Re: [galaxy-dev] GATK unified genotyper

2011-09-29 Thread Daniel Blankenberg
Hi Ilya, Something similar to this is planned, but directly referencing location files is being deprecated in favor of using the tool_data_tables mechanism. The validator implementation does not yet support data tables, but will be enhanced in the future. Additionally, the selection

[galaxy-dev] 2 questions about Galaxy's functional testing support

2011-09-29 Thread Paniagua, Eric
Hi all, I've read the Wiki page on Writing Functional Tests (http://wiki.g2.bx.psu.edu/Admin/Tools/Writing%20Tests) and I've been looking through test/base and test/functional and I am left with two questions: * Is it possible to write a test to validate metadata directly on an

[galaxy-dev] Additional eggs

2011-09-29 Thread Chorny, Ilya
Could you add PyX and Matplotlib(http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0.1/) to the eggs? They would be very useful for creating reports. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121

Re: [galaxy-dev] [galaxy-user] Add library to dataset performance metric: developer vs production instances

2011-09-29 Thread Jennifer Jackson
Hi Roman, This is a good question for the development community to provide feedback on, so I'll cross-post your question over to that list. Best, Jen Galaxy team On 9/19/11 2:30 PM, Roman Valls wrote: Hello, Today I was routinely adding a 27GB Illumina lane on my galaxy instance running

Re: [galaxy-dev] [galaxy-user] Add library to dataset performance metric: developer vs production instances

2011-09-29 Thread Duddy, John
We routinely put large compressed fastq files into data libraries by that method (linking, no copy) and it is very fast, since the patch that stopped it decompressing the files. You should probably make sure you specify the file format (fastqsanger) so Galaxy does not attempt to sniff the file

Re: [galaxy-dev] Setting http_proxy for Python

2011-09-29 Thread Nate Coraor
Hi Matloob, It looks like urllib, which Galaxy uses to fetch eggs, can't use authenticated proxies. urllib2 would do it: http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-proxy-for-a-python-http-connection But this would require some changes to the egg handling

[galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable

2011-09-29 Thread Haden, Kirt
Hi, When I run Galaxy under Python 2.7, I am unable to run SAM to BAM tools without getting the following error (below). The same configuration with Python 2.6 does not have an issue. The error seems to indicate bx_python eggs are not fetchable. What am I doing wrong? Error report below:

[galaxy-dev] FW: Galaxy tool error report from kha...@illumina.com

2011-09-29 Thread Haden, Kirt
Galaxy team, I am running a locally configured Galaxy instance using Python 2.7. I am getting an error on SAM_to_BAM unable to fetch eggs. When I change back to Python 2.6, the problem is removed and I can run the tool. Is there a quick fix for this problem? Thanks, Kirt

[galaxy-dev] bug report

2011-09-29 Thread KOH Jia Yu Jayce
Hi I'd like to enquire about the bug report. Apparently when someone sends a bug report, everyone in the mailing list and the sender himself are supposed to receive the bug report (as can be seen in the to field in the email sent out). However in our case the sender never receives the bug