This is really odd, and definitely not what should be happening. Would
you mind sharing your history with me so I can take a closer look?
While I'm looking into it, you should be able to manually change the
database to ce6 and then run SAM-to-BAM. We have everything needed for
I mapped illumina sequences using Bowtie on Galaxy server, I could not locate
the information, like how many there were total reads and in what percentage
they are mapped with mouse genome etc (samples were from mouse).
Help and suggestions are greatly acknowledged,
I can't help you with that, so I'm going to forward this to the
galaxy-user mailing list, firstname.lastname@example.org, where
presumably someone will know the answer.
On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge peter_ton...@hotmail.com wrote:
Hi, I have configured Galaxy on
To unpack this mystery, you need to follow the chain from
tool_conf.xml (that's what the tool menu is made from) to the actual
tool directory and xml file name - eg:
rerla@rosst61:~/rgalaxy$ grep -i group tool_conf.xml
tool file=stats/grouping.xml /
That means you need to look in
The tools in Text Manipulation, Filter and Sort, and Join, Subtract
and Group are designed to help with this type of file analysis (basic
stats). Please explore and let us know if you need help with any
On 4/18/11 7:47 AM, Sher, Falak
It turns out you discovered a bug in the cloud setup. We're missing a 2bit
file and a respective reference to the file for the extract genomic DNA
tool. We'll update the deployment but in the mean time you can configure the
instance yourself with just a few commands:
# connect to the
Take me off this list, please.
- Original Message -
From: Enis Afgan afg...@gmail.com
Date: Monday, April 18, 2011 1:41 pm
Subject: Re: [galaxy-user] database on the cloud
To: Randall, Thomas (NIH/NIEHS) [C] thomas.rand...@nih.gov
There may be another issue regarding metadata display we would like to
confirm. Would you have time to share a link to your history? Options -
Share or Publish. You can send the link directly to me. Please note
which dataset is the Bowtie result in question, if there are multiple
Genome assembly tools are available in the Galaxy Community Tool Shed.
Look under Browse by category - Assembly.
Tools are donated by our user community and are designed to work on
Please reply to the mailing list as emails to individual Galaxy
developers often get lost, and there are others on the list that might
be able to help you or benefit from this discussion.
Now, to your question: you're using the wrong GFF filtering tool,
which is an easy mistake to
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