Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

It's the same case as what I'm getting. I can see the output via "eye" icon on the history panel and able to download the files as well. On 1 November 2011 03:37, Mickael ESCUDERO wrote: > Hi there, > > I'm getting exactly the same problem with any job running on a TORQUE/PBS > cluster. The jobs

Re: [galaxy-dev] Re Acutal user code

It seems to be working but when I run BWA or Bowtie it finishes green but the files are empty. Doesn't give me much information. I also tried fastqc and it ran just fine. -Original Message- From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu] Sent: Monday, October 31, 2011 1:21

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

Thanks for the suggestions guys. I'm still struggling with a couple of things. How do I give the user a link to expose the file from extra_files_path as a history item and how would I set metadata like file format and db on the extra files? Things like PDF and text work fine, but I'd really like

Re: [galaxy-dev] Clusters, Runners, and user credentials

I modified drmaa.py to pass the galaxy users path variable to the actual user. As long as the galaxy user's environment is correct then the actual user's environment should be correct. -Original Message- From: Glen Beane [mailto:glen.be...@jax.org] Sent: Monday, October 31, 2011 4:20

Re: [galaxy-dev] data set import into current history

Oren, Not yet. Right now, the only path to accomplish this would be to upload via the API to a library, and then copy the contents to a history. This is a feature that definitely needs to be implemented, we simply haven't had a chance yet. If you're interested in writing it, I'm sure we'd we

Re: [galaxy-dev] Clusters, Runners, and user credentials

Many of us are using the PBS job runner (for TORQUE) and would definitely be interested in a port. How do you deal with making sure the user's environment is configured properly? We use a python virtualenv and load specific module files with tested tool versions in our galaxy users startup scr

[galaxy-dev] data set import into current history

Dear All, Is there an API call for importing data sets into the current history (or a new history)? This feature exists in the web UI. Thanks so much, Oren ___ Please keep all replies on the list by using "reply all" in your mail client.

[galaxy-dev] ImportError: No module named galaxy

Dear All, I am running the example_watcher_folder.py API script and it intermittently fails to run a workflow on a file dropped into the import directory (the file is imported and the workflow starts running, but its jobs hang or fail). Galaxy uses a condor dramaa job runner. When I look at t

Re: [galaxy-dev] Clusters, Runners, and user credentials

BTW, I am not sure if PBS works with drmaa. If not then the code will need to be ported to work with pbs. Ilya -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, October 31, 2011 3:27 PM To:

Re: [galaxy-dev] Clusters, Runners, and user credentials

Lyod, See Nate's email below Title: Actual user code. We have been working on implementing this feature in galaxy. The code is still in development but feel free to test it out and let us know how it works for you. Best, Ilya -Original Message- From: galaxy-dev-boun...@lists.bx.psu.e

[galaxy-dev] Clusters, Runners, and user credentials

I'm a systems administrator for an HPC cluster, and have been asked by a faculty member here to try to get galaxy to work on our cluster. Unfortunately, there are one or two outstanding questions that I can't seem to find the answer to, and I'm hoping someone here can help me out. In particular, i

[galaxy-dev] getting job's index position in the history from database

I am trying to get job's index in the history panel using SQL query (index number shown in the history when a job is submitted). I am unable to locate the necessary table-column for it. Any pointers in which table-column it is located will be really helpful. -- Thanks, Shantanu.

[galaxy-dev] Upcoming Galaxy Events

Hello all There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events

Re: [galaxy-dev] Running galaxy on external hard drive

Hi Hans, Thanks for your reply.The error I am getting is "Can't open folder /media/..." But I guess my question was more in general if I can have Galaxy run from an external drive so that it saves everything on it instead of /home, and if so, how (modifications etc..) Thanks A On Mon,

Re: [galaxy-dev] Re Acutal user code

Chorny, Ilya wrote: > Sweet!! Can't wait to see it. Have a look: https://bitbucket.org/natefoo/galaxy-central-ichorny/ Caveats: * job_working_directory has to be in a shared filesystem * outputs_to_working_directory must be True * set_metadata_externally must be True One thing

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

Hi, Jesse, IMHO, the Html datatype is perfect for this. By definition, the composite datatype can have any number of files (of any type!) in the files_path, but of course, your tool or wrapper will need to generate the legal html contents of that html page but that can be done when the files_path a

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

Have you checked out the barcode splitter? The output is quite similar, an HTML report with links to the split files. -Dannon On Oct 31, 2011, at 2:50 PM, Jesse Erdmann wrote: > I have an in-house Perl tool that generates a double digit number of > outputs that we'd like the user to have acces

[galaxy-dev] Appropriate method of coalescing tool output (not workflow)

I have an in-house Perl tool that generates a double digit number of outputs that we'd like the user to have access to, but don't necessarily need to be in the history. A complicating factor is that the exact number is determined at run time as user input can add any number of outputs that can't b

[galaxy-dev] Integrating a new display tool with bigwig format

Hello: I am trying to add a display tool to a local galaxy instance. However, I don't understand the scripts used. In the tutorial at: http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial The script for "Basic Topics" uses variables that are not traceable. Is ther

[galaxy-dev] Local Galaxy Instance MarkupSafe error

Hi there, I'm getting exactly the same problem with any job running on a TORQUE/PBS cluster. The jobs actually run fine as I can see the output and download it, but it's marked as failed in the galaxy history, with the following message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of

Re: [galaxy-dev] Running galaxy on external hard drive

Hi Allessia It is difficult to help you without knowing what kind of error you've got. What is the error message you get? Regards, Hans On 10/31/2011 03:35 PM, Alessia D wrote: Hi, I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-

[galaxy-dev] galaxy citation_url setting

Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help --> How to Cite Galaxy). Is it something hard-coded in the source? -- Thanks, Shantanu. ___ Please keep all replies on

[galaxy-dev] Running galaxy on external hard drive

Hi, I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can