Re: [galaxy-user] help for trim sequences

2013-11-25 Thread Geert Vandeweyer
You might also use ( / add to main) the CutAdapt tool, which is 
available in the main toolshed. It takes multiple adapters, allows 
3/5/both side adapters, and is fast.


http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=User.usernameoperation=view_or_manage_repositoryid=f19bc86bac946438

Best,

Geert

On 11/23/2013 03:19 PM, Peter Cock wrote:

On Fri, Nov 22, 2013 at 8:48 PM, Jennifer Jackson j...@bx.psu.edu wrote:

Hi Seung Hee,

I know we discussed this on the other list, but I didn't point you to the
open development ticket to (potentially) extend the functions of the Cut
tool. This is not being actively worked on right now, but you can follow it
for updates if you want.
https://trello.com/c/CbFSHrU5

Others are still welcome to comment about what types of solutions they might
have to offer. There is no specific tool to do this on Main right now (or in
the Tool Shed, from my checks). http://usegalaxy.org/toolshed

This tool of mine might do what Seung Hee wanted,
but I have not tried it on very large Illumina datasets:

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

Regards,

Peter
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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
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Re: [galaxy-user] receiving an email when a processing step finishes

2013-05-17 Thread Geert Vandeweyer

Hi,

Currently not. For local/cloud instances, you can install an extra tool 
for this from the toolshed:


http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/sendmail

best
geert

On 05/17/2013 03:01 PM, Nikolay N. wrote:

Hi,

I am using the main galaxy instance and have submitted several 
processing steps that seem to have been scheduled for execution. Is 
there a way to get an email notification when such a processing step 
finishes?


many thanks,
Nickyo


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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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Re: [galaxy-user] [galaxy-dev] Workflows

2013-01-18 Thread Geert Vandeweyer
Hi, 

I've put together some exempels for activating and using the api. You can find 
them here: 

http://geertvandeweyer.zymichost.com/index.php?page=readid=29

Best regards, 

Geert vandeweyer

Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven:

 Hi
Sorry if these questions are obvious but I just don’t know how to find the 
 answers.
  
 I’m trying to get one of the API examples to work in 
 http://wiki.galaxyproject.org/Learn/API/Examples .
  
 I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e 
 in the examples). I’ve created workflow but don’t know how to access this key.
  
 Also in the first example it states galaxy_url/api/workflows However I 
 don’t have the “api/workflows” directory structure in my galaxy-dist, do I 
 need to create this?
  
 Thanks
 Neil
  
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[galaxy-user] Lift Over bam files

2012-08-15 Thread Geert Vandeweyer

Hi all,

We have recieved some bam files that were aligned to hg18. What would be 
the easiest workflow to get a VCF file from GATK in build hg19 ? We are 
running a local galaxy with only hg19 for the moment. Lifting the bam 
file would be my first choice, providing support to hg18 by generating 
all indices would be my last :-)


Best regards,

Geert



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[galaxy-user] Create VCF file from samtools pile-up

2012-03-15 Thread Geert Vandeweyer

Hi,

This might be an easy question, but I can't find the solution in the 
standard galaxy tools it seems. How do I create a valid VCF file from a 
(filtered) samtools mpileup output?


Thanks in advance !

Geert
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Re: [galaxy-user] clipping from 5' end

2011-11-16 Thread Geert Vandeweyer

Hi,

with regard to the 5' clipping:

On the main (usegalaxy.org) server: it is possible using the NGS: QC 
and manipulation = Generic FASTQ Manipulation = FASTQ Quality 
Trimmer by sliding window.


If you are interested, we have recently adapted that tool a bit to 
improve speed (5'+3' clipping based of 62M reads in about 20 minutes). I 
can send you the perl script   xml for use in galaxy.


Best Regards,

Geert Vandeweyer
University of Antwerp,
Belgium


On 11/16/2011 03:44 PM, Soetkin Versteyhe wrote:

Hi all,

Does anyone know if it is possible to trim/clip a sequence from the 5’
end? Thank you.

Best, Soetkin.

*Soetkin Versteyhe, PhD**
*PostDoc**

*
University of Copenhagen
*Faculty of Health Sciences

*The Novo Nordisk Foundation*
*Center for Basic Metabolic Research*

Integrative Physiology

Blegdamsvej 3B *
*2200 København N

Denmark*
**
*PHONE +45 35337116*

*_soetkin.verste...@sund.ku.dk__
_http://sund.ku.dk
http://metabol.ku.dk http://metabol.ku.dk/*
**

*



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