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

How to get a shedtool to run locally
by Liisa Koski 24 Oct '12

24 Oct '12

Hello, I've installed a tool to my local Galaxy installation via my local ToolShed. I would like to run this tool locally, and not have it submitted to the grid. I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners] section. The tool id directly from the tool.xml file and the id from the shed_tool_conf.xml (same id found in the integrated_tool_panel.xml) tool = local:/// galaxy.server:9009/repos/user/tool/1.0 = local:/// My job still gets submitted to the grid. Any help would be much appreciated. Thanks, Liisa

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Trackster error
by Joachim Jacob 24 Oct '12

24 Oct '12

Hi all, I want to view two interval-type datasets in trackster on genome hg19 together with one BAM dataset. The interval datasets give an error (while the BAM is displayed nicely): [ti_index_core] bug in BGZF: 80048ed5001b < ffff80048ed50000 Thanks for any input, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Re: [galaxy-dev] trying to set up local toolshed
by Greg Von Kuster 24 Oct '12

24 Oct '12

Hi David, Setting the following in your community_wsgi.ini file should enable remote authentication in the tool shed. Features like this that are available in Galaxy itself are usually also available in the tool shed (and function the same way) since the code base supporting the features is shared across both applications. Let us know if you bump into problems with this, but please keep all communication on the dev list. # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy use_remote_user = True Thanks! Greg Von Kuster On Oct 24, 2012, at 1:53 PM, David Hoover wrote: > One more question. Is there any hope of having external authentication for the local toolshed? > > Thanks for your (ongoing) support! > > David >

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GMAP fails to install from mail toolshed
by Carlos Borroto 24 Oct '12

24 Oct '12

Hi, I get a "HTTPError: HTTP Error 500: Internal Server Error"(see full error trace below) when trying to install GMAP from the main toolshed. Is there a way to report this to the tool authors? Thanks, Carlos URL: http://galaxy.bfx.brel.local/admin_toolshed/prepare_for_install?tool_shed_u… File '/local/opt/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 205 in decorator return func( self, trans, *args, **kwargs ) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1178 in prepare_for_install response = urllib2.urlopen( url ) File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen return _opener.open(url, data, timeout) File '/usr/lib64/python2.6/urllib2.py', line 397 in open response = meth(req, response) File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib64/python2.6/urllib2.py', line 435 in error return self._call_chain(*args) File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain result = func(*args) File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error

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Re: [galaxy-dev] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error
by Joel Rosenberg 24 Oct '12

24 Oct '12

The galaxy webserver can solve this by allowing cross-domain resources from whatever toolsheds have been configured. http://en.wikipedia.org/wiki/Cross-origin_resource_sharing -Joel

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Galaxy, Apache, WSGI and mod_wsgi
by Paul Boddie 24 Oct '12

24 Oct '12

Hello, I have recently had the opportunity to look at the deployment of Galaxy together with Apache, and I saw that the recommendation is to run the Galaxy Web server behind Apache with the latter acting as a proxy: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Other than convenience - one can just put Apache in front of an existing server - is there any particular reason for doing things this way? It seems that Galaxy uses the built-in Web server provided by the Paste framework, which in turn is based on the Python standard library BaseHTTPServer framework, and although paste.httpserver seems to add capabilities to the underlying framework, each such server must still be constrained to running in a single process. I imagine that this then leads to the use of load balancing as described on the following page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… Given that Apache is an acceptable part of a large-scale solution, I would like to know if mod_wsgi has been considered for the deployment of Galaxy at all, and whether anyone has any positive or negative experiences with it. It seems to me that mod_rewrite is often something that should only be brought into play where other, typically more elegant, solutions cannot be used. Many Python-based Web applications have mod_wsgi as a recommended deployment option once their users look beyond CGI, and I wondered why this isn't the case with Galaxy. Paul

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Handling MS Excel output from Galaxy tool
by Peter Briggs 24 Oct '12

24 Oct '12

Hello We have some tools that wrap an in-house program which generates an Excel spreadsheet as one of its outputs, and wanted Galaxy to associate the correct mime type so that the user's browser knows how to handle it on view/download. The advice on the wiki at http://wiki.g2.bx.psu.edu/Admin/FAQ#Configuring_Galaxy_so_a_tool_can_proper… appears to be out of date, so instead as a workaround I've edited datatypes_conf.xml and replaced the existing "xls" type: <datatype extension="xls" type="galaxy.datatypes.data:Data" mimetype="application/vnd.ms-excel" /> This seems to work (in that clicking the eye icon now givens me a download dialogue rather than a server error message). However I'm wondering: - Would type="galaxy.datatypes.binary:Binary" be a better choice? - What are the consequences of replacing the original "xls" datatype? - More generally, is there a way to keep the locally defined datatypes separate from the main datatypes_conf.xml file? Thanks for any advice or comments (& apologies if I've missed anything obvious on the list or on the wiki) Best wishes, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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The blastdb_p.loc sample is wrong.
by Shane Sturrock 24 Oct '12

24 Oct '12

I've just been setting up our internal galaxy server and following the instructions to get the NCBI BLAST+ tool working but I kept getting stuck with it passing -db "" in rather than the actual database name. It turns out, because I had copied the examples in the blastdb_p.loc file, I had put two tabs in just as in the sample doc. This doesn't work. It has to be one tab. However, I would say that it would be better for the code to be fixed so it can handle a variable number of tabs rather than being so strict. Shane

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Galaxy Admin Tools
by lentaing＠jimmy.harvard.edu 24 Oct '12

24 Oct '12

Hi, We have some common admin-tasks that we would like to implement on our instance, but before doing so, we were wondering what Galaxy has already baked it. 1. Is the Galaxy team planning to implement job_walltime for the local runner? Currently, job_walltime is only implemented for the pbs runner--we believe that it would be a useful feature regardless of which runner one is using. 2. Is there a way to limit the number of active jobs a user can run at one time?--perhaps a record in universe_wsgi.ini (e.g. max_jobs) could be helpful. 3. This is a bug report--but on our version of Galaxy, rev 949e4f5fa03a, the sort-by-last login (on the manage users page), doesn't sort correctly. We are interested in deleting inactive users, and sorting by last-login is one way of doing this, but I was wondering if others out there have a better solution. Thanks! Len Taing Cistrome Development Team

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Manage Jobs: This Galaxy instance is not the job manager.
by Christos Kannas 24 Oct '12

24 Oct '12

Hi all, We have a locally installed Galaxy server that runs only a set of tools we are developing. It has been setup to run with 3 Web processes , 1 Job Manager and 4 Job Handlers. This setup is beeing run behind an Apache web server and we created a config file similar to the one found @ http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… . The problem we have is that Job Manager is not accessible, and we get error messages like the one below: This Galaxy instance (web1) is not the job manager (manager). If using multiple servers, please directly access the job manager instance to manage jobs. We do have the following RewriteRule: RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P] but it doesn't seem to work. Can you help me fix it? Regards, -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com Mob: (+357) 99530608

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