Re: [galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-03-23 Thread John Chilton
Hey Peter, Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d) that should make that error more informative. I don't know when that will get

Re: [galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-03-23 Thread Peter Cock
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton jmchil...@gmail.com wrote: Hey Peter, Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)

Re: [galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-03-23 Thread Peter Cock
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output

[galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-01-27 Thread Peter Cock
Hi all, I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails. https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad 2015-01-27 02:13:51 ... Tool