add-assembly translates absolute path to (wrong) relative path

[heavywatal]

jbrowse add-assembly modifies a given absolute path to a relative path, which is wrong if --target= is used.

mkdir target
echo "{}" > target/config.json
touch /tmp/my.fa.gz
npx jbrowse add-assembly -f --target=target --type=indexedFasta --load=symlink /tmp/my.fa.gz
ls -1 target/
# config.json
# my.fa.gz@ ⇒ ../../../../tmp/my.fa.gz
# my.fa.gz.fai@ ⇒ ../../../../tmp/my.fa.gz.fai

Symlinks are calculated for $PWD of command execution, not for the files in target/.

Expected behavior

1. Absolute paths should be kept as they are passed. jbrowse add-track works as expected because it keeps given absolute paths unchanged.
2. If relative paths are mandatory for some reasons, it should at least calculate relative paths correctly.

Screenshots

The command lines above should explain.

Version:

@jbrowse/cli/1.5.9 darwin-x64 node-v16.13.2

Additional context

Thank you for your great software and hard work.

[cmdcolin]

thanks for pointing this out, we do indeed convert some things to relative paths and so this is likely a bug for symlink handling.

possible fix here #2686

[heavywatal]

Thank you for the quick response! And sorry I forgot to report that it matters when --load=inPlace as well.

[cmdcolin]

good catch, thanks. I believe inPlace should be fixed now too, released as @jbrowse/cli 1.6.4