Re: [galaxy-user] Extract genomic DNA

2011-12-14 Thread Jeremy Goecks 
Rebecca,

You should be able to use a custom genome with this tool by selecting "History" 
from the "Source for Genomic Data" parameter.

The bug you're describing has, to the best of my knowledge, been fixed in 
Galaxy and should not be present anymore. On which Galaxy instance are you 
seeing this issue? If this is not the main Galaxy server ( 
http://main.g2.bx.psu.edu/ ), you'll want to contact the maintainers of the 
instance that you're using and ask them to update the instance.

Best,
J.

On Dec 14, 2011, at 1:31 PM, Rebecca C Mueller wrote:

> Hi all,
> Does anyone know if you can use the "Extract Genomic DNA" command with a 
> genome not in the database? I am working with an algal genome (C. merolae) 
> that isn't currently in the pulldown Database/Build menu. I keep getting the 
> "Unspecified genome build" error, and am assuming that's the problem, as my 
> other files appear to be formatted correctly (tab delimited without spaces 
> for the intervals, same names for chromosomes in interval and fasta file, 
> etc).
> Thanks!
> Rebecca
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
> http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
> http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] Looking for Galaxy related papers (or have written one)? There is a new Galaxy Group @ CiteULike

2011-12-14 Thread Dave Clements 
Hello all,

A new Galaxy Group
has been
created at the
CiteULike  social bookmarking service to organize
papers that are about, use, or reference Galaxy. The Galaxy
Groupis open
to any CiteULike user (and anyone can become a CiteULike user).
Group members can add papers to the group, assign tags, and rate papers.

CiteULike makes extensive use of *tags* to organize and categorize papers.
The Galaxy group uses this set of
tagsto categorize
papers.  If you want to help other Galaxy users and sites
find papers that are relevant to them, or help the Galaxy Project keep
track of what papers (and communities) are using Gaalxy, then please help
by adding relevant papers to the Galaxy Group
Libraryand/or
rating and tagging the papers that are there.
*We particularly need help with papers that were published before this
year, as very few of them are in the initial list. *
Links:
  http:/galaxyproject.org/wiki/CiteULike - Explanation of tags
  http://www.citeulike.org/group/16008/order/group_rating - Galaxy Group
list of papers

Thanks,

Dave Clements

PS: To cite the Galaxy Project, see
http://galaxyproject.org/wiki/Citing%20Galaxy.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] Extract genomic DNA

2011-12-14 Thread Rebecca C Mueller 

Hi all,
Does anyone know if you can use the "Extract Genomic DNA" command with 
a genome not in the database? I am working with an algal genome (C. 
merolae) that isn't currently in the pulldown Database/Build menu. I 
keep getting the "Unspecified genome build" error, and am assuming 
that's the problem, as my other files appear to be formatted correctly 
(tab delimited without spaces for the intervals, same names for 
chromosomes in interval and fasta file, etc).

Thanks!
Rebecca
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

[galaxy-user] Tophat jobs not starting

2011-12-14 Thread Magdalena Strzelecka 

Hi,

I have submitted some jobs to Tophat, but they have not started since  
yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have re- 
submitted everything again (2 jobs), but the same situation is  
happening. Is there some issue with Tophat at the moment?

Thanks.
M.

--
Magdalena Strzelecka, PhD

Heald Lab
University of California, Berkeley
Department of Molecular & Cell Biology
315 Life Sciences Addition # 3200
Berkeley, CA 94720-3200

phone: (510) 643-5002
fax: (510) 643-6791
e-mail: strzele...@berkeley.edu















___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Lastz very slow

2011-12-14 Thread Bob Harris 

Howdy, Andrew,

One possibility is that there are more jobs on the cluster.  I'm not  
familiar enough with the galaxy interface to know if there's an easy  
way to tell how much time the job sits on the cluster's queue waiting  
and how much time the job is actually running.


Assuming there's no cluster difference, are the data conditions  
similar between what you are mapping now vs two weeks ago?  I.e.  
number and length of reads, size of reference sequence, divergence,  
repeat content?


Bob H


On Dec 14, 2011, at 10:10 AM, Andrew South wrote:

Hi - is there a reason Lastz is very slow right now? I am mapping  
2-3,000, reads against a single, 11Kb, sequence and find that jobs  
are either returning an error or taking 16-24hrs to get done. This  
time frame was more like 30 minutes two weeks ago. Is there a way to  
speed this up? Thanks in advance for any help. Andy




Please consider the environment. Do you really need to print this  
email?


The University of Dundee is a registered Scottish charity, No:  
SC015096


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] Lastz very slow

2011-12-14 Thread Andrew South 
Hi - is there a reason Lastz is very slow right now? I am mapping 2-3,000, 
reads against a single, 11Kb, sequence and find that jobs are either returning 
an error or taking 16-24hrs to get done. This time frame was more like 30 
minutes two weeks ago. Is there a way to speed this up? Thanks in advance for 
any help. Andy
 
 
 
Please consider the environment. Do you really need to print this email? 

The University of Dundee is a registered Scottish charity, No: SC015096
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] abolut ftp setup

2011-12-14 Thread Richard Liao 
Dear all,
I'm a student at Fudan University in China. I was trying to enable ftp
uploading in my local version of GALAXY.
I tried the setting in
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the
following problems:
1. The galaxyftp seems to be a pasql database, shall I build it myself? or
does it already exists in galaxy directory?
2. the galaxy_user seems to be a table, shall I build it myself? and how
shall I update it and integrate it with galaxy?

Thanks for your attention, and looking forward to your reply!

Best wishes

Liao Ruiqi
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] GI error/shift in the output of megablast ?

2011-12-14 Thread Sandrine Hughes 
Dear all,

I have a trouble with the Megablast program available in NGS Mapping
and I hope that you can help. Indeed, I think that there might be a
problem with the table given in output, and notably a shift between
the GI numbers and the parameters associated.

Here are the details:

I. First, what I have done :
   I used the program to identify the species that I have in a mix of
sequences by using the following options:
   Database nt 27-Jun-2011
   Word size 16
   Identity 90.0
   Cutoff 0.001
   Filter out low complexity regions Yes
   I run the analyses twice and obtained exactly the same results (I
used the online version of Galaxy, not a local one).

II. Second, I analysed the data obtained for one of my sequence
(1-202). The following lines are the beginning of the table that I
obtained after the megablast and two lines with troubles:

 1-202   312182292   484 99.33   150 1   0   1 150
1   150 2e-75   289.0
 1-202   312182201   476 99.33   150 1   0   1 150
1   150 2e-75   289.0
 1-202   308228725   928 99.33   150 1   0   1 150
19  168 2e-75   289.0
 1-202   308228711   938 99.33   150 1   0   1 150
22  171 2e-75   289.0
 1-202   308197083   459 99.33   150 1   0   1 150
10  159 2e-75   289.0
 1-202   300392378   920 99.33   150 1   0   1 150
10  159 2e-75   289.0
 1-202   300392376   918 99.33   150 1   0   1 150
9   158 2e-75   289.0
 1-202   300392375   922 99.33   150 1   0   1 150
11  160 2e-75   289.0
 1-202   300392374   931 99.33   150 1   0   1 150
21  170 2e-75   289.0
 1-202   300392373   909 99.33   150 1   0   1 150
21  170 2e-75   289.0
 1-202   300392371   117299.33   150 1   0   1 150
9   158 2e-75   289.0
...
1-202   179366399   151762  98.67   150 2   0   1 150
   46880   47029   6e-73   281.0
1-202   58617849511 98.67   150 2   0   1 150
   21  170 6e-73   281.0


III. Third, what I’ve noticed:
   My first problem was that among all the species identified, two
were very different from the expected ones (2 last lines). So I
decided to search if that could be possible for this sequence and
performed independently a megablast on the NCBI with similar options.
I was not able to find these two species in the results.
   So, I decided to check the hits identified in the table above and
identified a second problem. In the table, the second column give the
GI of the database hit and the third column give the length of the
database hit. However, when I manually checked in NCBI the length of
the GI, this one was incorrect. Indeed, for the GI 312182292, the
length should be 580 and not 484.
   By checking different lines, I noticed that the length that is
given for a GI corresponds to the length of the GI-1. As you can see
in the above table, some GI are consecutive (300392376,
300392375,...). When checking the length of 300392376 in NCBI, I
should have 920. But when I checked 300392375, I found 918. And this
was true for the following lines : 300392374 give normally 922 and
300392373 give 931... My conclusion at that point was that there is a
shift of –1 between the GI and the other parameters of the line
(indeed the parameters for the remaining columns are in agreement with
the length of the GI-1). However, that’s not always true For some
GI given in the table (for example, the two last lines), if we check
the parameters of the GI-1, the parameters are completely different...
So, I suppose that there is a problem in the GI sorting during the
megablast but I’m not able to clearly define the problem.

IV. Fourth, confirmed with an other dataset
   In order to be sure that the problem was not linked to my data or
my process, I asked a colleague to do a megablast on independent data.
The  conclusions were similar to mine : a shift in the GI given in the
table and the parameters associated on the same line, that most of the
time but not always, correspond to GI-1.

Can you confirm that there is a problem with the output of the
megablast available in Galaxy ? If yes, do you think there is a way to
fix it ?

Thanks a lot,

Sandrine

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.