Re: [galaxy-dev] Question about GC

2011-02-01 Thread Xiandong Meng
Hi Enis, Thanks for your reply. Please share the guideline with me to install a customized Galaxy instance on Amazon. Thanks a lot, Xiandong On Mon, Jan 31, 2011 at 6:28 PM, Enis Afgan eaf...@emory.edu wrote: Hi Xiandong, Yes, it is possible to run a customized Galaxy instance and also use

[galaxy-dev] phastCons and phastOdds scores

2011-02-01 Thread David Hoover
Does anyone have a clear explanation of what files are required/available for Get Genomic Scores - Aggregate datapoints, Compute phastOdds (binned_scores.loc and phastOdds.loc files)? I know there are .mod and .pp files and .wigFix files from UCSC, but I can't figure out exactly what Galaxy

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-02-01 Thread Peter
Hi Kanewi, Sorry - make that three changesets on this branch to consider mering/transplanting: https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 Parameter handling, https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 Cope with errors on stderr,

Re: [galaxy-dev] Question about GC

2011-02-01 Thread Enis Afgan
Hi Xiandong, I made a wiki page with the necessary steps to customize you cloud cluster instance: https://bitbucket.org/galaxy/galaxy-central/wiki/Cloud/CustomizeGalaxyCloud Give it a shot and let me know if you have any questions. Enis On Mon, Jan 31, 2011 at 9:41 PM, Xiandong Meng

[galaxy-dev] Batch download of a history

2011-02-01 Thread Davide Cittaro
Hi all, ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Re: [galaxy-dev] Data Library - upload files from filesystem paths

2011-02-01 Thread Greg Von Kuster
Hello Nicki, On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote: Hi As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy,

Re: [galaxy-dev] Data Library - upload files from filesystem paths

2011-02-01 Thread Nicki Gray
Hi Greg thanks for your response, I have some questions about your reply. On 1 Feb 2011, at 16:14, Greg Von Kuster wrote: Hello Nicki, On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote: Hi As an admin I have created a data library on our local instance of galaxy, created folders in that

[galaxy-dev] Links to anchors in Pages

2011-02-01 Thread SHAUN WEBB
Hi, I am creating a tutorial using galaxy pages and I want to add a contents section at the top to link to headings further down the page. I can't quite figure out how to use the anchoring. Thanks for your help. Shaun Webb -- The University of Edinburgh is a charitable body, registered

Re: [galaxy-dev] histogram tool not working

2011-02-01 Thread David Hoover
R gives the error message 'x' must be numeric, so relevant questions are what version of R do you have, what version or rpy, and what version of Python (since Galaxy's tools tends to invoke R from Python via the ryp library - certainly the histogram tool does). python = 2.6 R = 2.10.0 rpy =

[galaxy-dev] Problem upgrading DB from 67 to 68

2011-02-01 Thread Assaf Gordon
Hi, Trying to upgrade DB schema ('sh manage_db.sh upgrade') from 67 to 68 fails with the following message: === sqlalchemy.exc.ProgrammingError: (ProgrammingError) syntax error at or near RENAME LINE 1: ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_i...

Re: [galaxy-dev] Problem upgrading DB from 67 to 68

2011-02-01 Thread Ramkrishna Chakrabarty
Hello Assaf, As you have rightly pointed out, the script is failing as ALTER SEQUENCE .. RENAME TO is not supported in Postgres 8.1. It works on 8.3 onwards which we have here. I will post a patch for this soon. Thanks rc On Feb 1, 2011, at 5:36 PM, Assaf Gordon gor...@cshl.edu wrote: Hi,

Re: [galaxy-dev] quality_scores.loc files

2011-02-01 Thread Guru Ananda
And, exactly what file(s) do you get from UCSC? I can find some for various organisms (goldenPath/[org]/bigZips/[org].quals.fa.gz), but hg18, hg19, mm8, and mm9 are not among them. UCSC doesn't host quality scores for hg18/hg19 since the sequence quality of these assemblies is very high.

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-02-01 Thread Kanwei Li
Committed On Tue, Feb 1, 2011 at 10:27 AM, Peter pe...@maubp.freeserve.co.uk wrote: Hi Kanewi, Sorry - make that three changesets on this branch to consider mering/transplanting: https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 Parameter handling,

[galaxy-dev] 2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands

2011-02-01 Thread Dave Clements
Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization,