On Tue, Oct 1, 2013 at 2:52 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Peter, dear John, dear all
Thanks very much. This is exactly what I need and the code changes
proposed work perfectly as they are. At a short glance even the
validators work as intended.
Now for the optional
Agreed Peter, this is essential functionality. Trello card created.
https://trello.com/c/J7aqer08
Thanks!
-John
On Fri, Oct 4, 2013 at 5:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Oct 1, 2013 at 2:52 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Peter, dear John, dear
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
with easily dozens of bam files.
Using the repeat in this case requires quite a bit of clicking. Is
there a more conventient way fo doing
On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
with easily dozens of bam files.
Using the repeat in this case
Thanks Peter,
Yeah, looking over unified_genotyper.xml, you would probably just
want to replace:
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam.input_bam} ${input_bam.input_bam.ext}
gatk_input_${i}
#if str(
Hi Ulf,
What I do:
1. make a history, doing the steps you want to do on one input file
2. create a workflow of that history
3. assemble all input files in one history
4. run the workflow and select the multiple input files to run the
workflow on.
5. Optionally: send the results to a new
Sorry, my answer doesn't fit your question. :-)
J
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote:
Hi Ulf,
What I do:
1. make a history, doing the steps you want to do on one input file
2. create a workflow of
Dear Peter, dear John, dear all
Thanks very much. This is exactly what I need and the code changes
proposed work perfectly as they are. At a short glance even the
validators work as intended.
Now for the optional special bonus:
Is there a way to define the size of the boxes? The ones I see
