Help with Summary Statistics
by D. A. Cowart
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
8 years, 8 months
SNP finding
by Xiefan Fang
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.
Thanks,
Xiefan
University of Florida
9 years, 2 months
posting supplementary information on galaxy server
by Jainy Tharun
Hello,
I would like to know whether I can post my supplementary data for an article in the galaxy server.
I have .docx files and .xlsx files. I am planning to upload these data in a folder and share the link at first and later publish it. When I tried uploading xlsx file, it is getting automatically converted to .xml files.
Please let me know if it is possible provide the supplementary information through galaxy that includes doc and excel sheets..
Thank you so much for your help
Jainy
9 years, 3 months
queue rules for multi-step workflows
by zuzmus
Dear Galaxy managers,
I would like to ask about the queuing rules for the workflows before
processed on the server?
I use my customized Galaxy workflow which contains 22 following steps
(basically, filtering, trimming and format change of NGS data). I guess the
server is generally very busy during last weeks/months (?), so my job was
waiting about 24 hours in a queue (which would not be a problem), and then
the first step of the workflow was processed, but the following 21 is
again/still waiting (already for another couple of hours...). It makes me
wondering about the queuing rules because I expected that the whole
workflow is queued as one job.. Then my question is if the whole workflow,
once submitted, is listed in the queue, or does the following step queue
only after the previous step is finished (which would mean to wait the
whole queue for each step of the workflow...)?
I routinely used those wrokflows before (months ago) without any
problems...
I tried to search similar question in the archive before I posted this
one...
Thanks a lot for your answer,
My best
Zuzana Musilova
--
Zuzana Musilova, PhD.
(zuzmus(a)gmail.com)
Zoological Institute
University of Basel
Vesalgasse 1, CH-4051 Basel
Switzerland - Europe
9 years, 4 months
URL problem
by Kucukural, Alper
Hi,
I have a problem in galaxy to get host/domain name in two different pages.
First one is in the tool installation from toolshed, I got the error below,
#####
Not Found
The requested URL /admin_toolshed/prepare_for_install was not found on this server.
#####
The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below.
#####
Not Found
The requested URL /history/list was not found on this server.
#####
I haven't seen these any other pages yet.
My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs.
In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error.
Thanks for your help,
Alper Kucukural
9 years, 4 months
bwa indexing not automatic?
by Joshua Orvis
I installed a new copy of galaxy today and then added the bwa_wrappers
tool. After I upload my reference genome and left/right reads I get output
like this each time I try to run bwa for illumina:
The alignment failed.
Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwt_restore_bwt] fail to open file
'/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'.
Abort!
/bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat
> /tmp/tmpMuj4l2/tmpUIdxXT
If I manually do the 'bwa index' command on dataset_4.dat it works but
in the past this seemed to happen automatically. Any clue what's
going on here?
9 years, 4 months
main galaxy server is down?
by garzetti
I have the same problem with the BWA mapping tool (jobs waiting for run
since Friday), but other tools (e.g. SAMtools) are working.
My analysis also depends a lot on these mapping data!
Debora
> Message: 1
> Date: Sat, 28 Sep 2013 16:47:01 +0000
> From: "Yardley, Nathan" <ny2217(a)cumc.columbia.edu>
> To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu>
> Subject: Re: [galaxy-user] main galaxy server is down?
> Message-ID:
> <9633FF819ABAF94A82A38D94B64B664501291F43(a)SGWAEXM003.mc.cumc.columbia.edu>
>
> Content-Type: text/plain; charset="us-ascii"
>
> I'm wondering the same. I have a mapping job that hasn't moved into the queue since I put it there on Thursday. It's the last sample set I need to move forward with some analysis and I've been trying to get it for more than a week now. :/
>
> Nathan
> ________________________________________
> From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Boaz Shaanan [bshaanan(a)bgu.ac.il]
> Sent: Friday, September 27, 2013 5:37 PM
> To: galaxy-user(a)lists.bx.psu.edu
> Subject: [galaxy-user] main galaxy server is down?
>
> Hi,
>
> Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already.
>
> Thanks,
>
> Boaz
>
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaanan(a)bgu.ac.il
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
> ___________________________________________________________
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>
--
Debora Garzetti, PhD Student
AG Rakin
Max von Pettenkofer-Institute, LMU
Pettenkoferstraße 9A
80336 Munich
E-mail: garzetti(a)mvp.uni-muenchen.de
Phone: +49 (0)89 2180 72915
9 years, 4 months
