April 2014 - galaxy-user - lists.galaxyproject.org

Can not delete data from my local galaxy
by Nishant THAKUR 10 Apr '14

10 Apr '14

Hello, I am using local galaxy server. I have disc storage problem and I noticed that galaxy is utilizing most of the space. I deleted old projects permanently, but they are appearing again in the saved history with one message which says "datasets were not removed from disk because that feature is not enabled in this Galaxy instance". Any suggestions how to enable this feature or delete dataset permanently from history. Galaxy installed on ubuntu 12.04 LTS, 3.5.0-44-generic, 64bit. Best regards Nishant Thakur

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server problem?
by Sarah Schaack 10 Apr '14

10 Apr '14

Hi there! I am teaching a workshop in East Africa, right this second, and we are trying to use a tool in galaxy (not too complex, files are not huge) to illustrate RNA-seq analysis. The server is SOOOOOOO slow-- is there a problem? Should we abandon ship and teach them Tophat using the command line? Please advise, at your earliest convenience-- I have a room full of impatient newbie hackers ;) Thank you! --Sarah **************************************** Sarah Schaack, PhD *Assistant Professor, Reed College* *Fulbright Scholar, Centre for Bioinformatics and Biotechnology, University of Nairobi**and Biosciences Eastern and Central Africa Hub, Int'l Livestock Research Institute* Email: schaackmobile(a)gmail.com Website: https://sites.google.com/site/schaackwork/ Phone (Kenya): +254 7 29 470 027 Workshop Info: https://sites.google.com/site/bioinfogenomicswrkshpea/

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Trackster error on dbkeys
by Aarthi Mohan 10 Apr '14

10 Apr '14

Hi all, I am setting up galaxy on a server running CentOS 6.5. I found that Trackster application hits me with an error "Could not load chroms for this dbkey: PF3D7", when I try "add new track" from Visualization. I am working with Plasmodium falciparum (PF3d7) genome, and I followed the instruction for setting visualization from " https://wiki.galaxyproject.org/Visualization%20Setup" and placed the 2bit, len files in the appropriate path. I have also made sure the genome build is present in the builds.txt under tool-data/shared/ucsc. For a test, I have the human chromosomes len files and Trackster loads it without any problem. Any suggestion would greatly help me. Thanks RT Log file: ----------- 127.0.0.1 - - [10/Apr/2014:12:29:44 +0800] "GET /visualization/trackster HTTP/1.1" 200 - "http://127.0.0.1:8081/" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" 127.0.0.1 - - [10/Apr/2014:12:29:45 +0800] "GET /api/genomes?chrom_info=True HTTP/1.1" 200 - " http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" 127.0.0.1 - - [10/Apr/2014:12:29:51 +0800] "GET /api/genomes/PF3D7?low=0&num=100 HTTP/1.1" 500 - " http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" Error - <type 'exceptions.IndexError'>: list index out of range URL: http://127.0.0.1:8081/api/genomes/PF3D7?low=0&num=100 File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 78 in decorator return to_json_string( func( self, trans, *args, **kwargs ) ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/webapps/galaxy/api/genomes.py', line 42 in show rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 292 in chroms rval = genome.to_dict( num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 153 in to_dict chroms[ fields[0] ] = int( fields[1] ) IndexError: list index out of range CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351' HTTP_HOST: '127.0.0.1:8081' HTTP_REFERER: 'http://127.0.0.1:8081/visualization/trackster' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/api/genomes/PF3D7' QUERY_STRING: 'low=0&num=100' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x6b37cd0> is_api_request: True paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351'>, 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x748eed0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x795c310> paste.parsed_querystring: ([('low', '0'), ('num', '100')], 'low=0&num=100') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'c1be491ec06811e39ed60025905a9e10' webob._parsed_query_vars: (MultiDict([('low', '0'), ('num', '100')]), 'low=0&num=100') wsgi process: 'Multithreaded' ------------------------------------------------------------

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Re: [galaxy-user] Filtering PhiX
by Jennifer Jackson 08 Apr '14

08 Apr '14

Hi Scott, Sorry to hear that you are having trouble. These are exact match hits to both? Contamination isn't out of the question with public databases, but I would start with filtering results first to see if that helps. If you still have concerns, a test versus the line-command version is the definitive answer. As you may have seen on the public Galaxy instance, the Megablast tool happens to have the ' phiX174' genome as a specific target, so you could use that. Most NGS mappers have a custom reference database option (however not Megablast, for resource reasons) and a local/cloud Galaxy can be configured to use any Galaxy-wrapped mapper (there are many, check the tool shed). Combined, these provide many options. Please send "reply-all" to keep questions on list going forward. Thanks! Jen Galaxy team On 4/8/14 10:26 AM, Scott Tighe wrote: > Jennifer > > Not in the case of Megablast. So sounds like there is no PhiX filter. > Also I noticed that when I selected megablast, all the reads went to > Bovine, but when I hand selected from galaxy a bunch of the sequences, > that blasted (using NR) to Pseudomonas and other bacteria which is > correct. I think your Megablast is not working properly. > > > > Scott > > Scott Tighe > Senior Core Laboratory Research Staff > Advanced Genome Technologies Core > NextGen Sequencing/Flow Cytometry > University of Vermont and Vermont Cancer Center > 149 Beaumont ave > Health Science Research Facility 303/305 > Burlington Vermont 05405 > 802-656-2482 (AGTC) > > On 4/8/2014 10:23 AM, Jennifer Jackson wrote: >> Hi Scott, >> >> This genome is available in most mapping tools, so a positive match >> could be used to identify the control. But if you just want to leave >> it behind, control should fall out during mapping against the >> sample's target genome (if available). >> >> Best, >> >> Jen >> Galaxy team >> >> On 4/4/14 12:33 PM, Scott Tighe wrote: >>> Dear Team Galaxy >>> >>> Is there a simple way to filter PhiX control from a sample set? >>> >>> S >>> >> > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Filtering PhiX
by Scott Tighe 08 Apr '14

08 Apr '14

Dear Team Galaxy Is there a simple way to filter PhiX control from a sample set? S -- Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC)

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setting dbkey in a workflow
by William Holtz 07 Apr '14

07 Apr '14

I'm working on making my first workflow in Galaxy, using a local server. A high level overview of the workflow is: 1) take a fasta file as input with dbkey set to organism1 2) blast input fasta file against organism2 database 3) manipulate the blast output into bed format 4) extract genomic DNA from organism2 based on the bed data I can't find a way to set the dbkey on the bed data to organism2. This results in the extract genomic DNA step failing, as it seems to default to the only dbkey that exists in my workflow, the dbkey from the input fasta file. (The names and intervals are not present in the organism1 genome, and thus the extract step fails.) I have found that if I set my the dbkey of my input fasta file to be organism2 (even though the sequences contained in it are actually from organism1), then my workflow successfully completes with the desired output. But this is a bit of a hack. I'd like to share my workflow with some coworkers and make it as easy to use as possible. Therefore I don't want to have to explain this hack to them. Is it possible to set the dbkey within a workflow? thanks in advance for your help! -Will

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illogical results in Tophat2 analysis
by Si Naftaly 07 Apr '14

07 Apr '14

Hello, I used a Tophat 2 analysis and got 99.2% discordant in the summary, while in fact I checked the distance between the reads and got 170 with std of 35 (this is the data i filled in the Tophat2). Why did the Tophat2 test found 99.2% discordant when it should have been much lower? The starting reads was 16665209, in a Bowtie2 test i got a logical outcome of 16567482, while on the other hand i got from Tophat2 35066991 and 34816158 - not logical. I tried to do the same test number of times with another data and got resemblance in the results. In all of the tests in Tophat2 i got discordant 99% and higher. What am i doing wrong? What is the correct way to feed data into the test? Thank you Si.

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Invitation to connect on LinkedIn
by Zhandong Liu 07 Apr '14

07 Apr '14

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Zhandong Zhandong Liu Assistant professor at Baylor College of Medicine Greater Philadelphia Area Confirm that you know Zhandong Liu: https://www.linkedin.com/e/psdo7u-htpaphru-20/isd/5858801440302051328/NhMsq… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/psdo7u-htpaphru-20/7wF3Dvdrn6R4dvztTwX5DLGm1Z4fwH… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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known name outputs shown in /database/files but not in galaxy windows
by ANGELICA GOMEZ ROIG 03 Apr '14

03 Apr '14

I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks

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GMOD Online Training 2014
by Amelia Ireland 03 Apr '14

03 Apr '14

Greetings GMOD community! Applications are now open for the 2014 GMOD online training course, to be held from May 19th - 23rd 2014. The course will cover the installation, configuration, and usage of core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database. The course is taught by experienced instructors and developers with deep knowledge of the tools. Although the course will be run online, students will be able to interact with the tutors and fellow attendees, ask questions, and so on. For more information and to apply, please see http://gmod.org/wiki/GMOD_Online_Training_2014 If you have any questions, please contact the GMOD help desk at help(a)gmod.org. Thanks! -- Amelia Ireland GMOD Community Support Generic Model Organism Database project http://gmod.org || @gmodproject

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