them out on the main site soon.
Thanks for a great package!
anton
--
Anton Nekrutenko
Professor of Biochemistry
and Molecular Biology
http://nekrut.bx.psu.edu
(814) 826-3051
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The new version is based on vcflib 386afcaafd.
GitHub -> https://github.com/nekrut/vcflib-tools
ToolShed -> https://toolshed.g2.bx.psu.edu/view/anton/suite_vcflib_tools_3_0
These will be on test and main instances shortly.
Any feedback is appreciated.
anton
--
Anton Nekrutenko
Profes
magic happens within the tool xml) and they produce BAM output.
a.
--
Anton Nekrutenko
Professor of Biochemistry
and Molecular Biology
*http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>*
(814) 826-3051
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> and other Galaxy lists, please use the interface at:
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Anton Nekrutenko
Profe
e
open to suggestions ... What we are thinking of lately is switching to
unaligned BAM for everyting. One of the benefits here is the ability to add
readgroups from day 1 simplifying multisample analyses down the road.
a.
Anton Nekrutenko
http://galaxyproject.org
On Sep 8, 2011, at 10:14 A
Glen:
Please, contribute it to Tool Shed once you are done with testing. This will be
much appreciated.
Thanks!
anton
Anton Nekrutenko
http://galaxyproject.org
On Oct 12, 2011, at 4:00 PM, Glen Beane wrote:
> I have an mpileup tool for Galaxy I've developed. After a lit
;
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Ant
Thon:
You can share a workflow through a URL, which you can send to all members of
the group.
anton
Anton Nekrutenko
http://www.galaxyproject.org
On Jan 31, 2013, at 10:52 PM, Anthonius deBoer wrote:
> Hi,
>
> I am trying to build some workflows for people that are part of a gr
Ry4an:
SAM output generated with bowtie can be converted into BED-like format with
NGS: Samtools -> Convert SAM to interval. However, it is not sorted.
Tx,
anton
On Jan 6, 2011, at 6:12 PM, Ry4an Brase wrote:
> I've got a user request for a converter from bowtie's map output to BED
> format
versity of Leeds,
> Leeds,
> LS2 9JT, UK.
> E-mail: l.d.hazelw...@leeds.ac.uk<mailto:l.d.hazelw...@leeds.ac.uk>
>
>
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
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Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
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x 08
> +33 4 26 55 67 85
> letex...@lyon.fnclcc.fr
>
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> h
Katie:
"Filter pileup" outputs 0-based coordinates if you use the "Convert
coordinates to intervals" option. So the issue may be related to aaChanges
tools. Can you give us a specific example, so we can track things down.
Thanks!
anton
galaxy team
Anton Nekrutenko
http
Thanks for letting me know. I'm also forwarding this galaxy-dev, so the thread
in complete.
Thanks,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On May 12, 2011, at 2:30 PM, Katie Hyma wrote:
> Hi Anton,
>
> You're right, sorry for the false
Dear Peter:
Yes, that would help. But, you patches are definitely not unnoticed. We'll
apply them (likely at the conference) and we are also in the process of
devising a strategy for doing so quickly and consistently.
See you on Tuesday.
a.
Anton Nekrutenko
http://nekrut.bx.psu.edu
Yann:
These tools are for testing only, and not yet supported/distributed.
Thanks,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 25, 2011, at 11:11 PM, Yann Surget-Groba wrote:
> Dear all,
> I'm trying to use the tool assembly statistics in
Casey:
Indeed. Will fix shortly.
a.
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jul 12, 2011, at 11:51 AM, Casey Bergman wrote:
> Dear Galaxy Team -
>
> We stumbled across a potential bug in the toolExample.pl script on the Galaxy
> Add Tool Tu
Casey:
This 'elegant' script has been fixed. Thank for poiting this out!
a.
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jul 12, 2011, at 11:51 AM, Casey Bergman wrote:
> Dear Galaxy Team -
>
> We stumbled across a potential bug in the toolExamp
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