JBrowse2: Revert from pif indexes for paf

[fubar2]

Painful.
The pif index is a GMOD thing - not tabix.
The utility works when tested with planemo/conda but fails with this node-js error using biocontainers so cannot be used. Tried making all the paths local - no difference. Something odd about node-js wanting to call uv_os_get_passwd in the biocontainer. Apparently it happens if a path cannot be found or is RO?

DEBUG:jbrowse:cd /tmp/tmpzefftlib/job_working_directory/000/17/outputs/dataset_1e09fe24-141b-439a-ba4d-e72140449478_files && cp /tmp/tmpzefftlib/files/c/c/5/dataset_cc53e7f1-20f8-44df-9069-dd99d8485e0b.dat ./temppif
DEBUG:jbrowse:cd /tmp/tmpzefftlib/job_working_directory/000/17/outputs/dataset_1e09fe24-141b-439a-ba4d-e72140449478_files && jbrowse make-pif ./temppif --out ./peach-grape-map.paf_10.pif.gz
node:os:359
    throw new ERR_SYSTEM_ERROR(ctx);
          ^

SystemError [ERR_SYSTEM_ERROR]: A system error occurred: uv_os_get_passwd returned ENOENT (no such file or directory)
    at userInfo (node:os:359:11)
    at Config._shell (/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/config/config.js:587:67)
    at Config.load (/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/config/config.js:309:27)
    at async Config.load (/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/config/config.js:167:9)
    at async Object.run (/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/main.js:62:20) {
  code: 'ERR_SYSTEM_ERROR',
  info: {
    errno: -2,
    code: 'ENOENT',
    message: 'no such file or directory',
    syscall: 'uv_os_get_passwd'
  },
  errno: [Getter/Setter],
  syscall: [Getter/Setter]
}

Node.js v22.9.0

[bgruening]

I guess we should try to find out why the container does not work.

https://stackoverflow.com/questions/61961485/a-system-error-occurred-uv-os-get-passwd-returned-enoent-no-such-file-or-direc

Indicates some permission problems. Which is very likely in a container setting.

[fubar2]

@bgruening: yes - likely a file permission error and well beyond my skills.

Meanwhile, synteny tracks do not work right. At least this reverts to working paf and retains the code - just need to set canPif true. Would prefer to merge this while someone figures out the real cause and fixes it.

[fubar2]

@bgruening: Until someone (not me!) figures out the fix, the current JBrowse2 is broken and this PR will fix it by reverting.
Please merge, then when you get the biocontainer/nodejs devils exorcised, I can easily re-enable PIF indexing by flipping a binary canPIF.

[bgruening]

Sorry, not a good week here ...

[fubar2]

Sorry you don't have enough monkeys to make every week a good one - sorry to add to your woes - thanks!