Re: [galaxy-dev] Adding a tool to Galaxy Main Server

Hello, New tools go into the Tool Shed, links with instructions are here: http://usegalaxy.org/toolshed http://wiki.galaxyproject.org/Tool%20Shed We tweet new tool additions to let the community know about them, info and recent tweets are here: http://wiki.galaxyproject.org/Galaxy%20on%20Twit

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Am Montag, den 07.10.2013, 14:07 +0100 schrieb Peter Cock: > On Tue, Oct 1, 2013 at 9:18 PM, Dave Bouvier wrote: > > I've done some investigating, and it looks like there is an irregularity > > with the installation of package_numpy_1_7, and somehow > > package_biopython_1_62 is not finding the (s

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Am Montag, den 07.10.2013, 10:36 -0500 schrieb John Chilton: > On Mon, Oct 7, 2013 at 10:22 AM, Peter Cock wrote: > > On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock > > wrote: > >> On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier wrote: > >>> Peter, > >>> > >>> I did some investigating, and it turns ou

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

Peter, Thanks for the information, it uncovered a problem with the testing framework that has been resolved in 10817:6b0c3592dde1. The listed repositories should start showing useful results next time the nightly tests run. --Dave B. On 10/04/2013 06:19 AM, Peter Cock wrote: On Fri, Oct

Re: [galaxy-dev] Dynamic job runner not being dispatched for a tool

Hi John, Thank you and Ilya for pointing this out. I was hitting my head on this for 2 days, convinced that I had misconfigured something. The tags didn't seem to have any effect, so I tried adding the .lower to the tool.get call. That did the trick. Thanks again, so much, for the help! You sa

Re: [galaxy-dev] Dynamic job runner not being dispatched for a tool

It might be due to this bug: http://dev.list.galaxyproject.org/Limit-number-of-Jobs-to-Trinity-tt4661790.html#a4661874 Ilya From: , Carrie L Date: Monday, October 7, 2013 1:46 PM To: "galaxy-dev@lists.bx.psu.edu" Subject: [galaxy-dev] Dynami

Re: [galaxy-dev] Dynamic job runner not being dispatched for a tool

I can look into this some more, but I have a couple quick questions. Can you try without the tags attributes, I am not sure what is going to happen since they do not match each other. Also, have you tried this fix, it looks like it could potentially be the same problem. https://bitbucket.org/galax

[galaxy-dev] Dynamic job runner not being dispatched for a tool

Hi List, I'm a bit baffled by a new tool I've tried to add to Galaxy. The job runner does not dispatch it correctly. I added the tool via the toolshed, set up the executable on the cluster side, and attempted to hook it up to the dynamic job runner. The destination always ended up set as local

Re: [galaxy-dev] GA file format documentation

Right, so you'd assemble the json clientside and use /api/workflows/upload to create it. See the import_new_workflow method for more details On Mon, Oct 7, 2013 at 12:31 PM, Philip Mabon wrote: > API allows for importing and exporting of workflows but nothing for > creating a new workflow. I w

[galaxy-dev] Adding a tool to Galaxy Main Server

Hi everybody, We are going to add our gene prediction tool to Galaxy Main server, anybody know whom we should contact? Thanks -- Hamid Reza Hassanzadeh, PhD Student & Graduate Research Assistant, Bioinformatics Lab, Center for Bioinformatics and Computational Genomics Joint Georgia Tech and Emory

Re: [galaxy-dev] GA file format documentation

API allows for importing and exporting of workflows but nothing for creating a new workflow. I will dig and see if anyone has published or presented on their internal libraries that create workflows on the fly. Thanks Takadonet On Mon, Oct 7, 2013 at 11:18 AM, Dannon Baker wrote: > Nothing form

Re: [galaxy-dev] GA file format documentation

Nothing formal. The .ga extension is simply the workflow dictionary exported as .json, if that helps -- there's no extra magic to the format. You may want to look at the workflow API, some users have had success integrating workflows created on the fly using it. -Dannon On Mon, Oct 7, 2013 at

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Mon, Oct 7, 2013 at 4:45 PM, Nicola Soranzo wrote: > actions_group is neither in stable nor in default branch of galaxy-dist > repository, it's present only in galaxy-central. > > Nicola i.e. for now only they can only be used and tested on the Test Tool Shed? It would be helpful if the bash

[galaxy-dev] error checking active jobs : KeyError: 'destination'

Hi List, I'm having this same issue - if I dispatch a job to dynamic job runner, and it then hands the job to pbs, then it will flip out if I restart the server. In my case, though, there is no error in the job state - it is sitting in the Torque queue where it should be. As far as I can tell,

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Mon, Oct 7, 2013 at 10:22 AM, Peter Cock wrote: > On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock wrote: >> On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier wrote: >>> Peter, >>> >>> I did some investigating, and it turns out that the if [[ condition ]] >>> syntax used in the ncbi tool dependency is o

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

actions_group is neither in stable nor in default branch of galaxy-dist repository, it's present only in galaxy-central. Nicola Il giorno lun, 07/10/2013 alle 11.24 -0400, Dave Bouvier ha scritto: > Peter, > > The platform detection code is not yet in the stable branch, but is > intended to be

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Peter, The platform detection code is not yet in the stable branch, but is intended to be included in the upcoming release. The automated testing framework does run the default branch, though, so the nightly tests will make use of the new definitions. --Dave B. On 10/07/2013 11:22 AM, Pe

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock wrote: > On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier wrote: >> Peter, >> >> I did some investigating, and it turns out that the if [[ condition ]] >> syntax used in the ncbi tool dependency is only compatible with bash, not >> sh. > > Does that mean the

[galaxy-dev] GA file format documentation

Is there any documentation on how exported workflow with '.ga' extension are structured? We are looking for the ability to create our workflows without using the workflow editor thru the web portal. Thanks Takadonet ___ Please keep all repl

Re: [galaxy-dev] fastx_toolkit not recognizing fastq files

Thanks Dannon! That was the fix. It's odd that it isn't part of the auto detect feature. -Ian On Oct 7, 2013, at 10:46 AM, Dannon Baker wrote: > If you look at the attribute details for one of your fastq files, what does > Galaxy say the filetype is? You most likely need to flip it from 'fas

Re: [galaxy-dev] fastx_toolkit not recognizing fastq files

If you look at the attribute details for one of your fastq files, what does Galaxy say the filetype is? You most likely need to flip it from 'fastq' to 'fastqsanger' so Galaxy will know how to handle the file, it doesn't automatically detect this. -Dannon On Mon, Oct 7, 2013 at 10:38 AM, UMD Bi

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier wrote: > Peter, > > I did some investigating, and it turns out that the if [[ condition ]] > syntax used in the ncbi tool dependency is only compatible with bash, not > sh. Does that mean the test system has switched between sh and bash and back to sh

[galaxy-dev] fastx_toolkit not recognizing fastq files

Hello, I've installed Galaxy on two separate machines. None of the fastx tools recognize my fastq files. They are not appearing in the drop down list on Galaxy for input options. I'm getting the same behavior on both machines. I've used the tool_shed to install fastx on one machine and I've done

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Peter, I did some investigating, and it turns out that the if [[ condition ]] syntax used in the ncbi tool dependency is only compatible with bash, not sh. For sh, the corresponding syntax would look like: if [ "$string" = "value" ] then echo "string is equal to value" fi However, it str

Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined

Hello all, I'm having this same issue with Functional Test being broken. I've switched between 'stable' and 'default' and it doesn't seem to fix the issue. Its possible that I'm not switching properly? This is my first local install of Galaxy so I'm new to the structure, detailed help would be

[galaxy-dev] GA file format documentation

Is there any documentation on how exported workflow with '.ga' extension are structured? We are looking for the ability to create our workflows without using the workflow editor thru the web portal. Thanks ___ Please keep all replies on the l

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Tue, Sep 24, 2013 at 10:58 AM, Peter Cock wrote: > Hi all, > > Some good news, the strange missing /bin/sh error has gone away > on the Test Tool Shed: > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc > > The BLAST+ wrapper tests also look good on the main Tool Sh

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Tue, Oct 1, 2013 at 9:18 PM, Dave Bouvier wrote: > I've done some investigating, and it looks like there is an irregularity > with the installation of package_numpy_1_7, and somehow > package_biopython_1_62 is not finding the (successfully) installed numpy > dependency. I duplicated the depende