Re: [galaxy-dev] microarray & NGS

Dear Eric, thank you for your answer. Your workaround works for the pheno file. A related question is: the affybatch and the eset file formats require to upload two files (rispectively the pheno and the eset/affybatch). Is it normal to have finally only the pheno one in the History? I. Hi Iva

Re: [galaxy-dev] microarray & NGS

Hi Ivan, That is correct, two files are uploaded. Both are stored in Galaxy's database (the filesystem part "database/files", not the relational part), and many subsequent operations on an affybatch or eset dataset will access the .affybatch or .eset file directly. Lines from the .pheno file

Re: [galaxy-dev] Name your own tool's output?

Hi Ross, That's excellent, thanks for jumping in! I've been charged with constructing a Galaxy tool kit for basic microarray data analysis for my group's Galaxy instance, and I looked at your Rgenetics / Rexpression (more the latter of course) as a starting point. I was wondering how the comp

[galaxy-dev] Newbie question for toolshed development

Hi Greg, I am in the process of trying to develop a set of Galaxy wrappers for the tools in my bedtools suite. I have read the Toolshed wiki, but I am still struggling with some very basic questions that I hope you can help me with. 1. How should a tarball repository be structured for the too

Re: [galaxy-dev] Name your own tool's output?

Hi Eric, I have no current resources or active users for microarray development so I can't contribute much and although the rgenetics code works fine with galaxy central the rexpression code is way out of date - which is why the metadata handling is so broken. There are ongoing problems in galaxy

[galaxy-dev] error in downloading bai files using shared history link

Hi, We are getting following error when a user tries to download bam index file (bai) files using a shared history link of following pattern - ' https://galaxy.mydomain/u/user1/h/awesome-analysis '. We are using external authentication and latest galaxy-dist code in our set up. {{{ Error Tr

[galaxy-dev] Delete toolshed repository

I want to delete a test repository I created on http://toolshed.g2.bx.psu.edu/repository?webapp=community. Is that possible? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.com

Re: [galaxy-dev] Delete toolshed repository

Hi Ilya, Do you plan to upload any tools to the tool shed in the future? If so, you can rename the repository to something more meaningful and use it when you are ready. To play with tool shed features, please use the Galaxy test tool shed at http://testtoolshed.g2.bx.psu.edu/. Thanks! On N

Re: [galaxy-dev] error in downloading bai files using shared history link

Shantanu, This is a bug and is fixed in galaxy-central changeset ccbee8d11a6a : https://bitbucket.org/galaxy/galaxy-central/changeset/ccbee8d11a6a/ Best, J. On Nov 18, 2011, at 12:37 PM, Shantanu Pavgi wrote: > > Hi, > > We are getting following error when a user tries to download bam index

Re: [galaxy-dev] error in downloading bai files using shared history link

Thanks for the fix Jeremy. -- Shantanu. On Nov 18, 2011, at 12:58 PM, Jeremy Goecks wrote: Shantanu, This is a bug and is fixed in galaxy-central changeset ccbee8d11a6a : https://bitbucket.org/galaxy/galaxy-central/changeset/ccbee8d11a6a/ Best, J. On Nov 18, 2011, at 12:37 PM, Shantanu Pavg

Re: [galaxy-dev] Problem with the Galaxy tool shed

Hi Marcel, This should now be working - sorry about the delay on this - a lot of enhancements came with it. Thanks for your patience on this one! Greg On Nov 16, 2011, at 12:19 PM, Marcel Schumann wrote: > Hi Greg, > > yes, I tried to change the synopsis. > Now I tried it again and noticed t

[galaxy-dev] November 18, 2011 Galaxy Development News Brief

November 18, 2011 Galaxy Development News Brief This release http://galaxyproject.org/wiki/News%20Briefs/2011_11_18 Release history http://galaxyproject.org/wiki/News%20Briefs Source http://getgalaxy.org Support http://galaxyproject.org/wiki/Support new: % hg clone http://www.bx.psu