Release v0.5.5 (documentation updated) 10-03-2024

RAPT rapt-45639894, with SKESA 2.5.0 and PGAP 2023-05-17.build6771

Updated stand-alone PGAP to version 2023-05-17.build6771 for:

• Better handling of species that changed name or taxonomic lineage.
• Addition of attributes (Gene Ontology terms, EC numbers, gene symbols) to more protein-coding features, by propagation from curated conserved domain architectures (CDD architectures)
• Incremental improvements in structural algorithm

Release v0.5.4 12-07-2022

RAPT rapt-41589182, with SKESA 2.5.0 and PGAPX 2022-10-03.build6384

Update PGAPX to 2022-10-03.build6384

Release v0.5.3 07-15-2022

RAPT rapt-39223259, with SKESA 2.5.0 and PGAPX 2022-04-14.build6021

This is a bugfix release. The methods to retrieve SRA and metadata have been modified to align with the recent change to the backend services

Release v0.5.2 05-04-2022

RAPT rapt-38092134, with SKESA 2.5.0 and PGAPX 2022-04-14.build6021

This release updates PGAP to 2022-04-14.build6021, and implemented --auto-correct-tax switch: when specified, in the case that the genome sequence is misassigned or contaminated and ANI predicts an organism with HIGH confidence, the system will use the predicted organism for PGAP instead of the one provided by the user.

Release v0.5.1 03-18-2022

RAPT rapt-37347638, with SKESA 2.5.0 and PGAPX 2022-02-10.build5872

This release updates PGAP to 2022-02-10.build5872

Release v0.3.2 (documentation updated) 03-19-2021

RAPT rapt-31854332, with SKESA 2.5.0 and PGAPX 2021-01-11.build5132

This release changes the default machine type for GCP-RAPT from n1-highmem-16 to n1-himem-8 as our cost-analysis shows the later is more cost-effective.

Release v0.2.0 (documentation updated) 11-02-2020

RAPT rapt-29571188, with SKESA 2.4.0 and PGAPX 2020-09-24.build4894

GCP-RAPT now displays job status in "joblist" command as "Done" and "Failed" instead of "Finished" and "Aborted" for more clarity; and more information has been added to the output of "jobdetails" command for easier problem identification. Log files are now included in the result archive "output.tar.gz" so that it is the only file to download under one jobid.

This release also provides a python script, run_rapt.py, to run RAPT agnostically on customer's own system with python and docker-compatible container system installed. Refer to the documentation for details.

Release v0.5.0 01-05-2022

RAPT rapt-36255426, with SKESA 2.5.0 and PGAPX 2021-11-29.build5742

This release updated PGAPX to 2021-11-29.build5742 and use dedicated program instead of curl to fetch SRA data.

The RAPT team

Release v0.4.2 10-25-2021

RAPT rapt-35244699, with SKESA 2.5.0 and PGAPX 2021-07-01.build5508

This release update SKESA to use a newer version of boost in order to handle some flavor of gzipped input file.

Release v0.4.1 10-12-2021

RAPT rapt-34986039, with SKESA 2.5.0 and PGAPX 2021-07-01.build5508

This release fixed a bug (double quote of version string that causes syntax error when running standalone run_rapt.py), added logic to tolerate minor taxonomy name mismatch, and retry upon SRA download failure caused by network glitches.