Sage-Bionetworks/genomeBrowsers

Name: genomeBrowsers

Owner: Sage Bionetworks

Description: null

Created: 2015-07-01 20:45:46.0

Updated: 2015-07-01 20:56:37.0

Pushed: 2015-07-10 19:44:22.0

Homepage: null

Size: 156

Language: Python

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README

Genome Browsers

Jbrowse

JbrowseConf.py

Required

Project - Project name

Jbrowse directory- Where Jbrowse-1.11.6 is installed (path)

Genome - Input (human/mouse) - hg19 and mm10 supported

Folder Path - Full path of folder with datafiles

optional arguments:

-h, –help: show this help message and exit

-N, –needRef: Need reference genome?

-A, –add: Append onto existing conf?

-D, –download: Download genome fasta files

-C, –create: Create Folder structure for project

Example:

For fresh jbrowse: python JbrowseConf.py [Project] [Jbrowse directory] [Genome] [Folder Path] -D -C -N

Biodalliance

CreateBDal.py

-h, –help show this help message and exit

-cu CONTROLURL, –controlURL CONTROLURL: Takes in list of control URL

-cau CASEURL, –caseURL CASEURL: Takes in list of case URL

-cf CONTROLFILE, –controlFile CONTROLFILE: Takes in list of control files

-caf CASEFILE, –caseFile CASEFILE: Takes in list of case files

-g GENOME, –genome GENOME: Input (human/mouse) hg19 or mm10 genomes