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
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
Could you add PyX and
to the eggs? They would be very useful for creating reports.
Ilya Chorny Ph.D.
Bioinformatics Scientist I
9885 Towne Centre Drive
San Diego, CA 92121
This is a good question for the development community to provide
feedback on, so I'll cross-post your question over to that list.
On 9/19/11 2:30 PM, Roman Valls wrote:
Today I was routinely adding a 27GB Illumina lane on my galaxy instance
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
It looks like urllib, which Galaxy uses to fetch eggs, can't use
authenticated proxies. urllib2 would do it:
But this would require some changes to the egg handling
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:
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?
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