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
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=http://your_proxy:port export ftp_proxy=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: alper@kucukural.com
On Feb 3, 2014, at 1:07 PM, Luca Toldo lucatoldo@gmail.com 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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Hi Luca,
On 3 February 2014 18:07, Luca Toldo lucatoldo@gmail.com 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-proxyhandle...
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/
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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%5C%5CSERVICEUSER:PASSWORD@myproxy.mydomain.de: proxyport/ export ftp_proxy=http://DOMAIN%5C%5CSERVICEUSER:PASSWORD@myproxy.mydomain.de: proxyport/
in addition to the tool installation, also the GET_DATA works now !!! That is amazing, congratulation to you all.
galaxy-dev@lists.galaxyproject.org
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Alper Kucukural -
Luca Toldo -
Saket Choudhary