Updated Ann Loraine. Tested it again, it's working as expected. https://bitbucket.org/lorainelab/findjunctions/pull-requests/1

Small change request:

• Please remove this repository reference from the POM: http://eos.transvar.org/nexus/content/repositories/freehep-maven/

Raised pull request: https://bitbucket.org/lorainelab/findjunctions/pull-requests/1. Please review and let me know if there are any issues.

I am able to build FindJunctions using mvn and then run the runFJ.sh to produce a bed file. I am also able to create a bed file using the FindJunction_exe.jar.

Ready for pull request.

Thanks Nowlan Freese for finding that out, I missed that -u option when running it from the terminal that's why I was getting the output from the terminal and not from the script. Updated the READMe file and included the script changes as well: https://bitbucket.org/jaya-sravani/findjunctions/branch/IGBF-3679

Jaya Sravani Sirigineedi - The example bash script above includes "-u" which outputs uniquely mapped reads only. My guess would be that the example reads in the 1.bam file are not uniquely mapped, and so the output was empty. When I removed the "-u" the bed files were no longer empty.

Edits to the Readme:

• I think you can get rid of lines 27-29 as they are included in the example.
• It may be worth including the current FindJunctions options (see below), or tell the user how to see them.
• What is the "-n 10" in the example for running the jar without building FindJunctions? Is that equivalent to the -f flank option?

FindJunctions options:

 -b,--twobit <2BIT>   2bit file with genomic sequence [required]
 -f,--flank <FLANK>   read bases required to flank intron [default is 5]
 -h,--help            print usage information
 -o,--output <OUT>    write output to file [optional]
 -u,--unique          uniquely mapped reads only [optional]
 -v,--verbose         enables debug logging [optional]

Fixed the build issue and modified the README.md file to include the steps to build and run the application. Updated code is available at the branch: https://bitbucket.org/jaya-sravani/findjunctions/branch/IGBF-3679. Also, I tried including this run step in a shell script file, but when i run the file the output bed file is empty when the same command is run in terminal it is working, Nowlan Freese could you please check this on your system as well and let me know if it's working for you. Clone the above branch and change the runFJ.sh file content to below:

#!/bin/bash

JAR="target/find-junctions-1.0.0-jar-with-dependencies.jar"
TWOBIT="src/test/resources/A_thaliana_Jun_2009.2bit"
BAM="src/test/resources/1.bam"
FLANK="10"
OUT="test.bed"

java -Xmx1g -jar $JAR -f $FLANK -b $TWOBIT -u -o $OUT $BAM
java -Xmx512m -jar $JAR -b $TWOBIT -u -f $FLANK -o test1.bed $BAM

With the instructions provided in the README.md file you should now be able to run the FindJunctions jar and get the bed file as output.

I've updated the FindJunctions page in the User's Guide (linked here) to mention Apache Maven and direct users to the BitBucket repo.

I'm unassigning myself from this ticket so that whoever has time to update the compilation instructions in the README can assign themselves and work on it.

If Jaya Sravani Sirigineedi or Kaushik Gopu has time this sprint, let's try to get this done.

Meaning: Explain how to compile the project using maven. Add the documentation to the repository itself as PRs.

Change line above to "Build the jar file using maven. See: [ insert link to bitbucket repository here ]."