trouble using sequenceTubeMap in chromium installed on WSL

I am trying to use the SequenceTubeMap repository and when I navigate to localhost:3000 in the browser, I am able to access the app but two red banners displays stating "vg view failed" and "vg chunk failed". In the terminal in which I ran npm run serve, two error messages print out stating:

"vg view exited with code -2"

and

"vg chunk exited with code -2". 
Error from vg chunk -x exampleData/internal/snp1kg-BRCA1.vg.xg -a exampleData/internal/NA12878-BRCA1.sorted.gam -g -c 20 -p 17:1-100 -T -b tmp/tmp-9bfa0550-f939-11ee-a678-9b562b148404/chunk -E tmp/tmp-9bfa0550-f939-11ee-a678-9b562b148404/regions.tsv

I am using a static binary of vg if that's relevant, and I believe I added it to my path variable. Any ideas?

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written 2.3 years ago by ayushm64 •

edit: when I try to upload a vg file some potentially useful information came up in the terminal:

Error executing "vg view": Error: spawn vg ENOENT
returning error: vg view failed
VgExecutionError: vg view failed
    at ChildProcess.<anonymous> (file:///home/ayush/sequenceTubeMap/src/server.mjs:1449:19)
    at ChildProcess.emit (node:events:513:28)
    at ChildProcess._handle.onexit (node:internal/child_process:289:12)
    at onErrorNT (node:internal/child_process:476:16)
    at process.processTicksAndRejections (node:internal/process/task_queues:82:21) {
  status: 500

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written 2.3 years ago by ayushm64 •

1 answer

Error: spawn vg ENOENT means that Node could not find the vg command when it tried to run it. It got back the ENOENT error code from Linux:

   ENOENT No such file or directory (POSIX.1-2001).

          Typically, this error results when a specified pathname
          does not exist, or one of the components in the directory
          prefix of a pathname does not exist, or the specified
          pathname is a dangling symbolic link.

This probably means that vg was not correctly added to the PATH variable.

If vg is correctly added to the PATH:

You will be able to type vg at the prompt and have vg print its help.
If you run echo $PATH, you will see a colon-separated list of directories, and one of those directories will be the directory that contains the vg binary. The path to the vg binary itself should not be on the list, only the path to the directory it is in.

If you edited your shell configuration file (~/.bashrc or similar) to add the directory with vg to the PATH, you will probably need to open a new terminal window for it to take effect. Older terminal windows will not be updated.

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written 2.3 years ago by anovak

This was a very helpful and detailed answer. Thank you so much!

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written 2.3 years ago by ayushm64 •