Hi James,
On 2 March 2011 19:44, James Taylor wrote:
> Hi Leon,
>
> Thanks for sharing this with the community!
>
> As far as similar activities, we are actively working on a solution for
> packaging and deploying tools. Enis can share more about that, it is what we
> use already to automaticall
Hi,
I've downloaded the Suite of Velvet assembler tools at
http://community.g2.bx.psu.edu/
and installed them as detailed in
http://gmod.827538.n3.nabble.com/attachment/868065/0/README?by-user=t
I've then run velveth in Galaxy using two files - a file each of corresponding
left and right paired-
This would be great. The 'tool dependency injection' part of Galaxy is
designed so any directory having this structure will work, and you can
have as many as you want and they will be searched in order.
On Mar 4, 2011, at 3:21 AM, David van Enckevort wrote:
The repository with the latest ver
Hi Glen,
Sorry for the delay in response.
> And how do I limit selections in an input drop down to just my specific file
> type? I'm guessing I need to extend the Tabular class, but I don't need to
> add any additional functionality at this point, I just want to limit how the
> tools can be c
Hi
When running bowtie on the command line I was able to use more than
one fastq file as input simply by listing them separated by a comma eg:
bowtie -p 3 -q -m 2 --best --strata --sam --chunkmb 256 /databank/
indices/bowtie/hg18/hg18 input1.fastq,input2.fastq output.sam
How can I do this
Dear Sir/Madam,
I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq
file into galaxy, but failed. Below is the error message.
OverflowError: signed integer is greater than maximum
How could I upload large data files into galaxy and process the data?
Any information fr
Nicki,
You are right that Galaxy's Bowtie only allows one input fastq. You
would have to combine your multiple input files into one before
running it in Galaxy. You can do this with the Concatenate datasets
tool (under Text Manipulation).
Let us know if you have any further questions.
Re
On Fri, Mar 04, 2011 at 04:28:20PM +, Yanji Xu wrote:
> Dear Sir/Madam,
>
> I installed galaxy in my local server, then I tried to upload a 4.7 Gb
> fastq file into galaxy, but failed. Below is the error message.
>
> OverflowError: signed integer is greater than maximum
>
> How could I uplo
Hi David,
Apologies for the late reply, but were trying to get you a complete
answer, but it is not ready. Meanwhile, perhaps this will help.
So, for phastCons:
Needs to be converted to binned array files using
wiggle_to_binned_array.py from bx-python.
The loc file points to a base directo
