Thanks.
I tried both File1 and 2 of SRR618542. Here's one of the links:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR618/SRR618542/SRR618542_1.fastq.gz
On Oct 14, 2013, at 8:01 PM, Vipin TS wrote:
>
> - bowtie2 does not show any built-in reference genomes
>
>
> by default Cloudman didn't ship the ge
> - bowtie2 does not show any built-in reference genomes
>
>
by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use
its own index set.
Usage: bowtie2-build [option] genome.fa index_basename
and add the entries in "bowtie2_indices.loc". Please make sure that the fields
are tab de
Thanks for the quick answer. Could access bowtie2 from command line without a
problem. Found that I had to include a line pointing to the wrapper in
tool_conf.xml. It wasn't there by default.
Now two new problems:
- bowtie2 does not show any built-in reference genomes
- when I try to import a
Hi
Stanislas,
Please check the PATH variable and make sure that you can access bowtie2
from command line and then restart the Galaxy service through cloudman
interface. I think that should work.
Vipin
>
> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
> distribution (
Dear all,
I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
distribution (ami-118bfc78). The instatiated Galaxy however does not contain
Bowtie2 and Tophat2, even after updating through the Cloudman Admin section.
Although the wrappers are there in the tools directory, w
