- galaxy-user - lists.galaxyproject.org

rgenetics and atlas
by Jelle Scholtalbers 26 Apr '10

26 Apr '10

Hi, I was wondering where I could find all the rgenetics dependencies as the link at the bottom of: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies doesn't seem to bring me anywhere. Furthermore it seems that I'm missing the module atlas for genetrack, although I haven't seen anything about the need for this dependency. Should this be added as a dependency or is this an egg that should be automatically fetched? Cheers, Jelle

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Galaxy server is down or Up ??
by Saurabh.V. Laddha 25 Apr '10

25 Apr '10

i am using mapping with Bowtie and its taking unexcepted time..i usally mapp data with bowtie in 30 mis or so but this time it is taking more than 18 hs.... so i wanted to know galaxy server is down or at my end problem ??? regards saurabh

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Re: [galaxy-user] A question regarding Galaxy
by Anton Nekrutenko 21 Apr '10

21 Apr '10

Caiti: I am forwarding your e-mail to galaxy-user list. To answer your question - you will soon be able to upload tarred gzipped datasets that may contain multiple files. a. On Apr 16, 2010, at 10:29 AM, Caiti Smukowski wrote: > Hi Anton, > > I am a graduate student in Mohamed Noor's lab at Duke University - I > believe you met at a conference where the Galaxy tool was discussed. > Mohamed suggested I contact you with a quick question. I am > interested in using Galaxy to do some linear regressions, but I am > encountering a problem. I have 640 individual datasets I would like > to look at. It seems I would have to individually upload each one or > alternatively upload them all as one file. I have decided to upload > them as one file, and then I was hoping to find a tool where I could > separate the file by row into different files once in Galaxy (file > consists of 3 columns and thousands of rows, the first column has > names in it that I would like to sort). So ideally, I would like to > sort the file by colum one (name) into individual files. Is there a > way to do this? > > Thanks. > > Best, > > Caiti Smukowski Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Question about FASTQ Groomer
by Timothy Hughes 17 Apr '10

17 Apr '10

Hi Jianchao, > I am asking this question because I used to use Maq's > sol2sanger (I guess it is just similar to your "Solexa") to convert all > data generated by Illumina 1.5. The different fastq formats are broadly summarised by: S - Sanger Phred+33, 41 values (0, 40) I - Illumina 1.3 Phred+64, 41 values (0, 40) X - Solexa Solexa+64, 68 values (-5, 62) However, at least in my version of the MAQ software (some months old), sol2sanger conversion converts from X to S and NOT from I to X. So if you feed I to the MAQ converter you are going to get slightly incorrect Sanger qualities (because it is expecting the input qualities to have been calculated using the Solexa formula but they have in fact been calculated using Phred). If you search on seqanswers.com you will find a post that details how you need to modify the MAQ conversion script to make the conversion from I to S. Could this explain the discrepancies you observe? Tim. > > ------------------------------ > > Message: 4 > Date: Fri, 16 Apr 2010 11:20:09 -0400 > From: "Yao, Jianchao" <jyao(a)cshl.edu> > To: <galaxy-user(a)bx.psu.edu> > Subject: [galaxy-user] Question about FASTQ Groomer > Message-ID: > <2A031782CDB83F44A26147B7A11C2C95013002CF(a)mailbox11.cshl.edu> > Content-Type: text/plain; charset="us-ascii" > > To Whom It May Concern: > > > > I am a new user to Galaxy. In the function of "FASTQ Groomer", I noticed > there is an option for "Input FASTQ quality scores type". My question is > what different conversions you will do when I choose "Sloexa" or > "Illumina 1.3+". I am asking this question because I used to use Maq's > sol2sanger (I guess it is just similar to your "Solexa") to convert all > data generated by Illumina 1.5. It seems like, based on your options, I > should have chosen other conversion (e.g., your "Illumina 1.3+") to > convert data generated by Illumina 1.5 > > > > Also, it looks like "Sloexa" and "Illumina 1.3+" just differ in the > quality score calculation. But, when I use BWA and SAMtools to do > mapping and call SNPs, I notice the size of the bam or pileup files are > very different between those two different conversions. Also, it looks > like even the coverage for some of the bases are different when choosing > different conversions. > > > > Can you tell me how the conversion can affect the final result in terms > of coverage? > > > > All your help will be greatly appreciated! > > > > -Jianchao Yao > > > >

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Question about FASTQ Groomer
by Yao, Jianchao 16 Apr '10

16 Apr '10

To Whom It May Concern: I am a new user to Galaxy. In the function of "FASTQ Groomer", I noticed there is an option for "Input FASTQ quality scores type". My question is what different conversions you will do when I choose "Sloexa" or "Illumina 1.3+". I am asking this question because I used to use Maq's sol2sanger (I guess it is just similar to your "Solexa") to convert all data generated by Illumina 1.5. It seems like, based on your options, I should have chosen other conversion (e.g., your "Illumina 1.3+") to convert data generated by Illumina 1.5 Also, it looks like "Sloexa" and "Illumina 1.3+" just differ in the quality score calculation. But, when I use BWA and SAMtools to do mapping and call SNPs, I notice the size of the bam or pileup files are very different between those two different conversions. Also, it looks like even the coverage for some of the bases are different when choosing different conversions. Can you tell me how the conversion can affect the final result in terms of coverage? All your help will be greatly appreciated! -Jianchao Yao

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setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

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data privacy?
by Peter Andrews 14 Apr '10

14 Apr '10

I ran into a researcher the other day who said her 'boss does not want me to put our data on galaxy'. What can I tell her to reassure them of privacy and safety? Thanks! -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

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Sending data to GBrowse
by Jelle Scholtalbers 13 Apr '10

13 Apr '10

Hi, I would like to be able to send data to my GBrowse2.0 instance. I have been trying some things based on the Epigraph tool but I can't seem to get it work. Below is a mail from Lincoln that was send to the GBrowse mailinglist about how to send data to GBrowse. If its possible, how should I configure the tool? Cheers, Jelle -------- In version 2.0 it is relatively easy. POST to the GBrowse URL (including the datasource part of the URL) with the following parameters: - action="upload_file" - file=<a multipart/form-encoded file upload> - upload_id=<any numeric id of your choosing> - id=<the id of the user that you are uploading to> Alternatively to providing the "file" argument you can provide a "data" argument with the uploaded data provided directly. The "id" argument indicates the id of the user that you are uploading for. You can get this ID by bookmarking a page -- the "id" parameter records the info. Alternatively, if you don't provide an ID, GBrowse will generate it for you and return the ID in the response cookie, in an argument called "gbrowse_sess". If you have administrator's mode enabled, then you can provide the ID of the administrator and the uploaded file will become part of the public set of tracks. Lincoln

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Sample management?
by Shawn Levy 13 Apr '10

13 Apr '10

I was at the recent ABRF meeting in Sacramento and one of the presentations from the Penn State core lab showed that Galaxy had a sample management/project management interface in development or possible available. I didn¹t see anything on the main pages or wiki and was wondering if Galaxy will be extended to include sample handling information. Thanks Shawn

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Problem w/Cheetah, repeating dataset input
by Jesse Erdmann 12 Apr '10

12 Apr '10

Hi all, I'm using the following XML: ... <inputs> <param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/> <param type="data" format="txt" name="lib_info" label="Label Info"/> <repeat name="to_merge" title="Evaluation Inputs and Results"> <param type="select" name="pmm" label="Mismatch %" help="Maximum % of mismatch between the construct sequence and the comparison sequence."> <option value="10">10%</option> <option value="15">15%</option> <option value="20">20%</option> </param> <param type="text" name="max_length" label="Max Construct Length" value="25" /> <param format="fasta" name="fasta_in" type="data" label="FastA Output"/> <param format="txt" name="seq_stats" type="data" label="Sequence Stats"/> </repeat> </inputs> ... <configfiles> <configfile name="file_info"> #for $merge_set in enumerate( $to_merge ) #silent sys.stderr.write($merge_set.__str__() + "\n") #silent sys.stderr.write($merge_set.fasta_in.__str__()) #end for </configfile> </configfiles> ... And getting the resulting output: 127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload HTTP/1.1" 200 - "http://localhost:8080/admin/reload_tool" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" 127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local runner galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched (0, {'seq_stats': <galaxy.tools.DatasetFilenameWrapper object at 0x572b390>, '__index__': 0, 'max_length': <galaxy.tools.InputValueWrapper object at 0x572b8d0>, 'fasta_in': <galaxy.tools.DatasetFilenameWrapper object at 0x572b810>, 'pmm': <galaxy.tools.SelectToolParameterWrapper object at 0x572b290>}) 127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure running job 234 Traceback (most recent call last): File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/__init__.py", line 386, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/tools/__init__.py", line 1364, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/jerdmann/Python/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py", line 86, in respond NotFound: cannot find 'fasta_in' while searching for 'merge_set.fasta_in' So, I'm printing the merge_set dictionary and seeing a fasta_in key, but when I try to use fasta_in it can not be found. I'm assuming this is probably a syntax oversight on my part, but I'm not seeing it. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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