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0.1.4

Date 📅 2025_02

Changes in detail

  • The 'mz_extractor' is now an optional process.

  • The conditions for selecting the 'decoyPYrat' and 'ThermoRawParser' processes have been changed.

Image Version history

  • bioDataHub (version 2.14):
    • Add new version of decoyPYrat (v3). In this version, the '|' character is replaced by '_'in the decoy comment line.
  • SearchToolkit (version 1.3):
    • 'mz_extractor': Change ProcessPoolExecutor to ThreadPoolExecutor.
Singularity image (version) Code Version
search_engine:0.1.4
MSFragger 4.2-rc14
ThermoRawFileParser 1.4.5
bioDataHub (DecoyPYrat) 2.14
SearchToolkit 1.3

0.1.3

Date 📅 2024_12

Highlights

  • Updated the sample input files.

  • Upgraded the MSFragger version (4.2-rc14) with a patch that extends the precursor mass range.

Changes

  • Upgraded the MSFragger version (4.2-rc14) with a patch that extends the precursor mass range.

  • Upgraded ThermoRawFileParser version.

  • Upgraded SearchToolkit version.

Image Version history

Version Singularity image Code Version
0.1.3 search_engine:0.1.3
MSFragger 4.2-rc14
ThermoRawFileParser 1.4.5
DecoyPYrat 2.13
SearchToolkit 1.2

0.1.2

DATE: 2024_11

Highlights

  • Search Adaptation: Added a module that inserts the ScanID into search engine results.

Changes

  • Created a 'SearchToolkit' repository to house the 'mz_extractor' program and other tools that adapt search engine results.

  • MSFragger adapted: execute process, then the output files overwrite the inputs (*.tsv).

  • Skip the method "mz_extractor" from a flag parameter (create_mzml).

Image Version history

Version Singularity image Code Version
0.1.2 search_engine:0.1.2
MSFragger 4.1
ThermoRawFileParser 1.4.2
DecoyPYrat 2.13
SearchToolkit 1.1

0.1.1

DATE: 2024_10

Highlights

  • DecoyPyRat: Optional outputs added when the database is copied.

  • Update the MSFragger version.

Changes

  • DecoyPyRat: Optional outputs added when the database is copied.

Image Version history

Version Description Singularity image Code Version
0.1.1 Update MSFragger version search_engine:0.1.1
MSFragger 4.1
ThermoRawFileParser 1.4.2
DecoyPYrat 2.13
MZ_extractor 1.0

0.1.0

DATE: 2024_07

Highlights

  • Release the first stable version.

Changes

Image Version history

Version Description Singularity image Code Version
0.1.0 First stable version
search_engine:0.1.0
MSFragger 3.8
ThermoRawFileParser 1.4.2
DecoyPYrat 2.13
MZ_extractor 1.0

0.0.X

DATE: 2024_XX

Highlights

  • Developing the beta version