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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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question history
by Liesbeth Van Rompay 01 Apr '14

01 Apr '14

Hi, Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do? Best regards, Liesbeth

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Job of format conversion waiting for over 5 days
by Eduardo Fox 31 Mar '14

31 Mar '14

Hello, Please I would like to know if it would be normal of a job to be queued for several days? It is a SAM to BAM conversion, and it has been waiting for over 5 days to run. I understand that the SAM file is pretty large but other similar conversions I made on the server recently were done within few minutes. Thanks! -- Eduardo G. P. Fox http://eduardofox.blogspot.com.br/ http://www.mendeley.com/profiles/eduardo-fox/

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April 2014 Galaxy Update Newsletter: GCC2014 Talk Abstracts due this Friday
by Dave Clements 31 Mar '14

31 Mar '14

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error while running Intogen.
by do kadya 28 Mar '14

28 Mar '14

Respected Sir / Ma'am, I was running Intogen using galaxy, I changes parameters name and then this error came. Can you please tell what is the meaning of this error ? Traceback (most recent call last): File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job job_wrapper.prepare() File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py", line 100, in respond NotFound: cannot find 'fimpact'

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