June 2013 - galaxy-dev - lists.galaxyproject.org

Galaxy on Cluster - how to set -a flag with username
by greg 12 Jun '13

12 Jun '13

In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like this: default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/ Is this possible? Thanks, Greg

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Recently Used Histories
by Jonathan Strickland 12 Jun '13

12 Jun '13

Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the "Options" button on the rightmost pane, "Saved Histories" in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the "History Lists" in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the "Saved Histories" or "Histories Shared With Me" grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default "Analyze Data" screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself!

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Toolshed bug related to readme files
by Lance Parsons 11 Jun '13

11 Jun '13

I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner… Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aa… -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Trackster error: not able to find the chrom len file
by Joachim Jacob | VIB | 11 Jun '13

11 Jun '13

Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. Trackster displays an error after opening a saved view: *********************** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *********************** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster Thanks for any advice, Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Pasted text in upload.py
by Daniel Gorelik 11 Jun '13

11 Jun '13

Hello, I am trying to understand how the upload.py file works. I have already spent a long time trying to figure this out, but I just cannot at all understand where, for example, a pasted text input is saved. Let's say, for example, I wanted to make any pasted text input all caps. Where would I put .upper? Thank you, Daniel Gorelik

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Trackster set display mode - Output looks all the same
by Linda Cham 11 Jun '13

11 Jun '13

Hi. Running Galaxy stable_2013.06.03 version on RH6.2 with postgresl db. Generated bam and vcf file to view under Trackster. Set up trackster by following http://wiki.galaxyproject.org/Learn/Visualization directions. No matter what I choose for "Set display mode", all I see is blocks of color for the vcf (is that the INTENSITY mode?) and a line for the BAM file which doesn't seem to be what the directions above for the Histogram, Line, Filled, and Intensity are supposed to look like. Not sure what the output supposed to look like so can't tell if it is correct or not. 1- Should the "Set display mode" give out different output? 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly? What is shown: Not sure if the 2 images that I had inserted above will be viewable after I send out the request. Thanks in advance. Linda

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Recently Used Histories
by Jonathan Strickland 11 Jun '13

11 Jun '13

Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the "Options" button on the rightmost pane, "Saved Histories" in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the "History Lists" in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the "Saved Histories" or "Histories Shared With Me" grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default "Analyze Data" screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself!

1 0

problems with exporting or importing data
by Edlund, Anna 11 Jun '13

11 Jun '13

Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select 'Import a History from an archive'. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedlund(a)jcvi.org<mailto:aedlund@jcvi.org>

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minor SQLAlchemy PostgreSQL issue
by Richard Burhans 11 Jun '13

11 Jun '13

The SQLAlchemy "postgres" dialect was renamed to "postgresql". Changing: database_connection = postgres:///... to: database_connection = postgresql:/// in the ini file causes Galaxy (tool_shed in my case) to fail to start as the "postgres" dialect is mentioned by name a few places in the code. Not a big deal, but I figured I'd report it. -rico

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Failed runtime validation of To
by Sameer Dixit 11 Jun '13

11 Jun '13

Hey all, I've been trying to run a workflow on Galaxy, which basically attempts to establish a correlation between the Chip-Chip, Polymerase binding and Dnase Hypersensitivity data. The input would be these 3 files, I am initially performing a liftover on the Chip-Chip data to convert from hg18 to hg19 and then using the output to establish the correlation. The following error keeps coming up 'Failed runtime validation of To (An invalid option was selected, please verify)' Can anyone please tell me what this might mean? This came up while attempting to run the following tool Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/runners/__init__.py", line 121, in prepare_job job_wrapper.prepare() File "/galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/__init__.py", line 656, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File "/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py", line 2343, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File "/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py", line 2382, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError Any assistance would be highly appreciated!! Thanks -Sameer

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