Re: [galaxy-dev] Error executing tool: 'hg19'

2012-02-14 Thread Joachim Jacob
First, thanks. I just created a new user, and I am ready to go with that user. FYI, the reset of the datatypes_conf.xml did not do the trick: following error appears on the custom builds page: NoConverterException: Conversion from 'fasta' to 'len' not possible Thanks, Joachim On 02/13/2012

Re: [galaxy-dev] Running workflows on mulitple paired-end data sets

2012-02-14 Thread Dannon Baker
Thon, Not currently, though the question comes up often enough that I'll try and bump it up my list. Instead of interlacing and deinterlacing a better workaround for now might be to use the API to execute over all these samples. -Dannon On Feb 13, 2012, at 8:46 PM, Anthonius deBoer wrote:

Re: [galaxy-dev] Error executing tool: 'hg19'

2012-02-14 Thread Jeremy Goecks
Can you confirm that the following lines are in your datatypes_conf.xml file? -- datatype extension=fasta type=galaxy.datatypes.sequence:Fasta display_in_upload=true converter file=fasta_to_tabular_converter.xml target_datatype=tabular/ converter

Re: [galaxy-dev] Galaxy server configuration question

2012-02-14 Thread huayan gao
Good point, Nate! I will move galaxy out of my documentroot then. Best, Huayan On Tue, Feb 14, 2012 at 1:21 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name

[galaxy-dev] cloudman/galaxy on EC2 - snapshot not found

2012-02-14 Thread Jorrit Boekel
Dear list, I am trying to deploy Galaxy as an environment for proteomics tools in amazon's EC2 cloud, probably/preferably via Cloudman. I have used both the biocloudcentral portal and a manual approach to set up cloudman/galaxy, but run into the same error message which seems to start with a

[galaxy-dev] Galaxy workflow data

2012-02-14 Thread Paul Gordon
Hi all, I have noticed that when I run a workflow with output to a new history, the data sets used as input to the workflow do not become part of the new history. Unfortunately, if a job fails in the workflow, the rerun interface for the job can't access the original dataŠit needs to be manually

Re: [galaxy-dev] Galaxy workflow data

2012-02-14 Thread Dannon Baker
Hi Paul, Thanks for this suggestion, it would definitely make sense to create a reference to the actual workflow inputs in the new history. I'll see what I can do! -Dannon On Feb 14, 2012, at 11:05 AM, Paul Gordon wrote: Hi all, I have noticed that when I run a workflow with output to a

Re: [galaxy-dev] Galaxy workflow data

2012-02-14 Thread Langhorst, Brad
Paul: I was about to suggest the same - great idea! ++ brad On Feb 14, 2012, at 11:08 AM, Dannon Baker wrote: Hi Paul, Thanks for this suggestion, it would definitely make sense to create a reference to the actual workflow inputs in the new history. I'll see what I can do! -Dannon

Re: [galaxy-dev] cloudman/galaxy on EC2 - snapshot not found

2012-02-14 Thread Dannon Baker
Hi Jorrit, There was a permissions issue with the new tool snapshot(snap-b28be9d5) created yesterday that I've fixed, it should work next time you start an instance. Thanks! -Dannon On Feb 14, 2012, at 10:37 AM, Jorrit Boekel wrote: Dear list, I am trying to deploy Galaxy as an

Re: [galaxy-dev] galaxy cloud help

2012-02-14 Thread Dannon Baker
Sure, I'm happy to help, though in the future it's probably best to mail galaxy-dev (cc'd for ticket tracking) directly as there are several of us that may be able to answer and get a response out sooner. That said, your problem is likely due to a permissions issue with the new tool

Re: [galaxy-dev] [galaxy-user] Result of annotation hg18 and hg19 on one file

2012-02-14 Thread Dannon Baker
Hi, Based on your previous questions, I'm going to guess that you're trying to add multiple tools, run both on an input dataset in series, and see the results in the History. Is this the case? If you're referring to how to combine these into one process, take a look at the Galaxy workflow

[galaxy-dev] No Display at UCSC Main link.

2012-02-14 Thread Luobin Yang
Hi, I have a local instance of Galaxy, but I found there is no Display at UCSC Main link for some datasets that can be viewed in GeneTrack or displayed by Ensemble, what has been wrong? Thanks, Luobin ___ Please keep all replies on the list

Re: [galaxy-dev] galaxy cloud help

2012-02-14 Thread brennac2
Perfect-- it works now. I will email to Galaxy-Dev next time Thank you, -CB On 2/14/12 11:50 AM, Dannon Baker dannonba...@me.com wrote: Sure, I'm happy to help, though in the future it's probably best to mail galaxy-dev (cc'd for ticket tracking) directly as there are several of us that may be

Re: [galaxy-dev] Problem previewing a tool in the Toolshed

2012-02-14 Thread Greg Von Kuster
Hi Carlos, Not every tool form parameter will properly display when previewing the tool in the tool shed because the tool shed doesn't have access to some Galaxy components (e.g., a Galaxy history ) that are required for some tool parameter types. When I get a chance, I'll take a closer look,

Re: [galaxy-dev] Batch limit on Wokflows

2012-02-14 Thread Petit III, Robert A.
Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or

Re: [galaxy-dev] Batch limit on Wokflows

2012-02-14 Thread Dannon Baker
I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and

Re: [galaxy-dev] Batch limit on Wokflows

2012-02-14 Thread Petit III, Robert A.
Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012

Re: [galaxy-dev] Batch limit on Wokflows

2012-02-14 Thread Petit III, Robert A.
Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To:

Re: [galaxy-dev] Uploading large file in browser

2012-02-14 Thread Nic Barker
Hi Nate, That's good to hear. Just letting you know that testing on my local install of galaxy, if the following stars align: -Google Chrome 17 / Firefox 10 (Mac os x) -Nginx as galaxy's front end web server -Nginx's optional upload module installed HTML uploading of large files to galaxy

Re: [galaxy-dev] Galaxy Cloudman - How to analyse 1TB data ?

2012-02-14 Thread Brad Chapman
Yves; I am currently investigating if Galaxy Cloudman can help us in analyzing large NGS datasets. I was first impressed by the simple setup, the autoscaling and useability of Galaxy Cloudman but soon ran into the EBS limit of 1 TB L I thought to be clever and umounted the

[galaxy-dev] Condor in bioinformatics pipeline

2012-02-14 Thread Jennifer Jackson
Hi Nathan, I am going to move your question over to the galaxy-...@bx.psu.edu mailing list to see if anyone in the development community has feedback. Galaxy-user is mostly a Q A list for scientists working with tools on the main Galaxy public server.

[galaxy-dev] Problem with python ./scripts/make_egg_packager.py

2012-02-14 Thread Jose William Valero Velasquez
Hi, I'm writing you because i'm trying to install galaxy in a server running suse behind a proxy, so i have to build the eggs like if the server were offline, in the guide says that i should execute the command ./scripts/make_egg_packager.py but i get the following error, and i don't really

Re: [galaxy-dev] No Display at UCSC Main link.

2012-02-14 Thread Jennifer Jackson
Hi Luobin, To display at UCSC, the datatype has to be a UCSC display type and the database has to be a UCSC genome browser. Often, small changes can be made to tune a dataset to help it fit into these requirements. Other times, a dataset will need to be transformed into another type or it

[galaxy-dev] Support for PolyPhen2

2012-02-14 Thread Praveen Raj Somarajan
Hi Dev Team, Do you have any plan to integrate PolyPhen2 to Galaxy? I feel, it would be good if you can, as this extends the functionality of NGS analysis and (definetly) it would be value addition to Galaxy as well. Let me know your comments. Best, Raj

Re: [galaxy-dev] No Display at UCSC Main link.

2012-02-14 Thread Jennifer Jackson
Hello again, The link is not a Galaxy Main public instance share link, which would start with: http://main.g2.bx.psu.edu Having the datatype as BED and the database as hg19 would (for all of the cases I can think of) bring up the View at UCSC link, if the instance is set up to have display

Re: [galaxy-dev] bug: unsorted bam files and import into data library

2012-02-14 Thread Jennifer Jackson
Hi Florian, I am fairly certain that this exact issue is still open, and so have opened a bitbucket ticket to track progress: http://bitbucket.org/galaxy/galaxy-central/issue/718/unsorted-bam-files-and-import-into-data If this has been corrected already, one of us will send an update