[galaxy-dev] LSF DRMAA/FedStage config-make errors

Hello all, I am trying to get a Galaxy server configured to submit jobs to an LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems. I have the Galaxy host as a client in LSF, but when I tried to configure/make/install the FedStage drmaa code, it errors out in the make

Re: [galaxy-dev] Blastxml error on Galaxy Cloudman

Hi Mohammad, Don't forget to CC the mailing list ;) It sounds like something has gone wrong with the update... Peter On Wednesday, August 29, 2012, Mohammad Heydarian wrote: > Hi Peter, > Thanks for your response. > > I am not using any of the Blast tools, I have only tried using the "filter >

[galaxy-dev] September 2012 Galaxy Update

Hello all, The September 2012 Galaxy Update is now available. *Highlights:* - 41 new papers(a new monthly high) - 3 new public Galaxy Servers

Re: [galaxy-dev] Modules

galaxy already has tool-dependencies which can be used. for example, velvet's tool XML would include: velvet the above will use the default version; or to specify a specific version: velvet in your tool-dependencies dir (as defined in universe_wsgi.ini): mkdir velvet cd velvet mkdir 1

[galaxy-dev] Error when downloading files through API

hey galaxy, Has anyone seen this error when downloading files through the API? "TypeError: display_data() got an unexpected keyword argument 'key'" It works for the majority of my files, but fails on "wig" files. This problem recently occurred when I updated my galaxy code about 2-3 weeks ago. Th

Re: [galaxy-dev] get wsgi headers

On Aug 24, 2012, at 9:48 AM, Mutlu Dogruel wrote: > Hi folk, > > Do you know any method for reading (the extended) WSGI HTTP headers > from a custom tool? > > If I put some debugging lines in > $galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py, I can > read the HTTP headers I want. B

Re: [galaxy-dev] Blastxml error on Galaxy Cloudman

Hi The BLAST+ tools and the definition of the blastxml format were moved to the tool shed. You should have seen a migration message during the update... If you are not using these tools, perhaps you have a legacy reference to the blastxml file which should be removed? If you are using BLAST+ the

[galaxy-dev] Blastxml error on Galaxy Cloudman

Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error: WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.data

[galaxy-dev] using data_ref to refer to column names?

Hi, I have some code that makes a plot and creates a legend from a given column name in the user's input data, which may have arbitrary column names. I'd like to create a dropdown list that has all the column names in it, but I don't know the names beforehand; I won't know them until the user uplo

Re: [galaxy-dev] Tool test question

On Jul 18, 2012, at 5:02 PM, christopher fletez-brant wrote: > Hi Nate, > > The test XML is: > > > > > > > > > > > > > > And the XML for the problematic parameter, indices_path, is: > > > > > >

Re: [galaxy-dev] xsendfile permissions

On Jul 17, 2012, at 3:16 PM, Julian Pradinuk wrote: > Hi all, > > I'm wondering if someone who has downloads working through apache (using > xsendfile) has encountered this error when downloading HTML files: > > (13)Permission denied: xsendfile: cannot open file: > /galaxy_data/production/tmp/

[galaxy-dev] Issues with database / metadata after upgrade

Hi Team, I had performed an upgrade of my Galaxy server and had experienced an issue with some of the database / metadata files have been corrupted. I have found instances where the dataset exists, but cannot be detected or read by galaxy when attempting to analysis data from a history. In so

Re: [galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)

Great, I am glad it was useful. Renaming the repository isn't needed, especially if you just have one pull request open at a time. But there have been times I have had maybe 4 or 5 open pull requests at once, so then it helps to keep track of which repository maps to which feature or bug fix. If I

Re: [galaxy-dev] upload files by cluster with pbs-python returns empty files

On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote: > Hi, > > We have set up a local instance of galaxy-dist, using pbs-python to > communicate with our HPC. Everything is working great, except for the upload > functionality. > > When I assign the upload1 to local:/// , uploading of small fil

Re: [galaxy-dev] Cannot install freebayes with migration script

That's pretty much what I had to do. Thanks for the full explanation so others will know! Philip Mabon Senior Bioinformatician National Microbiology Laboratory Public Health Agency of Canada On Wed, Aug 29, 2012 at 10:31 AM, Assaf Gordon wrote: > Hello Philip, > > Philip Mabon wrote, On 08/29

Re: [galaxy-dev] Cannot install freebayes with migration script

Hello Philip, Philip Mabon wrote, On 08/29/2012 10:08 AM: > Looks like I forgot to reset that value. So making progress... I can install > freebayes successfully (the front end timeout but it worked) > > However, samtools fails with the following message in web worker log: > > [localhost] local

Re: [galaxy-dev] missing slash when installing from toolshed?

Hi, Greg, Thank-you so much for taking the time to answer my question. You appear to be correct; I removed the virtual hosting configuration from apache (I had some redirection configured to automatically forward from port 80 to port 443), and this problem went away. I think I should be able to

Re: [galaxy-dev] Cannot install freebayes with migration script

You should be able to click on the link for the samtools dependency from the "Installed tool shed repository" page for freebayes. Clicking the link will allow you to browse the INSTALLATION.LOG on disk and see what caused the error. Your environment is probably missing some component required

Re: [galaxy-dev] Cannot install freebayes with migration script

Looks like I forgot to reset that value. So making progress... I can install freebayes successfully (the front end timeout but it worked) However, samtools fails with the following message in web worker log: [localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile Warning: local() enco

Re: [galaxy-dev] Cannot install freebayes with migration script

Hi Philip, What do you have for the following configuration setting in the [app:main] section of your universe_wsgi.ini file? The config setting for tool_dependency_dir should be a valid subdirectory that is writable by the user that starts your Galaxy server. # Location for installing tool d

Re: [galaxy-dev] Cannot install freebayes with migration script

I upgrade Galaxy to changeset 2531e085f262 and attempt to install freebayes from the admin panel. It installed the freebaye xml tool and appears in the tool panel but both dependencies did not install (freebayes itself and samtools) When I attempt to install either of them from the "Tool shed rep

Re: [galaxy-dev] Deleted jobs on the cloud keep running

This should be fixed in 7443:f1eb04839053, but the cloud is (by default) at 7166:1744124f8ee4. The default installation on the cloud will be updated next time we do a galaxy-dist release, but until then you can certainly update your own instance through the admin panel (or via terminal). -Dann

[galaxy-dev] Deleted jobs on the cloud keep running

Dear list, When running Galaxy/Cloudman on Amazon (on Ubuntu 12.04), I run into the following: - I start a job with in the tool.xml file. - Since I have use_tasked_jobs=True in universe_wsgi.ini, the job is split and divided over the instances on EC2 - I change my mind, and click on the dele

[galaxy-dev] Running apache as galaxy

Dear all, I had problems configuring apache, which were solved by running apache as user galaxy. Is this an security issue? The server will only be use for galaxy. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Se

Re: [galaxy-dev] How to restart the Galaxy process

Hi, try that in your galaxy directory: GALAXY_RUN_ALL=1 sh run.sh --stop-daemon GALAXY_RUN_ALL=1 sh run.sh --daemon Cheers, Bjoern > Hello, > > I modified the Galaxy configuration file and would like to stop and > re-start the Galaxy process. Can you tell me how to do that? > > Thank you. >