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

GenePeeks is hiring a Computational Geneticist
by Adam Cohn 20 Dec '12

20 Dec '12

Hello all, GenePeeks is hiring a Computational Geneticist. The position description is list below. We are also hiring a tools programmer and I will send another note with that position description. Thanks, Adam Position Description GenePeeks is a unique genetic information company with a mission to help families protect the health of their future children. We are searching for a highly skilled scientist to join our growing team and help develop leading-edge technologies in a fast-paced, early-stage environment. Primary Duties: * * - Manipulate and analyze whole genome and high complexity genotype data, including SNPs and Copy Number Variations (CNVs) from raw microarray data files. * * - Develop computational and data mining approaches to combine genotype information, molecular profiling data and other phenotypic information derived from NCBI and other online databases. * * - Develop protocols to predict the probability and severity of particular diseases and conditions related to SNP, CNV and other structural variations. * * - Participate in implementing a system to test for and identify those diseases * * - Test and assure the quality of automated analysis systems * * - Efficiently manage experimental data and data workflows * * - Monitor trends and innovations in the fast-moving world of genomic data, analytics, storage, * * and clinical diagnostics * * - Contribute to the ongoing design and development of GenePeeks technology * * - Other duties as assigned * * Our ideal candidate would have the following training and technical expertise: * * - Ph.D. in genetics, biostatistics, computer science or related field, or comparable training * * - Familiarity with and experience using related publicly available scientific datasources and tools * * (OMIM, DBSNP, GeneReviews, UCSC Genome Browser, Galaxy, HapMap) * * - Ability to implement tools using APIs that automatically interrogate publicly available scientific * * datasources and tools such as OMIM, DBSNP, GeneReviews, UCSC Genome Browser, * * Galaxy, HapMap * * - Familiarity with next-gen data analysis and whole genome data * * - Research experience with and /or knowledge of clinical aspects of the genetic causes of * * Autism, Schizophrenia and other neurological disorders * * - Experience analyzing SNP, CNV, GWAS (or NGS) data * * - Experience using automated bioinformatics tools * * - Experience working with whole genome sequence data * * - Proficiency with scripting language such as Python or R * * - Familiarity with 1000 Genomes Project or similar exposure * * General Requirements: * * - Ability and motivation to work independently * - Ability to interact proactively with a small group * - Strong written and verbal communication skills * - Desire to work in a fast-paced, loosely structured business environment - Sense of humor * * Location: * * - Cambridge, MA or New York, NY - Some travel may be required * * Contact Information: * * If you are interested in this role and fulfill the requirements, please send your CV and cover letter to jobs(a)genepeeks.com -- Adam S. Cohn Chief Technology Officer / Chief Operations Officer GenePeeks 175 Varick Street, New York, NY (646) 664-4268 (703) 473-8811 (mobile) adamcohn(a)genepeeks.com www.geenpeeks.com

1 0

Urgent: Seems like tophat2 does not support "--transcriptome-mismatches"
by Sachit Adhikari 20 Dec '12

20 Dec '12

It seems like tophat2 does not support "--transcriptome-mismatches" option but Galaxy is still configured to call tophat2 with this option when run with "Full parameter setting" option within Galaxy. Is there new wrapper with this fix? If not, how to remove this option from Galaxy so that tophat2 is not call with this option. I am assuming that this is specified somewhere in the wrapper. Thanks, Sachit

2 1

Reference Genomes for NGS Tools - A Couple Questions
by greg 20 Dec '12

20 Dec '12

Hi all, I'm finishing up installing Galaxy on our local cluster. I'm at this step regarding setting up reference genomes: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#Setting_Up_the_Refe… But it looks like a whole lot of manual work that needs to be done by a system administrator. I was kind of expecting this would be something end users would be able to do. I'm actually not sure we have the resources for a sys admin to install all of these reference genomes every time someone needs one. I guess here are my questions: Am I misunderstanding the process? Is there a different way that normal users can add reference genomes instead? Is there anything in the works that lets users easily add these? Is there a way to use NGS tools without installing reference genomes? Thanks, Greg

2 3

liftOver Exception caught attempting conversion
by Nikoloas Sidiropoulos 20 Dec '12

20 Dec '12

Hi I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each. "Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py", line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion" I also found this in the handler.log file: "galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' " Do you know how could this be sorted? Thanks in advance, Nikos

1 0

Integrating generated graphics from cli tool?
by Samuel Lampa 20 Dec '12

20 Dec '12

Hi, I'm looking into integrating some R scripts into Galaxy, which create some graphics / plots. We are interested in integrating those in galaxy somehow, or otherwise presenting them to the user in an as easy way as possible. I wanted to check if there is some support for this kind of functionality there already, or if I'll need to hack something together myself? (I couldn't really find anything here on the mailing list). Many TIA! Best // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se

4 5

Extracting bacterial seq from cordinates
by shamsher jagat 20 Dec '12

20 Dec '12

I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use. Thanks

2 3

feature or bug with the tool shed?
by David Gene Morgan 19 Dec '12

19 Dec '12

Hi, I just installed a galaxy server and ran into something that may be a deliberate feature or a genuine bug when trying to install a package from the main tool shed. I got the Admin tab working, went to the section dealing with tool sheds and selected "Search for valid tools" in the Galaxy main too shed. I was able to find the tool I wanted (NCBI Blast+, and I found multiple revisions) but I never found anything remotely like an "Install" button. There are bare-bones instructions for a manual install of the tool, but nothing automatic. However, if I start with "Browse valid repositories" and _then_ search for "ncbi blast" (and not "ncbi blast+"), I find a single revision that has a "Preview and install" option and an "Install into local Galaxy" button. So the only question here is whether this behavior is a bug or a feature. In other words, should I be able to automatically install packages using my first approach, or does Galaxy prevent this deliberately? -- David Gene Morgan cryoEM Facility 320C Simon Hall Indiana University Bloomington 812 856 1457 (office) 812 856 3221 (EM lab) http://bio.indiana.edu/~cryo

2 1

copying files via galaxy API
by Richard Park 19 Dec '12

19 Dec '12

Hi Everyone, Is there a way to directly copy files from galaxy with the proper file name? I'm currently using the galaxy API to download files via HTTP, but it is very slow and would like to speed up the process of copying files directly, but am having a hard time getting the proper file names. Are there any suggestions on how to copy files directly from galaxy without HTTP and with the proper filenames? # Looking up files via API $ ./display.py <api_key> http://localhost:8080/api/libraries/86cf1d3beeec9f1c/contents/32ff5cf1b96c1… Member Information ------------------ ldda_id: 32ff5cf1b96c1df7 misc_blurb: 10,028,615 lines name: H3K9me3_L3_FE_2.wig data_type: txt file_name: /galaxy-central/database/files/000/dataset_733.dat uploaded_by: rpark(a)bu.edu template_data: {} genome_build: ? model_class: LibraryDataset misc_info: uploaded txt file file_size: 48439126 metadata_data_lines: 10028615 message: id: 32ff5cf1b96c1df7 date_uploaded: 2012-12-15T01:53:08.655366 metadata_dbkey: ? # Downloading files using a URL like http://127.0.0.1:8080/datasets/a4975bc1e68708d4/display?to_ext=txt thanks, Richard

2 1

Problems with Internet Explorer 9?
by Peter Cock 19 Dec '12

19 Dec '12

Hello all, Are there (or were there) any known problems with Galaxy under Microsoft Internet Explorer 9? One of our biologists is now having problems with our local Galaxy server, probably after updating his browser. Specifically new history entries do not seem to automatically update from queued to running to done, and also the "peep" functionality to expand/collapse a history entry had stopped working. This was on a large history of about 100 entries. We installed Firefox 10, logged into Galaxy, and it was fine with this same history. A quick test on the public Galaxy with a single history entry seemed to work in both browsers, so perhaps this is something you've already fixed in the latest Galaxy - or perhaps it depends on the size of the history. Any ideas? Has anyone else seen something similar? Thanks, Peter

2 1

help configuring tools in Galaxy
by Tilahun Abebe 19 Dec '12

19 Dec '12

Hi, We installed a local galaxy a couple of days ago following the basic installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) The installation went well, all the tools are listed on the left. I can also upload data to Galaxy. However, an error occurs when I try to run RNA-seq analysis. I am thinking the tools are not configured properly. Can you give me tips to configure NGS tools? An example file with setup syntax will help as well. Thanks. Tilahun

4 5