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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
318 stars 120 forks source link

Grabix dependency uses git protocol #142

Closed heuermh closed 11 years ago

heuermh commented 11 years ago

I didn't notice until after gemini_install.py was running that one of the dependencies used the git protocol instead of https, which is a problem here since git is blocked by our firewall.

[localhost] local: git clone git://github.com/arq5x/grabix.git
Cloning into 'grabix'...
fatal: unable to connect to github.com:
github.com[0: 204.232.175.90]: errno=Connection refused

Fatal error: local() encountered an error (return code 128) while executing 'git clone git://github.com/arq5x/grabix.git'

Aborting.
Traceback (most recent call last):
  File "gemini_install.py", line 191, in <module>
    main(parser.parse_args())
  File "gemini_install.py", line 46, in main
    install_tools(gemini["fab"], cbl["tool_fabfile"], fabricrc)
...
heuermh commented 11 years ago

Looks like the declaration is here

https://github.com/chapmanb/cloudbiolinux/blob/f45a0360f0c0ced238135eab6c22afc7d7452484/cloudbio/custom/bio_nextgen.py#L550

so I'll create a pull request in chapmanb/cloudbiolinux.

chapmanb commented 11 years ago

Merged and fixed. Feel free to close

arq5x commented 11 years ago

@heuermh I am closing this, but please reopen if you have any more issues. Thanks for reporting this!

heuermh commented 11 years ago

Thank you, Brad, Aaron.