Hi Yan,
have a look at the blast2GO wrapper in the toolshed. If you already have
gene-ids you can download the GO in an appropriate format and intersect
with your ids.
Hope that works,
Bjoern
Hi everyone,
I got a list of differentially expressed genes from my RNA-seq data.
Is there a
Hi Bjoern,
Thank you very much for your reply! I am working on one species of oyster and
the gene_ids are created from the transcriptome dataset, which is in our own
defined format. I already have the gene_ids and GO annotation for each gene. I
would like to do the GO enrichment to see which
So I'm trying to install the recently migrated ncbi_blast_plus tool from the
Tool Shed to my local galaxy instance running in EC2 and am getting errors at
the installation step.
After clicking Install to local Galaxy I immediately get: Server Error An
error occurred. See the error logs for
On Mon, Oct 8, 2012 at 8:26 AM, Joel Rosenberg thisisj...@hotmail.com wrote:
So I'm trying to install the recently migrated ncbi_blast_plus tool from the
Tool Shed to my local galaxy instance running in EC2 and am getting errors at
the installation step.
After clicking Install to local
Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are
those tools must be installed in order to work in Galaxy. For example: I am
using Debian machine(Don't have tophat and bowtie installed). Will tophat
and bowtie work in my local galaxy? Thanks
Hi Sachit,
you need to install such tools by yourself, unless you are using some
new tools from the toolshed. For example the ncbi-tools or BWA from the
toolshed are capable of installing all dependency automatically.
In the future the plan is to move all heavy tools to the toolshed with
I don't think you understood my question very well. Tophat and Bowtie are
available by default in Galaxy. Tophat and Bowtie however is not installed
in my operating system. Will it still work in Galaxy?
On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de
I am running Galaxy online, excuting TopHat on a fastq file, something which I
previously have done without problems. This time, my data file is maybe double
the size and does not seem to ever get done (I'm on the fourth day or so).
Previously I have never experienced that this has taken more
Despite clearly all my files and histories, the history is red (using 100%) and
stating 'You are over your disk quota'.
Is there a way to remedy this situation?
Mark
___
The Galaxy User list should be used for the discussion of
Galaxy
Hi, there,
I just got two genome-wide Bisulfite sequences from BGI and start to
analyze the data.
I am trying to use Galaxy; but I find there is no such platform available.
Does anybody know where I can find this kind platform at Galaxy or other
places.
Thanks
David
On Fri, Oct 5, 2012 at
Hi Mark,
Galaxy still lets you reinstate deleted files unless you permanently
delete them. You can do this by hitting Purge Deleted Datasets, which
pops up in the list when you click on the gear icon in your history.
Hope this helps!
Kathy
-Original Message-
From:
Hi Sachit,
Björn answer is correct. The issue is what is a tool. There are what
Galaxy calls tools. Some of which are installed by default and some
of which you can install from the toolshed. There are in many cases
just wrappers to third-party tools that need to be installed and
available in the
Hi David,
please do not hijack a different thread :)
If you are analysing Bisulfite data i would recommend to have a look at
http://www.bioinformatics.babraham.ac.uk/projects/ ... especially at
bismark.
We have written a wrapper for bismark, its still in testing phase but if
you like to try it
Hi Kathy
I have just tried the Purge Deleted Datasets' and refreshed + logged in/out
but still have the 'You are over your disk quota.
Don't suppose you have any other suggestions?
BW
Mark
On 8 Oct 2012, at 16:02, So, Kathy GZ/US wrote:
Hi Mark,
Galaxy still lets you reinstate deleted
Hi Mark,
Did you have deleted data on multiple histories? The purging should have
permanently deleted data on your currently active history. Maybe try
going through your other histories and purging? You can navigate to them
by clicking on the gear icon and selecting Saved Histories.
Kathy
Ah, I'll check with them. Thanks for the user list clarification.
Date: Mon, 8 Oct 2012 09:55:18 +0100
Subject: Re: [galaxy-user] Cannot install ncbi_blast_plus or other tools from
Tool Shed: HTTP 500 error
From: p.j.a.c...@googlemail.com
To: thisisj...@hotmail.com
CC:
Dear Sir or Madam,
I had onpened multiple accounts at Galaxy Main, I did not know that it is
against policy. I noticed this policy when I found that all the accounts are
blocked. Would you please restore the account with email address
jia...@iupui.edumailto:jia...@iupui.edu?
If you are not
Thanks, I'll probably wait until that commit makes its way downstream.
Joel
From: eaf...@emory.edu
Date: Mon, 8 Oct 2012 17:17:02 +1100
Subject: Re: [galaxy-user] galaxyTools volume not given enough time to attach
To: thisisj...@hotmail.com
CC: galaxy-user@lists.bx.psu.edu
Hi Joel, This has
Hi Yan,
If you already have the GO terms, then the summary, counting, and
statistics tools for tab delimited are probably what you are looking
for. Tool groups to look in are:
Text Manipulation - Cut, Compute
Join, Subtract and Group - Group
Statistics
There is also the tool Phenotype
Hi Hiram,
Thanks for contacting us about the issue, I hope I can help to clarify.
Datasets in Galaxy histories exist until a user deletes them.
On 10/5/12 9:57 AM, Hiram Clawson wrote:
Good Morning Galaxy Universe:
What is the data expiration policy at Galaxy for user created
big* files
Hi Mark,
The suggestions Kathy has given are all exactly on target. In addition,
after purging, it may take up to a few hours (but usually less) for the
database to fully update.
If you need help, this wiki has help, including a screencast that walks
through how to check for deleted/purged
Hello Alicia,
There are two tools in the main Galaxy Tool Shed
(http://toolshed.g2.bx.psu.edu/) that would likely be helpful. Read the
input requirements for each to decide which is a better fit. Search for
'deseq' to find them:
deseq_and_sam2counts
deseq_hts
To use these tools, a
Bjoern,
I interested in trying Bismark under Galaxy. Could you please point me
where I can use it.
Thanks
Kanwar
On Mon, Oct 8, 2012 at 8:08 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi David,
please do not hijack a different thread :)
If you are analysing
Hi Kanwar,
I interested in trying Bismark under Galaxy. Could you please point me
where I can use it.
please have a look at the pull request ...
https://bitbucket.org/galaxy/galaxy-central/pull-request/73/bismark-wrapper-issue-626
Cheers,
bjoern
Thanks
Kanwar
On Mon, Oct 8, 2012 at
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