hicops_config

Command line tool that takes in the user paramters and generates a file, called uparams.txt, which is used as arguments to the hicops binary. This tool also generates a template user paramter file which can be modified as needed and then used used with hicops_config to generate the uparams.txt file.

Note: Regenerate a uparams.txt everytime you modify the user parameters.

Note: If you are working on XSEDE Comet, you can follow an easier workflow by following instructions here and using the hicops_comet tool.

General Syntax

Generate a template user parameters file

$ $HICOPS_INSTALL/bin/hicops_config -g
Generated: ./sampleparams.txt

SUCCESS

Parameters:

• -g: flag that specifies to generate a template user paramters file.

Generate uparams.txt from user params

$ $HICOPS_INSTALL/bin/hicops_config <params.txt>

Parameters:

• params: user parameters file, template generated via the -g flag and then edited for experiment.

Example Usage

$ $HICOPS_INSTALL/bin/hicops_config userparams.txt

*****************************
*  HiCOPS Configuration Gen *
*    PCDS Lab, SCIS, FIU    *
*****************************

Provided Parameters:
Workspace   = /lclhome/mhase003/workspace
Using cores/node  = 22
Processed DB Parts = /lclhome/mhase003/Data/Database/Digested/parts
MS/MS dataset = /lclhome/mhase003/Data/Dataset/PXD009072
Max mods/pep  = 3
Adding mod   = M 15.99 2
Min pep len  = 7
Max pep len  = 40
Min precursor mass = 500
Max precursor mass = 5000
Max frag chg = 3
Required min PSM hits = 4
Base Normalized Intensity = 100000
Intensity Cutoff Ratio = 0.01
Scratch Memory (MB) = 2048
Resolution   = 0.01
Peptide mass tolerance (dM) = 10.0
Fragment mass tolerance (dF) = 0.01
Top matches = 10
Max expect value to report = 20.0

Initializing Workspace at:  /lclhome/mhase003/workspace

SUCCESS

Written: /disk/raptor/lclhome/mhase003/repos/hicops/install-no-inst/bin/uparams.txt

You can now run HiCOPS as:

$ mpirun -np [N] [OPTIONS] /disk/raptor/lclhome/mhase003/repos/hicops/install-no-inst/bin/hicops /disk/raptor/lclhome/mhase003/repos/hicops/install-no-inst/bin/uparams.txt

After HiCOPS, run post-processing as:

$ /disk/raptor/lclhome/mhase003/repos/hicops/install-no-inst/bin/tools/psm2excel -i /lclhome/mhase003/workspace/output

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     Read More: https://github.com/pcdslab/hicops/blob/develop/README.md
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