Hi Greg,
On Mon, Nov 18, 2013 at 4:02 PM, Greg Von Kuster wrote:
> On Nov 18, 2013, at 10:33 AM, Peter Cock wrote:
>> On a closely related point, I understand Galaxy likes to store all
>> BAM files co-ordinate sorted and indexed - when a tool produces
>> a BAM file where does this happen? i.e. I
Hi Peter,
On Nov 18, 2013, at 10:33 AM, Peter Cock wrote:
> On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier wrote:
>> Peter,
>>
>> It turns out there were two problems. First, the test environment was not
>> resolving the upload tool's dependency on samtools, which I've now
>> corrected.
>
> Ex
On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier wrote:
> Peter,
>
> It turns out there were two problems. First, the test environment was not
> resolving the upload tool's dependency on samtools, which I've now
> corrected.
Excellent.
On a closely related point, I understand Galaxy likes to store
Peter,
It turns out there were two problems. First, the test environment was
not resolving the upload tool's dependency on samtools, which I've now
corrected. Second, the bam file detection on upload was broken due to
the bug in python 2.7.4's gzip module, which I've also corrected.
I have r
Hi Peter,
On Nov 14, 2013, at 11:27 AM, Peter Cock wrote:
> On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster wrote:
>> Hello Peter,
>>
>> Yesterday we discovered what Björn has communicated and added it to the
>> Trello card for this issue:
>>
>> https://trello.com/c/sN2iLCCn/99-bug-in-inst
On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> Yesterday we discovered what Björn has communicated and added it to the
> Trello card for this issue:
>
> https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
>
> ...
>
> becomes the following in your renam
Hello Peter,
Yesterday we discovered what Björn has communicated and added it to the Trello
card for this issue:
https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
It also seems that your tool is attempting to use samtools. Tgis is in your
config:
samtools
On Wed, Nov 13, 2013 at 10:43 AM, Björn Grüning
wrote:
> Hi Peter,
>
> sorry for coming late to this thread.
>
> I may be wrong, but you are only specifying a repository_dependecies.xml
> file. You probably only need to rename it to tool_dependencies.xml file,
> otherwise the tool can not import i
Hi Peter,
sorry for coming late to this thread.
I may be wrong, but you are only specifying a repository_dependecies.xml
file. You probably only need to rename it to tool_dependencies.xml file,
otherwise the tool can not import it. I guess the env.sh file is not
created if no tool_dependencies.xm
On Tue, Nov 12, 2013 at 2:37 PM, John Chilton wrote:
> This sounds a lot like this;
> http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
>
> When using the local job runner (as the test framework likely does), I
> believe samtools needs to be on Galaxy's path. I
This sounds a lot like this;
http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
When using the local job runner (as the test framework likely does), I
believe samtools needs to be on Galaxy's path. I don't think it is
enough to just have it available as a "tool
Hello Peter,
Thanks for reporting this - I've added the following Trello card for this issue.
https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
Greg Von Kuster
On Nov 12, 2013, at 7:07 AM, Peter Cock wrote:
> Hi guys,
>
> I have a new wrapper for samtools idxstats with a w
Hi guys,
I have a new wrapper for samtools idxstats with a working
unit test via run_functional_tests.sh run locally or on TravisCI:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html
However, this tool
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