Expanded Documentation at https://pughlab.mbg.cornell.edu/scriptmanager/
Scripts are generically categorized within semi-descriptive tabs and are designed to be run in parallel with each other and themselves.
Open ScriptManager-Tutorial.docx available in root directory
(after cloning this repo):
$ cd scriptmanager
$ ./gradlew build
The compiled JAR file will be output into the build/libs directory.
$ cd scriptmanager
$ singularity build --fakeroot scriptmanager.sif scriptmanager.def
To run the GUI verson of ScriptManager, you can double click the compiled JAR file or run the followinug command in the terminal
$ java -jar /path/to/jarfile
Running the CLI version of ScriptManager is similar to running the GUI. To view the list of command options, use the -h flag.
$ java -jar /path/to/jarfile -h
Example:
$ java -jar /path/to/jarfile coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
$ singularity exec scriptmanager.sif scriptmanager ${command}
Example:
$ singularity exec scriptmanager.sif scriptmanager coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
BAM Statistics:
-BAM Statistics
-Paired-End Statistics
-BAM Genome Correlation
BAM Manipulation:
-BAM-BAI Indexer
-BAM File Sorter
-BAM Remove Duplicates
-BAM Replicate Merge
-Filter for PIP-seq
BAM Format Converter:
-BAM to scIDX
-BAM to GFF
-BAM to BED
-BAM to bedGraph
File Utilities:
-MD5 Checksum
Peak Calling:
-Genetrack - still highly unstable
Peak Analysis:
-Align BED to Reference
-Filter BED by Proximity
-Genomic Coordinate Tile
-Generate Random Coordinate
-Signal Duplication
Coordinate File Manipulation:
-Expand BED/GFF File
-Convert BED/GFF to GFF/BED
-Sort BED/GFF by CDT
Sequence Read Analysis:
-Tag Pileup
-Calculate Scaling Factor
-Scale Matrix Data
-Aggregate Data
DNA Sequence Analysis:
-FASTA from BED
-Randomize FASTA
-Search Motif in FASTA
-DNA Shape from BED
-DNA Shape from FASTA
Figure Generation:
-Heatmap
-Merge Heatmaps
-4Color Sequence Plot