- galaxy-dev - lists.galaxyproject.org

pysam egg shows possible binary incompatibility
by Anthonius deBoer 05 Dec '12

05 Dec '12

Hi, I installed a fresh copy of galaxy-dist on my VM machines and I am seeing this as the first line of the log files. /mnt/ngs/analysis/svcgalaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * I am also seeing some issues with the metadata update of SAM files which I suspect is related to this error... What does this incompatibility message mean and is this the cause of the failed auto update of the metadata (If I run the update metadata manually, it runs fine) Thanks, Thon

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RFE: Adding tags to AWS resources created by Cloudman
by Shea Lovan 05 Dec '12

05 Dec '12

We are managing Galaxy/Cloudman clusters on AWS for a few research groups on campus. As is so often the case, we need to separate usage for billing purposes. This this is fairly simple to do with Amazon's CSV billing report with the "clusterName" tag included. However, it doesn't appear that I can configure Cloudman to set that tag on every resource it creates. This is forcing us to keep the scaling of the clusters under our control so that we can set the tags manually. What I was hoping, is that this feature could be added. It seems like a fairly simple patch; once the ID (instance, volume, or snapshot) is available, it's one more API call to create/set the clusterName tag. Any chance of getting this included? Thanks! -Shea -- ------------------------ Shea A. Lovan Manager, Server Operations and Architecture UCSB Life Sciences Computing Group Santa Barbara, CA 93106 805.893.2405

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Blast+ tools
by Shaun Webb 05 Dec '12

05 Dec '12

I have just installed the Blast+ tools from the Galaxy tool shed and tried to make a Blast DB from a fasta file in history. The tool runs ok and indicates that a blastdb has been created in: /storage/home/galaxy/production/galaxy-dist/database/files/085/dataset_85192_files/blastdb However there is no directory dataset_85192_files. I have blast installed and I'm able to run makeblastdb on the command line. Do I have to make any other modifications before I can use Blast tools? Thanks for your help Shaun Webb University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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segfault in libdrmaa -> galaxy front end failure
by Langhorst, Brad 05 Dec '12

05 Dec '12

Galaxy is failing due to a segfault in libdrmaa [9116874.391434] python[5211]: segfault at 0 ip 00007fcb9fd8ae62 sp 00007fcb9affe490 error 4 in libdrmaa.so.1.0[7fcb9fc29000+1b9000] I first started observing this in the last few weeks. After the first event I pulled in this changeset 4a95ae9<https://bitbucket.org/galaxy/galaxy-central/commits/4a95ae9a26d96f0dc9a0fe3…> Handle invalid job ids in the drmaa runner. but I'm still seeing the segfault. I think this is some correlated log information from before the patch… Error - <type 'exceptions.UnboundLocalError'>: local variable 'job' referenced before assignment URL: http://galaxy.neb.com/datasets/c3d98ec09a23e847/show_params File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 1025 in show_params return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects ) UnboundLocalError: local variable 'job' referenced before assignment after applying 4a95ae9 I see this galaxy.jobs.handler DEBUG 2012-12-05 10:34:20,968 Stopping job 25519: galaxy.jobs.handler DEBUG 2012-12-05 10:34:20,971 stopping job 25519 in drmaa runner galaxy.jobs.runners.drmaa DEBUG 2012-12-05 10:34:20,983 (25519/22378) User killed running job, but it was already dead 172.17.121.186 - - [05/Dec/2012:10:34:19 -0400] "GET /datasets/414fa4e8d28bb2be/delete_async HTTP/1.1" 200 - "http://galaxy.neb.com/history?status=done&show_deleted=False&filename=None&…" "Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; InfoPath.2; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)" galaxy.jobs.handler INFO 2012-12-05 10:34:21,073 (25520) Job unable to run: one or more inputs deleted galaxy.jobs.handler DEBUG 2012-12-05 10:34:22,251 Stopping job 25520: galaxy.jobs.handler DEBUG 2012-12-05 10:34:22,253 stopping job 25520 in drmaa runner Any ideas? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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question on installing galaxy on EC2 centos instance
by Sun, Wenping [USA] 05 Dec '12

05 Dec '12

Dear galaxy-dev members, I am new to the list and seeking some advices on working galaxy with ec2. I am working on installing galaxy on ec2 centos instance and have everything set up. Now when I execute run.sh and have the following message on ............................... Starting server in PID 1077. serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 However, I try to access the galaxy web via the ec2 instance site with http:// ec2-#######.compute-1.amazonaws.com:8080, the site was not be able to load. [cid:image003.jpg@01CDD2D0.C59306B0] Would anyone working with ec2 cloud provide some advice? Thank you in advance! Kind regards, Kathryn

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Trying to understand data libraries
by Sajoscha Sauer 05 Dec '12

05 Dec '12

Hi, I'm having some difficulties to understand what is going on when I try to access the data libraries. For example, we have a library with 20 folders and each folder contains datasets (up to 30) with ~1Gb of size. The files of the datasets are not stored locally but on file servers. So, the problem is, when I try to access this data library it takes ages to load. This can easily be half a minute. Could someone give me some insights on what happens when I try to access the libraries? Or even better, a way to speed it up? :) Thanks a bunch for your help! Sajoscha

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question on installing galaxy on EC2 centos instance
by Sun, Wenping [USA] 05 Dec '12

05 Dec '12

Dear galaxy-dev members, I am new to the list and seeking some advices on working galaxy with ec2. I am working on installing galaxy on ec2 centos instance and have everything set up. Now when I execute run.sh and have the following message on ............................... Starting server in PID 1077. serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 However, I try to access the galaxy web via the ec2 instance site with http:// ec2-#######.compute-1.amazonaws.com:8080, the site was not be able to load. Would anyone working with ec2 cloud provide some advice? Thank you in advance! Kind regards, Kathryn

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Edit login page
by Zinonas Antoniou 05 Dec '12

05 Dec '12

Hello, I need your help. I need to edit the login page of galaxy and show another way of login in our platform, except of simple login and openid options. I want to have another option for external login. Can you help me please, how to do it? Thank you in advance, Zinonas

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from shed to shed
by Ido Tamir 05 Dec '12

05 Dec '12

Hi, how do I get tools from one local toolshed (or the main galaxy toolshed) into another tool-shed? Is it possible to clone the content of a complete tool-shed - all repositories at once into another tool-shed? Can I then import all the tools at once into a local galaxy instance? We have a group with their own tool-shed. Unfortunately, I accessed it directly without a proxy on its port which leads to a problem described in issue 825 in galaxy-central. I want to a) clone the tool-shed as it is into my own tool-shed (rsync?) b) selectively or bulk install these tools into my galaxy server. thank you very much, ido

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Advice on running reports interface in production setting
by Peter Briggs 05 Dec '12

05 Dec '12

Hello The Galaxy reports interface (run_reports.sh) looks immensely useful for getting a handle on the usage of our local Galaxy, and I was wondering if anyone could offer advice on how they run the reports in a production environment. In terms of setting up and running the reports server, there doesn't appear to be much documentation however the instructions in the June 8th 2010 news brief covers the basics adequately: http://wiki.galaxyproject.org/DevNewsBriefs/2010%2006_08?highlight=%28repor… This looks okay for running in an ad-hoc fashion (i.e. start it up, look at the reports in a browser running on localhost, shut it down again as required) but does anyone run it in a more persistent set-up? Or is ad-hoc the way to go? Any suggestions welcome, many thanks 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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