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:
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
User name: dac330
Please I would like to know if it would be normal of a job to be
queued for several days? It is a SAM to BAM conversion, and it has
been waiting for over 5 days to run. I understand that the SAM file is
pretty large but other similar conversions I made on the server
recently were done within few minutes.
Eduardo G. P. Fox
Respected Sir / Ma'am,
I was running Intogen using galaxy, I changes parameters name and then this
Can you please tell what is the meaning of this error ?
Traceback (most recent call last):
line 123, in prepare_job
line 702, in prepare
self.command_line = self.tool.build_command_line( param_dict )
line 2639, in build_command_line
command_line = fill_template( self.command, context=param_dict )
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
line 1004, in __str__
return getattr(self, mainMethName)()
line 100, in respond
NotFound: cannot find 'fimpact'
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
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.
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?
>> 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:
>>> 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?
>>> 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:
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> To search Galaxy mailing lists use the unified search at:
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?
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?
Dr David A. Matthews
Senior Lecturer in Virology
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University of Bristol
Tel. +44 117 3312058
Fax. +44 117 3312091
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