galaxy-dev March 2012

galaxy-dev@lists.galaxyproject.org

110 participants
202 discussions

HMMER wrappers
by Peter Cock 26 Jul '12

26 Jul '12

Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter

4 16

Looking for recommendations: How to run galaxy workflows in batch
by Dave Lin 05 Jul '12

05 Jul '12

Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave

5 8

Exporting histories through API
by Martin Dahlö 25 Jun '12

25 Jun '12

Hello there As the subject hints, I am trying to export histories through the API. Doing it through the web interface is a breeze, but has it been implemented in the API yet? I could not find anything about it in the examples or by searching the web/this list. I am planning to only use Galaxy through the API to import my data and run some workflows on it, and then export the results. Preferably specific files from the history, but a bundled history like the one you get from the web interface 'Export history' would be ok as well. Has anyone done something like this, and can point me in the right direction? :) Mvh Martin Dahlö --- Bioinformatic support martin.dahlo(a)scilifelab.uu.se +46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se ---

3 3

Workflow API (runtime modification of tool parameters)
by Richard Park 21 Jun '12

21 Jun '12

Hello, I was wondering what would be the best way to extend Galaxy's API functionality to allow for runtime modification of tool parameters? I have successfully been able to run workflows programmatically using the API, following the basic steps in: scripts/api/execute_workflow.py. scripts/api/example_watch_folder.py However, it is unclear to me, what would be the best way to run workflows through API with specific parameters at various steps. Should I generate new workflows for every workflow that requires different parameters and upload this to galaxy? Or would it be better to extend the API to allow for runtime parameter configuration? If this is the case, any pointers on how to extend this would be greatly appreciated. Thank you, Richard Park

2 7

Galaxy server configuration question
by Huayan Gao 07 Jun '12

07 Jun '12

Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? Best, Huayan

4 16

LookupError: No section 'main' (prefixed by 'server') found in config
by Iry Witham 07 Jun '12

07 Jun '12

I have performed a new install of Galaxy for development and deployment purposes. However, when I run the run.sh script I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 274, in command relative_to=base, global_conf=vars) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 308, in loadserver relative_to=relative_to, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 210, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 363, in get_context object_type, name=name) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 528, in find_config_section self.filename)) LookupError: No section 'main' (prefixed by 'server') found in config /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini I have modified the universe_wsgi.ini to reflect the way our production server is configured. The following is the server section of that file: # # Galaxy is configured by default to be useable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: # # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer # # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. # examples of many of these options are explained in more detail in the wiki: # # Config hackers are encouraged to check there before asking for help. # ---- HTTP Server ---------------------------------------------------------- # Configuration of the internal HTTP server. [server:web0] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 2 [server:web1] use = egg:Paste#http port = 8081 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 3 [server:web2] use = egg:Paste#http port = 8082 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. #use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. #use_threadpool = True # Number of threads in the web server thread pool. #threadpool_workers = 5 # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. # These filters are disabled by default. They can be enabled with # 'filter-with' in the [app:main] section below. # Define the gzip filter. [filter:gzip] use = egg:Paste#gzip # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy My production server works fine, but this one will not run. What am I missing? Thanks, Iry

3 2

uploading multiple files into one dataset
by Jorrit Boekel 01 Jun '12

01 Jun '12

Dear list, Our lab's proteomics data is frequently outputted into >50 files containing different fractions of proteins. The files are locally stored and not present on the Galaxy server. We've planned to somehow (inside galaxy) merge these files and split them into tasks so they can be run on the cluster. We would either merge/split the files by concatenation, or untar/tar files at every job, depending on filetype and tool. No problems so far. However, I have been looking around for a way to upload >50 files simultaneously to galaxy and convert to one dataset, and this does not seem to be supported. Before starting to create a hack to make this work, which doesn't seem especially trivial to me, I'd like to know if I should instead use libraries. From what I've seen, libraries are not treated as datasets in Galaxy but rather contain datasets. If there was a "tar all sets in library and import to history" I'd be using that, but I've only encountered "tar/zip sets and download locally" which would be a bit of a workaround. I haven't found much on this subject in the mailing list, has this functionality been requested before? cheers, jorrit boekel

2 2

Galaxy administrators - admin_users setting
by Peter Cock 30 May '12

30 May '12

Hi all, To make someone an administrator on a local Galaxy install, do I just need to add their email (login) to the comma separated setting admin_users in universe_wsgi.ini? https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface I have this working on one server, but it doesn't seem to have any effect on a second server. Both are now running the current release (changeset 50e249442c5a). Is there some other setting needed to enable the admin interface? Thanks, Peter

2 4

Batch limit on Wokflows
by Petit III, Robert A. 29 May '12

29 May '12

Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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how is metadata generated
by KOH Jia Yu Jayce 28 May '12

28 May '12

Hi Just wondering how metadata files in galaxy-dist/database/files/_metadata_files are generated? Are there any configurations in the xmls that specify these to be generated? Thanks

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galaxy-dev March 2012