Re: [galaxy-dev] adding new genome to local galaxy instance

2013-08-29 Thread Vipin TS
H i Jen & Ricardo, Thanks for the suggestions. It is resolved now. The problem was due to the tab delimiter. In my local workstation the tab was preset to four spaces. regards, Vipin > Is it not showing up under the list of databases/genomes when you at > these locations: > > 1 - Get Data ->

[galaxy-dev] How to get the import of BAM files to create its index on the cluster

2013-08-29 Thread Anthonius deBoer
Hi,I am looking how to improve the import of BAM files into galaxy.I often use the Upload tool in the Data Libraries to upload a number of BAM files into galaxy (after recombining several readgroups into a BAM file for the library, which I unfortunately have to do OUTSIDE of galaxy since it cannot

Re: [galaxy-dev] Better packaging for toolshed binaries

2013-08-29 Thread John Chilton
On Thu, Aug 29, 2013 at 4:17 PM, Guest, Simon wrote: >> > There is a similar but probably larger set of Debian packages >> > available via Debian-Med and Bio-Linux too. The catch here is can you >> > install arbitrary versions of a tool in parallel? And I think the >> > answer sadly is no. >> >> T

Re: [galaxy-dev] Better packaging for toolshed binaries

2013-08-29 Thread Guest, Simon
> > There is a similar but probably larger set of Debian packages > > available via Debian-Med and Bio-Linux too. The catch here is can you > > install arbitrary versions of a tool in parallel? And I think the > > answer sadly is no. > > This is the crucial concern for us. The standard OS packagin

Re: [galaxy-dev] No zebrafish Zv9 build

2013-08-29 Thread Jennifer Jackson
Hi Tiffany, This build is included in the public Main Galaxy instance at https://main.g2.bx.psu.edu (usegalaxy.org) and in the most current CloudMain AMI (by default). This is the full name: If you are working with a local instance, then the g

Re: [galaxy-dev] adding new genome to local galaxy instance

2013-08-29 Thread Jennifer Jackson
Hi Vipin, On 8/28/13 1:34 PM, Vipin TS wrote: Hello, I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration) I have edited th

Re: [galaxy-dev] adding new genome to local galaxy instance

2013-08-29 Thread Ricardo Perez
Hello, I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration) I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new A

Re: [galaxy-dev] Postgresql database cleaning

2013-08-29 Thread Dannon Baker
Can you get a dump of table sizes for us to compare with? http://wiki.postgresql.org/wiki/Disk_Usage On Thu, Aug 29, 2013 at 12:05 PM, Nate Coraor wrote: > On Aug 29, 2013, at 11:50 AM, Nate Coraor wrote: > > > On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote: > > > >> Hi everybody, >

Re: [galaxy-dev] Postgresql database cleaning

2013-08-29 Thread Nate Coraor
On Aug 29, 2013, at 11:50 AM, Nate Coraor wrote: > On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote: > >> Hi everybody, >> >> The python scripts to clean histories, datasets, users etc.. are fine... >> However, the records are not really removed from the postgresql database and >> as a

Re: [galaxy-dev] Postgresql database cleaning

2013-08-29 Thread Nate Coraor
On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote: > Hi everybody, > > The python scripts to clean histories, datasets, users etc.. are fine... > However, the records are not really removed from the postgresql database and > as a result, this one gets bigger and bigger with unused record

Re: [galaxy-dev] Better packaging for toolshed binaries

2013-08-29 Thread James Taylor
On Thu, Aug 29, 2013 at 3:36 AM, Peter Cock wrote: > There is a similar but probably larger set of Debian packages > available via Debian-Med and Bio-Linux too. The catch here > is can you install arbitrary versions of a tool in parallel? And > I think the answer sadly is no. This is the crucial

Re: [galaxy-dev] Help with cluster setup

2013-08-29 Thread Nate Coraor
On Aug 14, 2013, at 7:48 AM, Jurgens de Bruin wrote: > Hi > > just to keep things up to date I have the the cluster up and running jobs are > being submitted. Last problem I am facing is: > > 21: UCSC Main on Pig: refGene (chr18:1-61220071) > error > An error occurred with this dataset: The re

Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why?

2013-08-29 Thread Nate Coraor
On Aug 14, 2013, at 8:39 AM, Boaz Shaanan wrote: > Hi, > > On my local galaxy installation (updated to the latest version yesterday), it > takes ages (hours!) to upload a fastq files. I attach a report from the the > computer on which galaxy is installed. The fastq file is uploaded from > 132

Re: [galaxy-dev] Better packaging for toolshed binaries

2013-08-29 Thread Peter Cock
On Thu, Aug 29, 2013 at 5:45 AM, Guest, Simon wrote: > Dear Galaxians, > > This email is about difficulties with the current approach for installing > tool dependency binaries from the Galaxy Toolshed, and what might be done to > improve the situation. It comes down to this: packaging software