Increase usablity on other systems by updating (SLURM)/scripts/juicer.sh

[bclaremar]

Juicer is supposed to be able to run on several systems.
You have come a long way but there are some hardcoded bugs, more or less hidden in the scripts.
This issue refers to (SLURM)/scripts/juicer.sh but may possibly apply for the other schedulers as well.

• <blank-space> are not allowed before #SBATCH lines, like row 665, in the batch script parts (jid='sbatch << ...) and at more places (search for <blank>#SBAT)

  • error output is not spot on so troubleshooting this took a while!!!
  • please change to <tabs>

• Possibly this applies to <blank>$userstring as well!

• add "-A project" as possible input instead of user

[GouZiHui]

Did you run the SLURM scripts successfully? I really confused by it .

[bclaremar]

Yes, the whole workflow works today.
I'm staff at a HPC center and had conversations with a researcher for more than half a year until everything worked.
For each step we found new things.
There were some updates for other tools needed in the later steps as well .

I see that I have modified:

• juicer.sh
• juicer_hiccups.sh
• split_rmdups_sam.awk
• link: juicer_tools.jar -> juicer_tools.jar.v2.13.07

I cannot give support for the tool.
But would you like to see our solutions for our cluster and get inspired to your local changes?

[GouZiHui]

Hi！
Thank you so much for sharing! I would be happy to take a look at your solutions. Feel free to contact me via email at [email protected].
Best regards,
Xiaohui