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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
62 stars 8 forks source link

Unable to access jarfile umicollapse.jar when running from another directory #24

Closed divibisan closed 9 months ago

divibisan commented 1 year ago

It's possible this is an issue with my setup, but whenever I try to run UMICollapse from any directory than the one it's installed in (I've added the UMICollapse directory to my PATH), I get the following error Error: Unable to access jarfile umicollapse.jar. I do not get this error if I cd into the UMICollapse directory and call it from there, or if I edit umicollapse to give the full, absolute path to umicollapse.jar in the -jar argument.

I'm using openjdk version "11.0.19" 2023-04-18 LTS on an EC2 instance running Amazon Linux. I've gotten the same issue when UMICollapse was installed on the same EBS as the data (in my home folder) and with it installed on a mounted EFS.

I can deal with this issue, but it makes it more difficult to incorporate into my pipeline. Thanks!

Daniel-Liu-c0deb0t commented 1 year ago

Yup the umicollapse script looks for the jar file locally. You should just edit the script and insert the absolute path to work around this issue. Alternatively, you could make the path relative to the script location: https://stackoverflow.com/a/24112741