PCLServer

Usage

Basic Usage

 PCLServer -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>

Detailed Usage

package "PCLServer"
version "1.0"
purpose "PCLServer that serves pcl data to client"

section "Main"
option  "port"              p   "Port to listen to"
                                string typestr="9000"
option  "input"             i   "Input PCL directory"
                                string  typestr="directory" yes
option  "sinfo"             s   "Sinfo directory"
                                string  typestr="directory" yes
option  "prep"              q   "Prep directory"
                                string  typestr="directory" yes
option  "gene"              g   "Gene map file"
                                string  typestr="file"  yes
option  "platform"          P   "Platform directory"
                                string  typestr="directory" yes
option  "dset"              x   "Dataset listing"
                                string  typestr="file"  yes
option  "quant"             Q   "quant file (assuming all datasets use the same quantization)"
                                string  typestr="filename"  yes
                        
section "MISC"                              
option  "additional_db"     B   "Utilize a second CDatabase collection. Path to the second CDatabase's setting file."
                                string default="NA" 

Flag	Default	Type	Description
-i	stdin	Text file	Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene names (matching those in the input DAT/DAB files).
-d	.	Directory	Input directory containing DB files
-D	.	Directory	Output directory in which database files will be stored.
-x	.	Text file	Input file containing list of CDatabaselets to combine