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biocommons / biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences
Apache License 2.0
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OSError: Unable to open SeqRepo directory /projects00/tmp/usr/hgvs/bin/seqrepo/latest #72

Closed ypchan closed 4 years ago

ypchan commented 4 years ago

bash code and error

` SEQREPO_ROOT=/projects00/tmp/usr/hgvs/bin/seqrepo

mkdir $SEQREPO_ROOT

seqrepo --root-directory $SEQREPO_ROOT init

seqrepo --root-directory $SEQREPO_ROOT load --namespace dog Can.fna

seqrepo --root-directory $SEQREPO_ROOT show-status

Traceback (most recent call last): File "/psd/biosoft/anaconda/envs/Python-3.7/bin/seqrepo", line 10, in sys.exit(main()) File "/psd/biosoft/anaconda/envs/Python-3.7/lib/python3.7/site-packages/biocommons/seqrepo/cli.py", line 545, in main opts.func(opts) File "/psd/biosoft/anaconda/envs/Python-3.7/lib/python3.7/site-packages/biocommons/seqrepo/cli.py", line 420, in show_status sr = SeqRepo(seqrepo_dir) File "/psd/biosoft/anaconda/envs/Python-3.7/lib/python3.7/site-packages/biocommons/seqrepo/seqrepo.py", line 56, in init raise OSError("Unable to open SeqRepo directory {}".format(self._root_dir)) OSError: Unable to open SeqRepo directory /projects00/tmp/usr/hgvs/bin/seqrepo/latest `

Hello, sir, when I used seqrepo to build a local seqrepo, a OSError error happened. Although I fixed the problem by doing this:

`#ap.add_argument("--instance-name", "-i", default=DEFAULT_INSTANCE_NAME_RO, help="instance name")

modifed the default

ap.add_argument("--instance-name", "-i", default=DEFAULT_INSTANCE_NAME_RW, help="instance name")

` I hope you fix this error in future change. Anyway， thank you for your great program.

reece commented 4 years ago

This command is working as intended, although I agree that the RO/RW split across subcommands is very confusing.

The interface is likely to change in the next several months in order to accommodate new features. The issue you raise provides additional incentive to do that soon. Thanks!