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This wiki is out-of-date! Please visit http://pughlab.mbg.cornell.edu/scriptmanager for the latest documentation
Welcome to the ScriptManager wiki!
A tool written in Java for analyzing sequencing data and generating figures.
Both Graphical User Interface (GUI) and Command Line Interface (CLI) execution options are available.
Open your terminal and move to the directory where you want to install scriptmanager and type the following commands.
git clone https://github.com/CEGRcode/scriptmanager
cd scriptmanager
./gradlew build
The ScriptManager jar file will be created in the build/libs directory. As long as you have this file, you can move it wherever you want and do whatever you want with the rest of the scriptmanager files (even delete them).
To run the GUI version of ScriptManager, execute the jar file without any arguments or flags:
java -jar /path/to/ScriptManager.jar
To run the CLI version of ScriptManager, you must append the two subcommands corresponding to the tool you wish to run and any input arguments and options. The subcommand structure reflects the organization of the GUI tool.
java -jar /path/to/ScriptManager.jar <TOOLGROUP> <TOOLNAME> <INPUTS> <OPTIONS>
The TOOLGROUP corresponds to one of the tabs in the GUI tool while the TOOLNAME corresponds to the specific tool within the TOOLGROUP group. Each tool will have its own set of input requirements and options. You will have to rely on the -h flag for usage help or the documentation here for the input arguments.
For more information on CLI usage, see Command Line Overview.
The -h documentation is very useful so at any point in constructing your command you get stuck, use the -h to see what your options are and what you might be missing.
- For Bugs: email Olivia/Will or open a Github issue with the following info
- command you ran
- entire stack trace (error messages that followed execution of the command)
- Detailed tool documentation
- File format specifications
- Javadoc
aggregate-data
bam-correlation
bam-indexer (GUI only)
bam-to-bedgraph
bam-to-bed
bam-to-gff
bam-to-scidx
bed-to-gff
composite (CLI only)
dna-shape-bed
dna-shape-fasta
expand-bed
expand-gff
fasta-extract
filter-bed
filter-pip-seq
four-color
gff-to-bed
heatmap
md5checksum (GUI only)
merge-bam (GUI only)
merge-heatmap
pe-stat
peak-align-ref
rand-coord
randomize-fasta
remove-duplicates (GUI only)
scale-matrix
scaling-factor
se-stat
search-motif
signal-dup
sort-bam (GUI only)
sort-bed
sort-gff
tag-pileup
tile-genome