How to install tool-shed behind proxy with authentication ?

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How to install tool-shed behind proxy with authentication ?

Luca Toldo
dear Galaxians,
my server is behind a proxy with user authentication.
Wget and hg work fine however unfortunately when I try to install from the tool shed I get error since the system is using urllib2 that is known not to be compatible with proxy with authentication.

How should one locally install tool-sheds  ?

Is it possible with hg or with wget ?

Looking forward your advice.
Thankyou


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Re: How to install tool-shed behind proxy with authentication ?

nephantes

Hi Luca,

I had a similar issue and I exported proxy url’s in run.sh and toolshed started working. It might be helpful.

run.sh:

#!/bin/sh

cd `dirname $0`
export http_proxy=<a href="http://your_proxy:port">http://your_proxy:port
export ftp_proxy=<a href="http://your_proxy:port">http://your_proxy:port


Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: [hidden email]



On Feb 3, 2014, at 1:07 PM, Luca Toldo <[hidden email]> wrote:

dear Galaxians,
my server is behind a proxy with user authentication.
Wget and hg work fine however unfortunately when I try to install from the tool shed I get error since the system is using urllib2 that is known not to be compatible with proxy with authentication.

How should one locally install tool-sheds  ?

Is it possible with hg or with wget ?

Looking forward your advice.
Thankyou

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Re: How to install tool-shed behind proxy with authentication ?

saketkc
In reply to this post by Luca Toldo
Hi Luca,



On 3 February 2014 18:07, Luca Toldo <[hidden email]> wrote:
> dear Galaxians,
> my server is behind a proxy with user authentication.
> Wget and hg work fine however unfortunately when I try to install from the
> tool shed I get error since the system is using urllib2 that is known not to
> be compatible with proxy with authentication.
>

This was fixed by this PR:
https://bitbucket.org/galaxy/galaxy-central/pull-request/299/add-proxyhandler-to-auto-detect-system/diff

As Alper pointed out, you can export http_proxy to your environment,
to get this working.

Saket

> How should one locally install tool-sheds  ?
>
> Is it possible with hg or with wget ?
>
> Looking forward your advice.
> Thankyou
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: How to install tool-shed behind proxy with authentication ?

Luca Toldo
Thankyou so much Saket and Alper  for your so fast reply !
I confirm, I've modified run.sh as follows:

after the "cd dirname $0" I've added the following 2 lines and then re started the service ... and then from the Admin panel the installation works ! That is great and I would strongly suggest to add it to the FAQ.. for those behind proxy with authentication.

export http_proxy=http://DOMAIN\\SERVICEUSER:[hidden email]:proxyport/
export ftp_proxy=http://DOMAIN\\SERVICEUSER:[hidden email]:proxyport/

in addition to the tool installation, also the GET_DATA works now !!!
That is amazing, congratulation to you all.


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