.