Error on pip galaxy-upload

1

Hi, I’m trying to upload a large .bam file to my galaxy account using galaxy upload. I did those steps but still getting errors that I’m not able to fix. Please help!
$ pip install galaxy-upload
$ python3 -m venv ~/galaxy-upload
$ . ~/galaxy-upload/bin/activate
$ pip install galaxy-upload
(galaxy-upload) (base) TS261@PHS024050 outs % galaxy-upload --url https://usegalaxy.org \ –api-key cae08ba0d4323e26716c58de5cb3c4 --history-name ‘RNA’ -i \ –file-name possorted_genome_bam.bam

Usage: galaxy-upload [OPTIONS] [PATH]…

Try ‘galaxy-upload --help’ for help.

Error: Missing option ‘–api-key’.

2

I dont see a pip error so I think your question is not correctly formulated.
It looks like galaxy-upload is installed but your command is not correct.
Based on your command it should be something like:

galaxy-upload --url https://usegalaxy.org --api-key cae08ba0d4323e26716c58de5cb3c4 --history-name 'RNA' possorted_genome_bam.bam

You have –api-key instead of --api-key

3

Hi, Thank you for your reply!
I fixed the command but still getting the error and not able to upload the bam file to my galaxy account. Do you have any suggestions? I’m not sure what I’m doing wrong. This is what I’m getting:
(galaxy-upload) (base) TS261@PHS024050 ~ % galaxy-upload --url https://usegalaxy.org \
–api-key bfdf58ba226efa18da654f47224b2e4c --history-name ‘RNA’ -i \ –file-name possorted_genome_bam.bam
Usage: galaxy-upload [OPTIONS] [PATH]…

Try ‘galaxy-upload --help’ for help.

Error: Missing option ‘–api-key’.

4

You are showing the same command as your orignal question. Besides the api key the use of --file-name is also not correct. Look at this galaxy-upload — galaxy-upload 1.0.0 documentation

You could also try to upload your file with galaxy itself on the webinterface.

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