Attached to the card, thanks Peter.
J.
On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote:
> Hi Jeremy
> No problem - zip file with the two patches is attached, please let me know if
> there's a problem.
> Best wishes
> Peter
>
> On 28/02/13 15:07, Jeremy Goecks wrote:
>> Hmm, I don't see a patc
Hmm, I don't see a patch for your changes to the wrapper script. Can you please
bundle up and send along your tool definition + wrapper script changes and I'll
add it to the card?
Thanks,
J.
On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
> Hi Jeremy - that's awesome, thanks!
>
> One thing:
Hi Jeremy - that's awesome, thanks!
One thing: not sure if I read this right (I'm a Trello newbie) however
it looks like only the patch to the tool XML has was attached to the
card. This change also requires a patch to the python wrapper script
(should have been attached to my earlier message)
Thanks it is working now.
Best wishes,
Alex
On Wed, Feb 27, 2013 at 9:35 AM, Peter Briggs wrote:
> Hello Alexander
>
> I've made some changes to our local copy of the bowtie tool files
> (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing
> bowtie's stderr output and ad
Thanks Peter. I've added your patch to the Trello card tracking incorporation
of community contributions to the Bowtie wrapper:
https://trello.com/c/TdYxdbkm
Best,
J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
> Hello Alexander
>
> I've made some changes to our local copy of the bowtie
Hello Alexander
I've made some changes to our local copy of the bowtie tool files
(bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of
capturing bowtie's stderr output and adding it as an additional history
item (here the statistics in this output is used as input to a local tool).
You can change the bowtie wrapper to save the stderr of the bowtie part.
The command line is (bowtie2_wrapper.py):
cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - -
> %s'
Change it to something like:
cmd = 'bowtie2 %s -x %s %s %s 2> bowtie_stderr_filename | samtools view -
