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

local instance upload data failed
by 刘阳 05 Dec '12

05 Dec '12

I just installed postgres, and modified the database_connection option in universe_wsgi.ini to database_connection = postgres://postgres:postgres@localhost:5432/galaxy Then I tried to upload a fasta format file (about 4KB), what confused me is that it is uploading on and on. I think the uploading process is pending. The console gave a lot of message like this: 127.0.0.1 - - [06/Dec/2012:12:10:01 +0800] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://127.0.0.1:8080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/536.11 (KHTML, like Gecko) Ubuntu/12.04 Chromium/20.0.1132.47 Chrome/20.0.1132.47 Safari/536.11" Is it caused by the wrong configuration of postgres? I can't figure it out. Does anyone encountered similar problem? Jacky Lau

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Tool runners don't "listen" to settings in [galaxy:tool_runners]
by Anthonius deBoer 05 Dec '12

05 Dec '12

Hi, In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section... This is the setting for bwa_wrapper in my universe_wsgi.ini: bwa_wrapper = drmaa://-V -q long.q -pe smp 4/ and this is what the job admin page shows: It's in a different queue and does not use the smp setting I ask for...(It's the default setting) any ideas? 7 X 26 minutes ago toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 running python /mnt/ngs/analysis/svcgalaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="4" --fileSource=indexed --ref="/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta" --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=false drmaa://-V -q all.q -pe smp 1/ 4440144

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Re: [galaxy-dev] Main toolshed broken??
by Adam Carr (NBI) 05 Dec '12

05 Dec '12

Hi, I hadn't caught this as I posted my query to the list, I'm having trouble uploading to a brand new repository. Could my issue described here: http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Cras…, be related? Many Thanks, Adam. --- Adam Carr Linux Support & Developmnent E adam.carr(a)nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory -----Original Message----- > > Hi list, > > Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error.. > > This is the repo: http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark > > Is anyone having the same issues?? I could just delete the repository but no option for that is given.. > > Thanks, > > Franco >

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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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