Re: [galaxy-dev] RE : Error with get data function

2014-04-29 Thread Martin Čech
Hi Noémie, the special characters are probably in the file path, so some of your folders, or your file name or your computer user name may contain these and when our server gets that path he does not like it and throws an error. Like I said, it is a problem on our side but you can get around it

[galaxy-dev] Get the user credentials from the tool.

2014-04-29 Thread Dmitry
Hello, Is there any way to provide a protected resource link to the external application? My tool is supposed to call a Web service via SSL which should access to the Galaxy resources. In ideal it would be something like ftp://user:passw...@mygalaxy.net/fasta.gz The Web service then

Re: [galaxy-dev] Galaxy Error Message

2014-04-29 Thread Daniel Blankenberg
Hi Bradley, For your inputs, don’t use periods (‘.’) within the param names. Thanks for using Galaxy, Dan On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf2...@gmail.com wrote: The XML file is: tool id=pathview name=pathview version=1.0 description Pathview is a tool set for

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Saket Choudhary
Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’:

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Björn Grüning
Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this?

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

2014-04-29 Thread Björn Grüning
Hi, I updated the test and the tool shed accordingly to Dave suggestion. I'm just wondering, the TS tests were passing with the old version, anything I should worry about? :) Thanks and sorry for the inconvenience! Bjoern Am 29.04.2014 16:07, schrieb Peter Cock: On Tue, Apr 29, 2014 at

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Saket Choudhary
Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py install The documentation mentions the following options: PycURL Unix options: --curl-config=/path/to/curl-config use specified curl-config binary

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Greg Von Kuster
Hello Saket, I'm not a system-level expert, so please ignore my attempt at helping if it is incorrect. Your recipe for installing and compiling pycurl may be assuming that certain dependencies exist in the Galaxy environment into which it is being installed for testing, but they do not.