[galaxy-dev] Cannot see data when selecting "Display Data in Browser"

up and the file has permissions of 644. I don't see any reason why I shouldn't be able to view or download this file through galaxy. Any ideas? Thanks, Dave --- Dave Walton Manager Scientific Computing The Jackson Laboratory Bar Harbor, Maine dave.wal...@jax.org The information in thi

Re: [galaxy-dev] [Newsletter] Re: Interested in speaking with other institutions deploying Galaxy locally?

JAX would be interested in this. Dave From: Ryan Golhar mailto:ngsbioinformat...@gmail.com>> Date: Friday, April 27, 2012 3:14 PM To: Ann Black-Ziegelbein mailto:annbl...@eng.uiowa.edu>> Cc: "galaxy-dev@lists.bx.psu.edu" mailto:galaxy-dev@lists.bx.psu.edu>> S

Re: [galaxy-dev] Multiple Workflows broken?

disregard this email and except my apology for reporting a known issue. Dave On 1/30/12 2:20 PM, "Dave Walton" wrote: We just upgraded our Galaxy server last week to the one from change-set b258de1e6cea. We have several workflows that leverage the ability to select multiple in

[galaxy-dev] Multiple Workflows broken?

We just upgraded our Galaxy server last week to the one from change-set b258de1e6cea. We have several workflows that leverage the ability to select multiple input files, that in turn launches an instance of the workflow per input file. When I use these workflows, it now only runs a single insta

Re: [galaxy-dev] Setting the output label based on input parameters?

; those, the base name (which we routinely use for metadata needed at > some final amalgamation step, such as experimental condition) is hard > to find in all the cruft. > > > > On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton wrote: >> This is similar to something w

Re: [galaxy-dev] Setting the output label based on input parameters?

This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but si

Re: [galaxy-dev] Display BAM with IGV

Minor correction. It wasn't commented out... # Force everyone to log in (disable anonymous access). require_login = True But yes, changing to Require_login = False Fixed the problem. Thanks Iry. Dave On 9/1/11 8:42 AM, "Iry Witham" wrote: > Hi Nate, > > We have found the solution to

[galaxy-dev] Selective storage of galaxy files

ould be like so that we could get institutional funding to develop the functionality. Thanks for any input you can provide. Dave -- Dave Walton Computational Sciences The Jackson Laboratory Bar Harbor, Maine ___ Please keep all replies

Re: [galaxy-dev] Display names accessible from Tool XML?

or. Are things like this documented somewhere? I couldn't find it in the wiki, and it took digging into the code and quite a bit of trial and error to figure it out. Thanks, Dave On 6/16/11 9:08 AM, "Dave Walton" wrote: > I'm building a tool that needs the "di

[galaxy-dev] Display names accessible from Tool XML?

I'm building a tool that needs the "display name" of a file inside the output of the tool. To clarify, I have a tool that merges gene expression result from cufflinks for many samples. It generates a "matrix" tab-delimited file that provides the results with genes or transcript down one axis and

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

he path of determining the cause. You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain brows

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

our "development server" in your response. Are you running only > 1 Galaxy instance, or more than 1? > > Is the behavior occurring for all of your users or just a few? Does it occur > with different browsers, or is it related to a certain browser brand? > > What vers

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

gt; for sure by deleting the cached templates in > ~//database/compiled_templates/user assuming you have not changed the setting > for the template cache in your universe_wsgi.ini file. If you have, delete > the files in the user directory where you have them stored. > > Greg V

[galaxy-dev] Error getting to http://galaxy/user/create on local instance

We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.2

[galaxy-dev] Database/Build

I'd like to get a better understanding of the point of the database/build attribute, and pose the question of when is the appropriate time to have it set? In our case at the Jackson Laboratory, the most common build is NCBI37/MM9. However, the feeling of many folks here, is that this should not

Re: [galaxy-dev] More on multiple inputs to a workflow

30 AM, "Dannon Baker" wrote: > On May 9, 2011, at 10:49 AM, Dave Walton wrote: >> First the new... So I have a workflow that does analysis on paired end mRNA >> Seq data. My workflow for single end works great, but with paired end, I >> can see an obvious way to su

Re: [galaxy-dev] Wrapper generator.

An alternative might be to have something like GenePattern has. It's not as seamless for the person who wants the wrapper as what's been suggested here, but it's easier than creating a lengthy XML file. GenePattern has an HTML Form interface for entering all the components of your tool, including

[galaxy-dev] Concatenation as first step in workflow

We have samples that span multiple lanes of our sequencer, that are the same sample. We'd like to have workflows where the first step is to concatenation the fastq files for one sample, and then feed it to the rest of our workflow (for RNA Seq). Unfortunately, when I use the Concatenation module

[galaxy-dev] More on multiple inputs to a workflow

So we loaded the change set that was developed at the hack-a-thon to our instance of galaxy. For the case where I have a directory of input files, where I want to run the same workflow for each, this change works great. There is one new issue I see, that I'd be interested in input on, and an old

Re: [galaxy-dev] Display BAM with IGV

Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Thanks, Dave On 4/27/11 9:07 PM, "Dave Walton" wrote: I’m getting this same err

Re: [galaxy-dev] Display BAM with IGV

I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave On 4/27/11 12:33 PM, "Daniel Blankenberg" wrote: Hi Alex,

Re: [galaxy-dev] No Menu after submitting workflow

nning workflows, though I haven't seen any > errors like this yet. > > Also, what's different about the two workflows (history destinations, > multiple-inputs, rename actions, etc.)? > > -Dannon > > On 04/19/2011 03:01 PM, Dave Walton wrote: >> I'm ge

[galaxy-dev] No Menu after submitting workflow

I'm getting inconsistent behavior when I run a workflow. I have one workflow,that when I run it, the green box indicating my workflow has been submitted shows up in the middle panel with Tools to the left, histories to the right, and menu above. For another workflow, I submit it successfully, but

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

p/NBIC_Galaxy_Hackathon_project#Loop_over_files_i > n_a_directory > > Since they had only 2 days, it will need some polish, but I heard this hack > already made it into the development branch of Galaxy, so we may see something > like this in the near future :) > > Cheers, &

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

the same. Where are the docs and information for the Galaxy API? Wondering if I could program this exact functionality in the script that the tool would execute. thanks, Leandro On Fri, Apr 15, 2011 at 4:28 PM, Dave Walton wrote: I've essentially asked the same question of the list in the

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

I've essentially asked the same question of the list in the past and gotten no real response. I have the same interest, but from a workflow perspective. * A module that allows me to select multiple datafiles (say fastq files) * Then pass each data file to a separate instance of a workflow that r

[galaxy-dev] Workflow variables and the workflow API

I'm working on a module that involves calling a workflow multiple times over a set of data. The workflow has a "variable" that I use for renaming output files. I see, using the workflow_execute.py example how to pass in file names, but I don't see how to pass in a value for this variable. When

Re: [galaxy-dev] Output file naming / dataset's label

I get it now!! I did my Rename Dataset/output_file with a variable ${input}. I chose that because I thought that would give me the name of the input file to that module, which I'm looking to carry on through out the run of my workflow (though actually I'd like the file name minus the file ext

Re: [galaxy-dev] Recommended Specs for Production System

This is very close to our config, except - We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise Server 11 (x86_64) with 16 GB of memory. Instead of SGE our HPC cluster uses Torque/Moab for scheduling. Also, we've set up a separate IO Node for upload of data files from the

Re: [galaxy-dev] Running a workflow programatically

When is this functionality expected to make it into galaxy-dist? Thanks, Dave On 3/16/11 6:07 PM, "Dannon Baker" wrote: > That's not actually what I expected, but I see what's going on here. The > workflows API expects explicit "Input Dataset" steps for mapping datasets, add > one of those a

Re: [galaxy-dev] Galaxy workflow with variable inputs

erm needs. Thanks, Dave On 3/18/11 11:23 AM, "Dave Walton" wrote: > I'm curious if there is a way to create a workflow as follows (or if anyone > else thinks this is a good idea, or for that matter has a good suggestion of > another solution): > > 1) User sel

[galaxy-dev] Galaxy workflow with variable inputs

I'm curious if there is a way to create a workflow as follows (or if anyone else thinks this is a good idea, or for that matter has a good suggestion of another solution): 1) User selects N groomed fastq files and puts them in a history 2) User selects a workflow that allows them to select the N