bcbio not found

[nbisweden]

bcbio not found

[CristianRiccio]

Hurray, everything worked this time. I got to the EMBLmyGFF3 help page. So maybe the problem was due to a slow connection. Thanks for your help.

[Juke34]

Could copy past the result of this command please ?
pip --version

[CristianRiccio]

pip --version
pip 9.0.3 from /Users/user/anaconda/envs/python2env/lib/python2.7/site-packages (python 2.7)

[Juke34]

I'm wondering if the pip version could be the problem. I was using the 9.0.1. I just updated to 10.0.1 and bcbio-gff==0.6.4 is still listed.
Try to install it by yourself with that command:
pip install bcbio-gff==0.6.4

If it doesn't work do:
pip info bcbio-gff==0.6.4 to check if pip knows something about the package

otherwise update pip:
pip install --upgrade pip

[CristianRiccio]

pip install bcbio-gff==0.6.4 gives

Collecting bcbio-gff==0.6.4 Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/bcbio-gff/ Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/bcbio-gff/ Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/bcbio-gff/ Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/bcbio-gff/ Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/bcbio-gff/ Could not find a version that satisfies the requirement bcbio-gff==0.6.4 (from versions: ) No matching distribution found for bcbio-gff==0.6.4

pip info bcbio-gff==0.6.4
gives
ERROR: unknown command "info"

and

pip install --upgrade pip gives
Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/pip/ Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/pip/ Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/pip/ Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/pip/ Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', error(54, 'Connection reset by peer'))': /simple/pip/ Requirement already up-to-date: pip in /Users/user/anaconda/envs/python2env/lib/python2.7/site-packages

[Juke34]

It looks like you re using a proxy and pip is unable to access data registry on the web.
Could you check you connexion and try without any proxy ?

[CristianRiccio]

I am not sure what a proxy but I am not connected through any VPN. I am on a wifi network.

[CristianRiccio]

Do you think installing it as described here would work:

https://github.com/bcbio/bcbio-nextgen

?

[Juke34]

Yes sure, but pip is made to make your life easier. So if you cannot use pip it's really a problem.

[Juke34]

I guess the easier is just to use another internet access.

[Juke34]

Maybe you have installed pip through conda. In that case try to upgrade it like that:
conda upgrade pip

[Juke34]

Please, let us know if you have succeeded to solve your problem.

[CristianRiccio]

I will let you know. I go back to a high-speed internet tomorrow. I'll see if that helps.