[galaxy-dev] Browse Galaxy main tool shed - Connection Reset error

Hi, I am running a local instance of galaxy, which has been functioning fine until 2 weeks ago. However, now when I go to the Admin section, then to ‘Search and browse tool sheds’ and click ‘Galaxy main tool shed’ the browser waits for a while then I get a ‘Connection was reset’ error instead

Re: [galaxy-dev] gzipped fastq reader

On Mon, Jul 8, 2013 at 11:21 PM, Robert Baertsch wrote: > I respectfully disagree, If you want an extensible system, you should > always wrap primitive system level calls. > > Any tools that opens a file that could be compressed would be affected. > That is a huge number of tools. Do you really w

Re: [galaxy-dev] gzipped fastq reader

On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch wrote: > Peter and Dan, > I like the idea of replacing all open() with galaxy_open() in all tools. You > can tell the format by looking at the first 4 byes (see C code below from > the UCSC browser team). Is there some pythonic way of overriding ope

[galaxy-dev] Connecting to new Galaxy Cloudman by FTP

Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group set

Re: [galaxy-dev] ToolShed dependencies KeyError: 'invalid_repository_dependencies'

Hello Peter, Thanks for reporting this - I have committed a fix in changeset 10206:86efa5ac1fae, which is currently running on the test tool shed. Greg Von Kuster On Jul 8, 2013, at 11:35 AM, Peter Cock wrote: > Hi Greg, > > Previously my workflows had hard coded dependencies on the main > T

Re: [galaxy-dev] Error Uploading Directory of Files

Hi Nicholas, as pointed out by Peter and here: http://www.biostars.org/p/76021/ please check your white spaces and provide a little bit more information. Btw. what is wrong with biostar? Why the double post? Cheers, Bjoern > Hi, > > Our lab recently installed a local version of Galaxy on a m

[galaxy-dev] Setting up reference genomes for GATK Genotyper

Hi, I am running an instance of Galaxy that I setup using Cloudman. We are trying to use the GATK Unified Genotyper, but we are missing the reference genomes. I saw in your website instructions on how to setup reference genomes for some other tools, but not for the Unified Genotyper. Where can I f

Re: [galaxy-dev] Galaxy on a server without internet connexion try to contact toolshed.g2.bx.psu.edu

Hello Ghislain, Thanks very much for repostring this issue. I have committed a fix in changeset 10205:2accb50ef103. Greg Von Kuster On Jul 4, 2013, at 7:21 AM, Ghislain Fournous wrote: > Hi, > > I installed Galaxy on a server located on a secure Network without internet > connexion follow

Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml

Hello Björn, Thanks very much for the patch - I've committed alsightly alterered verson of it in changetset 10204:afec613d77fa which is currently running on the test tool shed. Greg Von Kuster On Jul 7, 2013, at 6:59 PM, Björn Grüning wrote: > Hi Greg, > > bitbucket has a downtime so I hav

[galaxy-dev] ToolShed dependencies KeyError: 'invalid_repository_dependencies'

Hi Greg, Previously my workflows had hard coded dependencies on the main Tool Shed, which currently is a bit of a problem on the Test Tool Shed. Therefore I'm update my Tool Shed workflows using a repository_dependencies.xml with implicit repository and revision fields (i.e. the latest revision w

Re: [galaxy-dev] Error Uploading Directory of Files

On Mon, Jul 8, 2013 at 3:36 PM, Nicholas Kline wrote: > Hi, > > Our lab recently installed a local version of Galaxy on a mid-2012 Mac > Pro computer. We can access the Galaxy server and sign in as an > administrator. Today we tried creating a Data Library, adding a > dataset to it, and uploading

[galaxy-dev] Error Uploading Directory of Files

Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation ( http

Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml

I'll soon be committing a slightly altered version of your patch which includes a language attribute for the template_command action type. On Jul 8, 2013, at 10:02 AM, Björn Grüning wrote: > Hi James, > >> It probably makes sense to specify the template type in this case. >> Maybe an addition

Re: [galaxy-dev] How were liftover and nib files generated?

liftOver files come from the UCSC genome browser, derived from pairwise alignments. A variety of tools can create nib files from fasta, however we prefer the use of the twoBit format now, which can be created using faToTwoBit from the UCSC utilities. -- James Taylor, Assistant Professor, Biology/

Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml

Hi James, > It probably makes sense to specify the template type in this case. > Maybe an additional attribute, language='cheetah' ? My first suggestion was to reflect the template engine. I'm fine with both. > On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning > wrote: > > > > #if env.get('X

Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml

It probably makes sense to specify the template type in this case. Maybe an additional attribute, language='cheetah' ? On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning wrote: > > #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): >./configure --prefix=$env.INST

Re: [galaxy-dev] CloudMan Error

Hi guys, Any thoughts on this? I'm kind of stuck. (Even some pointers on where to look for more clues would be extremely helpful.) Thanks, Greg On Fri, Jul 5, 2013 at 11:10 AM, greg wrote: > Hi guys, > > I'm hitting an error using CloudMan using the Share-an-Instance > option. It says: > >

Re: [galaxy-dev] [GSoC2013] Week 2 Accomplishments and Week 3 Plans

Week 3 and Week 4 Plans: http://galaxy-gsoc2013.blogspot.in/2013/07/week-3-accomplishments-and-week-4-plans.html On 6 July 2013 16:46, Saket Choudhary wrote: > Here is a short post explaining the data model. Not ver elaborately > written, so incase you you find a mistake or something poorly > exp

Re: [galaxy-dev] gzipped fastq reader

On Thu, Jul 4, 2013 at 9:49 PM, Robert Baertsch wrote: > Dan, > Do these readers support gzip files? > >reader = fastqVerboseErrorReader > reader = fastqReader Presumably you are writing a Python script using this library? The answer is a qualified yes. Instead of passing them a n

Re: [galaxy-dev] Galaxy Server Processes Dying?

Hi Dan, That's old code. Updating will probably help. Logging level just takes disk space, but just in case you haven't followed http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance leaving debug = True uncommented used to fill al

[galaxy-dev] Tool Error: Failure Preparing Job

Hi all, I'm working on a local Galaxy instance and I want to integrate TASSEL's GLM pipeline into it. But when I run the tool, it prompts: "tool error An error occurred running this job:* failure preparing job*" This is how the log looks like: galaxy.jobs.handler INFO 2013-07-08 16:00:47,648

Re: [galaxy-dev] [galaxy-user] Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"

Thank you Björn and Ross. I will install the tools from the admin interface. On Mon, Jul 8, 2013 at 12:35 PM, Björn Grüning < bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > Hi Sachit, > > we are working currently on a DESeq2 wrapper. Not yet finised sorry. > There is also a edgeR Test repo