Hemant,
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
ce6
Hi Colleagues,
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,
Thank you for
Hi Peter,
I can't help you with that, so I'm going to forward this to the
galaxy-user mailing list, galaxy-user@lists.bx.psu.edu, where
presumably someone will know the answer.
Scott
On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge wrote:
>
> Hi, I have configured Galaxy on my desktop and it appe
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
..
..
That means you need to look in [galaxyroot]/tools/stats for
groupin
Hello all,
We have a good news / bad news situation here.
The good news is that people have now been able to unsubscribe without any
problems. That's also the bad news. We don't know if the problem has been
fixed, or if it is merely intermittent. Our system logs indicate that all
unsub emails
Hello Falak,
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
particular tool,
Best,
Jen
Galaxy team
On 4/18/11 7:47 AM, Sher, Fal
Hi Thomas,
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 ins
Take me off this list, please.
- Original Message -
From: Enis Afgan
Date: Monday, April 18, 2011 1:41 pm
Subject: Re: [galaxy-user] database on the cloud
To: "Randall, Thomas (NIH/NIEHS) [C]"
Cc: "galaxy-user@lists.bx.psu.edu"
> Hi Thomas,
> It turns out you discovered a bug in
Hello Falak,
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
Hello Vaibhav,
Genome assembly tools are available in the Galaxy Community Tool Shed.
http://community.g2.bx.psu.edu/
Look under "Browse by category" -> "Assembly".
Tools are donated by our user community and are designed to work on
local installs.
https://bitbucket.org/galaxy/galaxy-central/
Vasu,
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 m
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