NuPoP is a software tool for Nucleosome Positioning Prediction. For more information on NuPoP please refer For more information on NuPoP and the methods, please refer http://nucleosome.stats.northwestern.edu/
For comments, please contact: email@example.com
Vipin T Sreedharan customized the fortran program and wrote a pythonic interface to integrate in Galaxy service.
1) It can handle multiple fasta sequence in a query file to predict nucleosome positioning.
2) Multiple output, Plain text based result and Wiggle fixedStep format based on users request. In addition to this it will create binary files of nucleosome occupency score and corresponding positions in the genomic sequence. The binary file path can be found in NuPoP Log file.
How to integrate into your Galaxy:
1. Unpack the compressed file and move the resulting folder to anywhere you want.
2. Under the resulting folder run perl code by type "perl changePath.pl". This command set up the Fotran codes input file path according to the exact location.
3. Please make sure that Biopython is installed in your machine.
4. Edit the <command> tag in NuPoP.xml move into your Galaxy root.
5. Set the correct path for fortran program(NPred.f90) in NuPoP.py. Always below the line of #TODO line number
6. Move the test_nupop_* files to galaxy test-data folder.
Npred.f90 : Fortran program (core).
NuPoP.py : A pythonic interface to the core program.
NuPoP.xml : Tool configuration file.
changePath.pl : Seeting the CWD path in core program.
profile/ : NuPoP dependencies.
test_nupop_chr1.fa : genome sequence in FASTA format.
test_nupop_pred_chr1.txt : prediction result in text format.
test_nupop_pred_chr1.wig : prediction result in Wiggle format.
Please let me know if you find any difficulty to integrate into Galaxy. I can be reached at firstname.lastname@example.org