- galaxy-dev - lists.galaxyproject.org

How do I contribute a bug-fix?
by Pablo Cingolani 23 Jun '10

23 Jun '10

Could someone please tell me (or point me to) the proper procedure to contribute a bug fix? Thank you :-) P.

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More flexible use of Sun Grid Engine by Galaxy
by Peter van Heusden 23 Jun '10

23 Jun '10

Hi there At the moment Galaxy's choice of Sun Grid Engine settings are done on a per-tool basis - that is, you can define different queues and projects on a per-tool basis. However, I've got two use cases that currently aren't supported. 1) Per-user settings. The SGEJobRunner potentially has access to user information (via the job.session_id), and while all jobs get run as user galaxy, per-user settings could be simulated by mapping Galaxy users to SGE projects. Then the SGE admin can do load-balancing, etc on a per-project basis. For a site with a relatively small and static set of users this could work. Alternately you need to map Galaxy users to SGE users - this is much trickier, requiring elevated privileges and thus probably a separate job runner daemon. 2) Queue selection. Again this could be done on a per-tool basis, but usage patterns don't always support that. So for example, our site has two queues - a long running one and a short running one. Certain resources are reserved for only the short running queue's usage. How to select a different queue for jobs raises a bit of a design problem for me - effectively you're telling Galaxy "I want to run this workflow, but with this extra parameter" - its almost like having a "meta parameter" since clearly you don't want to have queue selection as an input for any particular tool. So I'd be interested in the Galaxy team's input as to how best to address these two use cases. Thanks, Peter

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Error when dowloading large compressed data library
by padioleau 23 Jun '10

23 Jun '10

Dear Galaxy developers, When I try to download a large data library (from the Data Libraries tab) as any compressed file I encounter this error: ### Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request POST /galaxy_dev/ library_common/act_on_multiple_datasets. Reason: Error reading from remote server ### If I download file per file (no compression) it's working. Ismael -- Padioleau Ismael EMBL Heidelberg ( V205)

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query on upload files from file system path
by Vipin TS 23 Jun '10

23 Jun '10

Hi Galaxy team, I had updated my galaxy instance and tried to upload files from system path, but the pop-up menu doesn't shows the option. I can only see 3 options, they are: 1. Upload files 2. Upload directory of files 3. Import dataset from current history. happy to hear from your side. Vipin T S

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problems with Explorer(6) on WinXP when looking at "Saved Histories"
by Hans-Rudolf Hotz 22 Jun '10

22 Jun '10

Hi Last weekend, we successfully upgraded our galaxy installations to changeset "3894:837aabec314e" (according to the 'June 8, 2010 New Development News Brief'). We have no problems on Mac and Linux. However if you want to look at your "Saved Histories" on WinXP with Explorer(version 6) the browser freezes. This was not the case before, when we used "3545:2590120aed68" I just checked your public website (http://main.g2.bx.psu.edu/) using WinXP with Explorer and the browser freezes as well. Unfortunately, we (still) have a lot of Windows/Explorer users. So we are a little bit stuck at the moment, as I don't want to downgrade our Galaxy servers...(and it might take a while for our "PC support" to install Firefox) Thank you very much for your help Hans

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problems with install on OSX 10.5, Python 2.5.1
by Arlin Stoltzfus 22 Jun '10

22 Jun '10

Hello. I'm a Python newbie having problems trying to install galaxy on a Mac (PPC) running OSX 10.5.8 and Python 2.5.1. Do I need to upgrade my Python or OSX version? If not, below are the gory details for anyone who wants to help. Arlin ----------------------------- gory details (narrative description followed by transcript) --------------------- I've been through this several times and loaded various packages manually, and it all seems to come down to numpy 1.3.0 and bx-python 0.5.0. I installed more recent versions of these myself (numpy 1.4.1 and bx-python 0.6.0), and verified that they were installed correctly, but Galaxy seems to want specific versions that are not the current versions. I found a binary of numpy 1.3.0 but the installer would not let me install it on the grounds that it requires "System Python 2.5", which is confusing because thats what I thought I had. I haven't found bx-python 0.5.0 anywhere though I suppose I could just build an old release from the source repository. camel12:dev arlin$ uname -a Darwin camel12.umbi.umd.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC Power Macintosh camel12:dev arlin$ python --version Python 2.5.1 camel12:dev arlin$ hg clone http://bitbucket.org/galaxy/galaxy-dist (works fine) camel12:dev arlin$ cd galaxy-dist/ camel12:galaxy-dist arlin$ sudo sh setup.sh . . . (lots of messages) Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.5.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources .working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Library/Python/2.5/site-packages/distribute-0.6.10-py2.5.egg/ pkg_resources.py", line 565, in resolve ) pkg_resources.DistributionNotFound: bx-python==0.5.0-dev-f74aec067563 ----------------------- end of gory details -------------------------------------- ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org

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NGS data library construction
by Terrence Barrette 22 Jun '10

22 Jun '10

Hi All, I'm working on building a local instance of the galaxy server. I've got the application up and its proxied behind a local apache. The base OS is redhat 5.5 kernel 2.6.18-194, python 2.6, on an hp dl385 with 8 cores and 20 GB of ram. The local drive is 1 TB SAS and I have a few TB of nfs space mounted as /exds/galaxy for holding the datafiles as a repository. I've got about 1 TB of solexa seq I want to make available to the various tools, bowtie, bwa, ... for analysis by the group but I'm a little uncertain how to proceed. It seems that I should make a file similar to faseq.loc in the tool-data folder that points to the individual files in a folder in the nfs space, but I'm not sure how that will make it available to the different tools that could use it and how to keep it a single copy as different users access it and choose from the fastq files to make datasets for analysis. In the galaxy-wiki it said to write to galaxy-dev(a)bx.psu.edu, on the galaxy site it links to galaxy-bugs(a)bx.psu.edu, at bitbucket I was just going to add this question as a issue. What is the preferred way to ask questions like this? Thanks Terry ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Lunch job as connected user
by Mariette 22 Jun '10

22 Jun '10

Hi, We have galaxy working on our cluster and we require user to be logged in using our ldap server. However jobs are owned by root when runing on the cluster as this user lunch galaxy. How can we configure galaxy, so the connected user is the user who own the runing job ? thanks for your help, Jerome

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Running Galaxy behind Apache Proxy
by Michael Siebauer 22 Jun '10

22 Jun '10

Hey, I have a problem running Galaxy behind an Apache Proxy. I followed the ApacheProxy Tutorial: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy loaded the proxy, proxy_http and rewrite modules and added | <Directory /var/www/> RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] |To the Apache configuration. When I try to access the Server via address http://bioapp07/ I get an "Internal Server Error" and the Galaxy Debug log shows: |Starting server in PID 1077. serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 52475) Traceback (most recent call last): File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 194, in __call__ path_info = self.normalize_url(path_info, False)[1] File "/homes/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 118, in normalize_url "URL fragments must start with / or http:// (you gave %r)" % url) AssertionError: URL fragments must start with / or http:// (you gave 'HTTP/1.1') ----------------------------------------| Is there some other module missing, or what am I doing wrong? Ciao, Michael ;-)

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MySQL
by SHAUN WEBB 22 Jun '10

22 Jun '10

Hi, I am trying to set up a MySQL database on our computer cluster as a backend to Galaxy. I had no trouble with this conversion on our local server installation but now I am faced with an error. The full traceback is below, I'm not really sure what the problem is. If any one could give me some idea that would be great. Thanks Shaun Webb galaxy.model.migrate.check INFO 2010-06-04 16:16:40,360 No database, initializing Traceback (most recent call last): File "/exports/work/biology_cell_galaxy/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/exports/work/biology_cell_galaxy/galaxy/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/exports/work/biology_cell_galaxy/galaxy/lib/galaxy/model/migrate/check.py", line 67, in create_or_verify_database migrate_to_current_version( engine, db_schema ) File "/exports/work/biology_cell_galaxy/galaxy/lib/galaxy/model/migrate/check.py", line 108, in migrate_to_current_version changeset = schema.changeset( None ) File "/exports/work/biology_cell_galaxy/galaxy/eggs/py2.4-noplatform/sqlalchemy_migrate-0.5.4-py2.4.egg/migrate/versioning/schema.py", line 173, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/exports/work/biology_cell_galaxy/galaxy/eggs/py2.4-noplatform/sqlalchemy_migrate-0.5.4-py2.4.egg/migrate/versioning/repository.py", line 170, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/exports/work/biology_cell_galaxy/galaxy/eggs/py2.4-noplatform/sqlalchemy_migrate-0.5.4-py2.4.egg/migrate/versioning/version.py", line 161, in script assert ret is not None AssertionError -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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