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
When will megablast be working again
by Scott W. Tighe
Dear NCBI and Galaxy Team
I have sent a note to determine when the Megablast option will be
active again. Whether you use Galaxy or NCBI directly, it is
inoperative.
Scott
--
Core Laboratory Research Staff
Advanced Genome Technologies Core
Deep Sequencing (MPS) Facility
Vermont Cancer Center
149 Beaumont Ave
University of Vermont HSRF 303
Burlington Vermont USA 05045
802-656-AGTC
802-999-6666 (cell)
6 years, 5 months
Megablast database identity
by Scott W. Tighe
Jennifer
I am megablasting a simple 500,000 line dataset that is certainly in
galaxy fasta.
For a week i have been seeing numerous errors. So i have reprocesed
the data multiple times.
The error message is "could not find specified database directory"
Is there an alternative approach? I did try ncbi directly and that
failed too. They say they have a database issue
Scott Tighe
Core Laboratory Research Staff
Advanced Genome Technologies Core
Deep Sequencing (MPS) Facility
Vermont Cancer Center
149 Beaumont Ave
University of Vermont HSRF 303
Burlington Vermont USA 05045
802-656-AGTC
802-999-6666 (cell)
6 years, 5 months
"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
by Sarah Maman
Hello,
I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (genome_test.len in
galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc
fils in tool-data/) but "Intersect multiple sorted BED files" gives this
error message :
An error occurred running this job: /Epilog : job finished at lun. mars
24 15:55:04 CET 2014
Error: The requested genome file
(/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could
not be opened. Exiting!
So, /I have integrated the code modification submitted in Galaxy Central
(https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3...):
- chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+ chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )
But I always have the same error message.
Could you please help us ?
Thanks in advance,
Sarah
//
--
--*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
--*--
6 years, 5 months
'filter pileup' not working on 'generate pileup' output
by Matthew
I used Bowtie2 on a fastq file. Then, generate pileup on the output
of Bowtie2. When I try to use 'Filter pileup', there is no file
recognized as input even though I have the output from the 'Generate
pileup'.
Matthew
6 years, 5 months
Is the Server Down?
by Scott Tighe
Jennifer
I have been trying to megablast some sequences for a few days now but it
seems that the server is down. Can you advise?
Scott
--
Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
NextGen Sequencing/Flow Cytometry
University of Vermont and Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
802-656-2482 (AGTC)
6 years, 5 months
Announcing the Galaxy Biostar Forum
by Jennifer Jackson
Dear Galaxy Community,
Galaxy has teamed up with Biostar to create a Galaxy User support forum
at https://biostar.usegalaxy.org!
We want to create a space where researchers using Galaxy can come
together and share both scientific advice and practical tool help.
Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if
you have something to say about Using Galaxy, this is the place to do it!
Current integration with usegalaxy.org
* We imported the whole history of galaxy-user(a)bx.psu.edu mailing list
into Biostar
* If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy
Biostar) you will be automatically logged in.
* A Galaxy Biostar account will be created for you if it did not
previously exist. To obtain this account’s password please use the
password reset feature of Galaxy Biostar
(https://biostar.usegalaxy.org/accounts/password/reset/).
* When you have a question, search Biostar directly from any Galaxy tool
page.
Read more about how to get started at
https://wiki.galaxyproject.org/Support/Biostar
Roll-out phase
* Galaxy Biostar is available at http://biostar.usegalaxy.org and will
be our primary avenue for support
* The galaxy-user(a)bx.psu.edu mailing list will continue to be supported
during the transition but starting now please use the
biostar.usegalaxy.org forum to ask all questions about using Galaxy.
* Please do not double post to both Galaxy Biostar and
galaxy-user(a)bx.psu.edu
* Send us feedback through the forum's post "Welcome to Biostar" to tell
us what you think.
What’s next
* Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is
retired.
* Archives of galaxy-user(a)bx.psu.edu will remain accessible.
We hope you will like the change and look forward to any feedback you
may have.
Thank you for using Galaxy!
The Galaxy team
6 years, 5 months
GCC2014 Poster Abstracts due April 25, THIS FRIDAY
by Dave Clements
Hello all,
This is just a reminder that poster abstracts for the 2014 Galaxy Community
Conference (GCC2014) *are due this Friday. *
Abstracts can be submitted at
https://wiki.galaxyproject.org/Events/GCC2014/Abstracts
Note that posters are reviewed and accepted on a rolling basis, until all
slots are full. The deadline is this Friday but sooner may be better.
In other news:
- We are delighted to have Steven Salzberg as the keynote
speaker<https://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker>
.
- Registration for the GCC2014
hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon>is
now open
- Early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register>for
the GCC2014
Training Day and
Meeting<https://wiki.galaxyproject.org/Events/GCC2014/Program>are also
open
- Abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>for
accepted talks will start showing up on the website this week.
Thanks, and hope to see you in Baltimore,
Dave C
On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements
<clements(a)galaxyproject.org>wrote:
> Hello all,
>
> *We are pleased to announce that Early Registration
> <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and
> Poster Abstract Submission
> <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for
> the 2014 Galaxy Community Conference (GCC2014)
> <https://wiki.galaxyproject.org/Events/GCC2014>.*
>
> GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at
> the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/home...>of Johns
> Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>,
> United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training
> Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring
> four *five* parallel tracks, each with three, two and half hour long
> workshops. There are 13 different topics spanning the full Galactic
> spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>
>
> *Early registration
> <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open.
> Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training
> Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main
> meeting) starting at $140 for post-docs and students. Registration is
> capped this year at 250 participants, *and we expect to hit that limit*.
> Registering early assures you a place at the conference and also a spot in
> the Training Day workshops you want to attend.
>
> You can also book affordable conference housing at the same time you
> register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options.
>
> *Abstract submission
> <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral
> presentations and posters is also open. Abstract submission for oral
> presentations closes April 4, while poster submission closes April 25.
> Poster authors will be notified of acceptance status within two weeks of
> submission, while presentation authors will be notified no later than May2.
> *Please consider presenting your work. If you are dealing with big
> biological data, then this meeting wants to hear about your work.*
>
> The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data
> Intensive and Reproducible Research" series announced for the last
> conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>,
> *and is continuing to take submissions for this year's meeting and beyond*.
> BGI is also continuing to cover the article processing charges until the
> end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibil...>.
>
>
> Thanks, and hope to see you in Baltimore!
>
> The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> http://wiki.galaxyproject.org/
>
--
http://galaxyproject.org/GCC2014
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
6 years, 5 months
