- galaxy-dev - lists.galaxyproject.org

Galaxy-LIMS and multiple sample
by Davide Cittaro 19 Feb '14

19 Feb '14

Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d

1 0

Sending tool output to input parameters of downstream tool(s)
by Peter Cock 19 Feb '14

19 Feb '14

Hi all, I was recently wondering how it might be possible for an output from tool A to be used as a parameter when calling tool B (without modifying tool B to take a data configuration file or anything like that). To clarify, I'm thinking about simple parameters like a single integer/float/string like "median insert size" or "average coverage" which map to a single input parameter in a downstream tool. Workflow parameters basic $variable support is similar to what I'm thinking about here, see: https://wiki.galaxyproject.org/DevNewsBriefs/2011_01_31 Perhaps one day in addition to tool outputs being files, they can include setting $variables (local to the history), which could then be used within downstream tools? I can see this has downsides with tracking the providence of each variable though... thus: Another idea would be extra filetypes for each parameter type (Unix philosophy - make everything into a file), e.g. integer_parameter, float_parameter, ... which "Tool A" could define as an output, and write to. Galaxy would then need to offer these history entries to the user when a later tool (e.g. "Tool B") asked for a parameter of that type (e.g. an integer, or a float). (This idea could be extended further, with data files using JSON or something to hold a structured set of parameter values which Galaxy could then offer to fill later tool's inputs.) Crazy, or is there some mileage in this idea? Peter

1 0

anybody know how to use #{input} in a workflow with the XY plotting tool?
by Langhorst, Brad 19 Feb '14

19 Feb '14

This tool can have multiple inputs, so there would need to be a way to select which one to use. (see attached ) i’m just using one and #{input} produces an empty string. tried #{input0} #{input1} #{input[0]) all to no avail. Any ideas? [cid:7D98BFD9-B958-4E7B-A556-B06C6856F949@neb.com] Brad -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

2 1

Role-based tool availability.
by Luca Toldo 19 Feb '14

19 Feb '14

dear Galaxians, the users of my galaxy service are quite eterogenous, and would like to have the toolbar customised only with subsets of the available tools. Such customisation should be possible a) at user group level b) at individual level A possibility for group-level tool availability could be to create separate galaxy sites and then upon login redirect the user to the specific one. For individual level customisation of the toolbar, one would need a different infrastructure, i guess. I would appreciate learning your views / experiences on the topic. Sincerely your Luca

2 1

Acceleration Card Optimization
by Panzer, Adam 18 Feb '14

18 Feb '14

Hello All, I recently was gifted an ioFusion ioFX acceleration card to help speed my bioinformatics work along and I am wondering how best to integrate it into my instance to make Galaxy more efficient. Is it sufficient to merely ensure that the datasets being operated on are on the flash storage (I guess by placing the main Galaxy directory there) or are there other elements that should also move lest they create bottlenecks elsewhere (tmp directory, files related to proxy/ftp server, tool shed, etc.)? Suggestions will be greatly appreciated. Thanks, Adam The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

2 1

Renaming in workflow - bis
by Charles Girardot 18 Feb '14

18 Feb '14

Dear all, I am looking into options for renaming output files automatically in workflows and I found this thread : http://dev.list.galaxyproject.org/Renaming-in-Workflows-td4656426.html#a465… I managed to use the following in test workflow: - ${} to create input variable to the workflow - #{} to reuse the tool input(s) In the post indicated earlier, I read that one can even manipulate input string with basename, upper and lower e.g. #{ input | basename} All this is really awesome and my questions are : - are there other ways to fetch existing e.g. env variables than ${} or #{} - what other variables can be fetched e.g. maybe this 'on_string' ? - are there string functions other than basename, upper and lower that can be used ? Is there a list? Thx a lot Charles

1 0

Galaxy Tool Shed packages for Biopython
by Peter Cock 18 Feb '14

18 Feb '14

Hi all, I've send this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, start here: http://galaxyproject.org - while the easy to guess Biopython website is at http://biopython.org Brad Chapman and I are both Biopython core developers, and are also both on the "IUC" Galaxy Tool Shed committee because we've been quite involved in wrapping and writing tools for use on Galaxy. Fellow committee member Björn Grüning has done a lot of the hands on work defining package definitions for dependencies within the Galaxy Tool Shed ecosystem - including defining them for Biopython, NumPy, SciPy, MatPlotLib, etc. We're very grateful for his hard work - most of which is now available under the IUC group account: http://toolshed.g2.bx.psu.edu/view/iuc/ http://testtoolshed.g2.bx.psu.edu/view/iuc/ The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to: http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/ This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/ We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages Currently the "Galaxy packagers" team on GitHub which has read and write access to this new repository is just me, Brad and Bjoern. Regards, Peter

2 3

Setting access role for datasets through the API
by Joseph Ward 18 Feb '14

18 Feb '14

Hi, I'm trying to use the API to upload data into galaxy, setting the access and modify roles as I do so. I've managed to get the roles working for the libraries (using LIBRARY_ACCESS_in and LIBRARY_MODIFY_in) but when it's uploaded the access roles for the datasets are all set to my personal role. I had a poke about the form for modifying the permissions of a dataset and took a shot at setting DATATSET_ACCESS_in but with no luck. Is it possible to set the access role for individual datasets using the API? Would this be possible to do at the upload stage or would I need to go over each of the datasets in the library after they've been uploaded and set the access role? Many thanks, Joe Ward (First time posting to anything like this, so please let me know if I've not gone into enough detail etc)

2 1

Attempting to bind to AMQP message queue, but kombu dependency unavailable
by Peter Cock 18 Feb '14

18 Feb '14

Hi all, I just updated my development server, and ran into what looks like a missing dependency: $ ./run.sh ... galaxy.jobs.manager DEBUG 2014-02-18 11:58:06,422 Starting job handler galaxy.jobs INFO 2014-02-18 11:58:06,422 Handler 'main' will load all configured runner plugins galaxy.jobs.runners DEBUG 2014-02-18 11:58:06,423 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2014-02-18 11:58:06,425 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2014-02-18 11:58:06,460 Starting 3 LWRRunner workers Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxy/galaxy-central/lib/galaxy/app.py", line 130, in __init__ self.job_manager = manager.JobManager( self ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 31, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 576, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 496, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/lwr.py", line 45, in __init__ self.client_manager = build_client_manager(**client_manager_kwargs) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/lwr_client/manager.py", line 41, in build_client_manager return MessageQueueClientManager(**kwargs) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/lwr_client/manager.py", line 89, in __init__ self.exchange = LwrExchange(self.url, self.manager_name) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py", line 37, in __init__ raise Exception(KOMBU_UNAVAILABLE) Exception: Attempting to bind to AMQP message queue, but kombu dependency unavailable $ hg summary parent: 13557:75b13d642f94 tip Allow LWR runner to publish/consume messages via message queue. branch: default commit: 9 modified, 240 unknown update: (current) (Local modifications mostly extra logging lines; nothing which looked relevant here) Regards, Peter

2 3

SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)
by Wang, Xiaofei 18 Feb '14

18 Feb '14

Dear, Is it possible to use SnpEff with genomes of other species (e.g. Drosophila) other than C.elegan on galaxy website (not local)? It seems the only option for the genome menu (Caenorhabditis elegants : WS220.64). In fact, I am trying to use CloudMap (the EMS Variant Density Mapping workflow) to analyze data for Drosophila. So, I have to edit the workflow based on my own data. For SnpEff on the workflow, I tried to change "Genome" to other species from Caenorhabditis elegants : WS. But, there is no other options. Then, I changed it "to be set at runtime". When I run the workflow, I still can not change it to other species. Then, I went to see the SnpEff tool on galaxy website and found that there is no other options for "Genome" option. So, could you help me about this? Could I use SnpEff and CloudMap (the EMS Variant Density Mapping workflow) other than worm? Or, I have to install galaxy locally for this objective? Thank you so much! Have a nice day!

3 4