May 2012 - galaxy-dev - lists.galaxyproject.org

Error starting Galaxy after upgrade.
by Luobin Yang 08 Jun '12

08 Jun '12

Hi, I upgraded Galaxy to the latest version using the command: "hg pull -u", then when I run "sh run.sh" I got the following error messages: Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 546, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: mercurial==2.1.2 Fetch failed. What happened here? Thanks, Luobin

2 1

Toolshed error with proprietary datatypes
by Björn Grüning 08 Jun '12

08 Jun '12

Hi, has anyone encountered that problem or has an idea how to solve it? Traceback (most recent call last): File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line 26, in load_proprietary_datatypes load_datatype_items( self.app, tool_shed_repository, relative_install_dir ) File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036, in load_datatype_items app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=repository_dict, deactivate=deactivate ) AttributeError: 'UniverseApplication' object has no attribute 'toolbox' All files are in one repository ... xml, the python-class und the converters. I was able to successfully upload it to our test-toolshed but after installing it (also successfully) galaxy is not able to start. Also the converters are recognised as tools in the toolshed is that intended? Thanks! Bjoern

2 7

AttributeError: 'module' object has no attribute 'FakeSocket'
by Sarah Diehl 07 Jun '12

07 Jun '12

Hi all, today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in <module> from galaxy.util.shed_util import * File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in <module> from mercurial import ui, commands File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py", line 12, in <module> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py", line 12, in <module> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py", line 11, in <module> import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py", line 11, in <module> import changelog, byterange, url, error File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py", line 13, in <module> import httpconnection as httpconnectionmod File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py", line 16, in <module> from mercurial import httpclient File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py", line 48, in <module> import socketutil File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py", line 82, in <module> class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket' Any help appreciated. Thanks. Sarah

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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

Is there a way to dynamically assign Queues in Galaxy
by Anthonius deBoer 06 Jun '12

06 Jun '12

Hi, I often find my self having to battle with other users of the cluster, even for the one-off jobs that someone runs interactively... We have setup Fast/short queues and Long queues... Is there a way for a tool to sometimes be placed in the fast queue and sometimes in the long queue? I know I can setup a tool in the universe file and add a -pe option there...But is there a way to dynamically assign jobs sometimes to one queue and sometimes to another? Even an option in the UI would work, since I could make the short queue the default for interactive work and people could turn it off in workflows that will run for a long time or will run with many samples.... Thanks Thon

5 10

Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?
by Anthonius deBoer 05 Jun '12

05 Jun '12

Hi, I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?). Thanks Thon Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view >> return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view >> return template.render( **data ) Module mako.template:296 in render view >> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view >> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view >> callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view >> __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)

2 3

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

Error executing tool: cannot find 'database'
by Marine Rohmer 31 May '12

31 May '12

Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the <command>, <param> etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface. However, when I execute my tool, Galaxy says to me : Error executing tool: cannot find 'database' And in my shell, I can see : 127.0.0.1 - - [30/May/2012:10:47:01 +0200] "GET /tool_runner?tool_id=myTool HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 333, in execute data.name = fill_template( output.label, context=params ) File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=myTool" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04) All help will be very very appreciated ! Thank you, Marine

3 6

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