DeNovoCLI
DeNovoGUI Command Line Interface
The command line interface to DeNovoGUI, referred to as DeNovoCLI, makes is easy to use DeNovoGUI in a command line setting, for example as part of a bigger software pipeline.
DeNovoCLI takes a set of spectrum files as input and uses the PepNovo+, DirecTag, pNovo+ (beta) and Novor algorithms to de novo sequence each spectrum according to the given search parameters.
Note that the spectra must be provided in the Mascot Generic File (mgf) format.
The recommended way to generate an identification parameters file is via the DeNovoGUI graphical user interface. But the file can also be created using the IdentificationParametersCLI. The folders used in the processing can be set via PathSettingsCLI.
General command line:
java -cp DeNovoGUI-X.Y.Z.jar com.compomics.denovogui.cmd.DeNovoCLI [parameters]
Mandatory parameters:
-spectrum_files Spectrum files (mgf format), comma separated list or an entire folder.
Example: "file1.mgf, file2.mgf".
-output_folder The output folder.
-id_params A search parameters file. Generated from the GUI
or using the IdentificationParametersCLI.
Optional common parameters:
-pepnovo Turn the PepNovo+ sequencing on or off.
(1: on, 0: off, default is '1')
-directag Turn the DirecTag sequencing on or off.
(1: on, 0: off, default is '1')
-pnovo Turn the pNovo+ sequencing on or off.
(1: on, 0: off, default is '0')
-novor Turn the Novor sequencing on or off.
(1: on, 0: off, default is '0')
Optional advanced parameters:
-pep_novo_folder The folder where PepNovo+ is installed.
Defaults to the version provided with DeNovoGUI.
-directag_folder The folder where DirecTag is installed.
Defaults to the version provided with DeNovoGUI.
-pnovo_folder The folder where pNovo+ is installed.
Defaults to the version provided with DeNovoGUI.
-novor_folder The folder where Novor is installed.
Defaults to the version provided with DeNovoGUI.
-threads The number of threads to use for the processing.
Default is the number of cores available.
PathSettingsCLI
Standard command line
java -cp DeNovoGUI-X.Y.Z.jar com.compomics.denovogui.cmd.PathSettingsCLI [parameters]
Generic temporary folder
-temp_folder A folder for temporary file storage. Use only if
you encounter problems with the default configuration.
-log Folder where to write the log files.
Specific path setting
-denovogui_matches_directory
Folder where identification matches are temporarily saved to reduce the memory footprint.
-utilities_user_preferences
Folder containing the compomics utilities user preferences file.
-ptm_configuration Folder containing the PTM user preferences file.
-fasta_indexes Folder containing the indexes of the protein sequences databases.
-gene_mapping Folder containing the gene mapping files.
-pride_annotation Folder containing the PRIDE annotation preferences.
Comma Separated List
When using comma separated lists as input for the mgf files or the PTMs, please pay attention to the quotes required. Surround the full content of the option in quotes and not the individual items:
-spectrum_files "C:\..\file_1.mgf, C:\..\file_2.mgf"
-variable_mods "oxidation of m, phosphorylation of s"
Examples
Here is an example for Windows using a search parameters file. X, Y and Z have to be replaced by the actual version of DeNovoGUI and my folder by the folder containing the desired files:
java -cp DeNovoGUI-X.Y.Z.jar com.compomics.denovogui.cmd.DeNovoCLI
-spectrum_files "C:/my_folder"
-output_folder "C:/my_folder/output"
-search_params "C:/my_folder/DeNovoGUI.parameters"
Note that for readability the commands are here split over multiple lines. When used the commands should of course be single lines.
Help
If you experience any problems with the command line or have any suggestion please contact us via the DeNovoGUI mailing list.