release 1.9.0 #388
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release 1.9.0 #388
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… argument. If --custom-quant-dir is set, psm and frag parquet files are not saved to the workflow directory, but to a the directory specified, which is necessary to perform distributed searches.
…lurm. outer.sh coordinates first search, mbr library building, second search and lfq, inner.sh performs the respective searches. parse_parameters.py creates necessary subdirectories & config files to process input files in chunks.
… improved job-specific logging.
…in base.py: if the custom_quant_directory is provided, the entire workflow folder is saved there instead of '.progress' in the output directory.
…e and decide whether to get library from library_path argument or existing config file.
…tolerances and inference independently
…ut any search-run specific input files
update separate_configs branch for distributed search with development
…rce instead of copying the spectral library to each chunk folder.
remove speclib copying step
merging separate_configs into rename_progress_folder to solve conflicts before reverse merge
introduce rawfilemanager
Add rt length to output ii
… and second search
# Conflicts: # alphadia/workflow/base.py # alphadia/workflow/peptidecentric.py # docs/methods.md
Addressed main points for distributed search: - overall code clarity and robustness - unifying quant directory naming, removing the name 'custom-quant-dir' - Documentation and user guide in docs - Handling of partial config files to prevent stale settings in default configs for first or second search - reading the spectral libraries from one location instead of copying them to each chunk folder This implementation was tested on 90 .raw files processed in 30 chunks.
alpharaw hdf reader
Transfer Library Bug
update and layout docs
Bump version: 1.8.2 → 1.9.0
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