Can not open up another session after using reference genome that was added #4325
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chemist-ian
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the admin-server basically requires that you paste only URLs instead of using the file chooser to open a local file on your computer for the error you are seeing with the CLI, i think you need to update the version of node.js on your computer |
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I've installed jbrowse server and have using the GUI to install the hg38 reference genome through the admin server. Once I close the admin server, and start the main server I can not access use the reference genome and get the above error. The Show Stack Trace gives the following:
Error: file ("hg38.fa") was opened locally from a previous session. To restore it, go to track settings and reopen the file
../../../packages/core/util/io/index.ts:64:13
../../../plugins/sequence/src/BgzipFastaAdapter/BgzipFastaAdapter.ts:12:27
../../../plugins/sequence/src/IndexedFastaAdapter/IndexedFastaAdapter.ts:67:26
../../../plugins/sequence/src/IndexedFastaAdapter/IndexedFastaAdapter.ts:37:34
../../../packages/core/assemblyManager/assembly.ts:508:18
../../../packages/core/assemblyManager/assembly.ts:392:15
JBrowse 2.10.3
I've tried to set a default session but that doesn't allow me to reload the reference genome unless I delete it and re-add it in the admin server.
I've tried to also the reference through the jbrowse add-assembly hg38.fa --load copy --out /var/www/html/jbrowse but get a terminal error:
/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/command.js:45
delete this.baseFlags?.json;
^
SyntaxError: Unexpected token '.'
at wrapSafe (internal/modules/cjs/loader.js:915:16)
at Module._compile (internal/modules/cjs/loader.js:963:27)
at Object.Module._extensions..js (internal/modules/cjs/loader.js:1027:10)
at Module.load (internal/modules/cjs/loader.js:863:32)
at Function.Module._load (internal/modules/cjs/loader.js:708:14)
at Module.require (internal/modules/cjs/loader.js:887:19)
at require (internal/modules/cjs/helpers.js:74:18)
at Object. (/usr/local/lib/node_modules/@jbrowse/cli/node_modules/@oclif/core/lib/index.js:4:19)
at Module._compile (internal/modules/cjs/loader.js:999:30)
at Object.Module._extensions..js (internal/modules/cjs/loader.js:1027:10)
So I've defaulted to using only the GUI version. Any assistance would be great, as of right now the web version is less useful than a local version.
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