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
6 years, 4 months
question history
by Liesbeth Van Rompay
Hi,
Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do?
Best regards,
Liesbeth
6 years, 6 months
error while running Intogen.
by do kadya
Respected Sir / Ma'am,
I was running Intogen using galaxy, I changes parameters name and then this
error came.
Can you please tell what is the meaning of this error ?
Traceback (most recent call last):
File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 123, in prepare_job
job_wrapper.prepare()
File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 702, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py",
line 2639, in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py",
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py",
line 100, in respond
NotFound: cannot find 'fimpact'
6 years, 6 months
Globus World 2014
by Ravi K Madduri
Dear All
I wanted to send a note to folks about Globus World 2014. I apologize before hand for spamming both the developer list and the users list also but I thought this may be relevant to folks on the lists. Please let me know if you have any questions.
GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomicsin the main meeting, including a keynote by Nancy Cox and these accepted talks:
Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev,
Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu
Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath
Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan
Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld.
--
Ravi K Madduri
MCS, Argonne National Laboratory
Computation Institute, University of Chicago
6 years, 6 months
Re: [galaxy-user] Trackster Error
by Jeremy Goecks
Hi Suzanne,
Thanks for sharing your history. This is a file format issue on our side. We’ll get it taken care of and let you know when it’s fixed.
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
>
>
> On Mar 27, 2014, at 9:27 AM, Jeremy Goecks <jgoecks(a)gwu.edu> wrote:
>
>> Hi Suzanne,
>>
>> Can you share your history with me and I’ll take a look?
>>
>> Thanks,
>> J.
>>
>> --
>> Jeremy Goecks
>> Assistant Professor of Computational Biology
>> George Washington University
>>
>>
>>
>> On Mar 24, 2014, at 5:08 PM, Suzanne Gomes <suzanneluziagomes(a)gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I am trying to look at an output from Tophat using Trackster, but I keep getting the following error:
>>>
>>> Could not load chroms for this dbkey: dp4
>>>
>>> This is not a custom dbkey - I just selected it from the list of available ones on Trackster.
>>>
>>> I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results.
>>>
>>> Any ideas why this is happening and what I can do to fix it?
>>>
>>> Thanks
>>>
>>> Suzanne
>>> ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>
>>> http://galaxyproject.org/search/mailinglists/
>>
>
6 years, 6 months
Trackster Error
by Suzanne Gomes
Hello,
I am trying to look at an output from Tophat using Trackster, but I keep getting the following error:
Could not load chroms for this dbkey: dp4
This is not a custom dbkey - I just selected it from the list of available ones on Trackster.
I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results.
Any ideas why this is happening and what I can do to fix it?
Thanks
Suzanne
6 years, 6 months
ftp not working
by David Matthews
Hi,
I'm still not able to use ftp - keeps saying connection refused either through the command line or through cyberduck - is anyone else seeing this?
Best Wishes,
David.
_________________________________
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax. +44 117 3312091
D.A.Matthews(a)bristol.ac.uk
6 years, 6 months
Question regarding storage space
by Alexandre Maia
I am using Deeptools at the main public server and was adding some files
initially to test. Now I have removed all my files (hidden and unhidden)
and history, but my usage is still at 38%. How can I remove all the files
to have a 0%?
My user name is alexandre.gaspar.maia(a)gmail.com
Thanks.
A
6 years, 6 months
