Re: [galaxy-user] help for trim sequences
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 ___ 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/ -- 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/in/geertvandeweyer ___ 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/
Re: [galaxy-user] receiving an email when a processing step finishes
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 ___ 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/ -- 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 ___ 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/
Re: [galaxy-user] [galaxy-dev] Workflows
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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/
[galaxy-user] Lift Over bam files
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 ___ 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/
[galaxy-user] Create VCF file from samtools pile-up
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 ___ 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/
Re: [galaxy-user] clipping from 5' end
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/* ** * ___ 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/ ___ 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/