March 2011 - galaxy-dev - lists.galaxyproject.org

missing setup.sh in galaxy source code
by Zhi-Wei Lu 07 Mar '11

07 Mar '11

Hi Galaxy developers, I have download the galaxy code via mercurial hg clone https://bitbucket.org/galaxy/galaxy-central The downloaded code, however, does not contain the "setup.sh" file. Could you let me know how do I run "setup" now? Thank you.

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phastCons and phastOdds scores
by David Hoover 04 Mar '11

04 Mar '11

Does anyone have a clear explanation of what files are required/available for Get Genomic Scores -> Aggregate datapoints, Compute phastOdds (binned_scores.loc and phastOdds.loc files)? I know there are .mod and .pp files and .wigFix files from UCSC, but I can't figure out exactly what Galaxy is looking for. Do I need to install PHAST and generate these score files? David Hoover Helix Systems Staff http://helix.nih.gov

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Map with Bowtie for Illumina - multiple input fastqs
by Nicki Gray 04 Mar '11

04 Mar '11

Hi When running bowtie on the command line I was able to use more than one fastq file as input simply by listing them separated by a comma eg: bowtie -p 3 -q -m 2 --best --strata --sam --chunkmb 256 /databank/ indices/bowtie/hg18/hg18 input1.fastq,input2.fastq output.sam How can I do this within galaxy? The "Map with Bowtie for Illumina" tool only allows for 1 input fastq file as far as I can see. Thanks, Nicki --------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434

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custom datatypes
by Glen Beane 04 Mar '11

04 Mar '11

I've created a custom file type based on the Galaxy Tabular type (this is so some tools I'm developing can declare this type as input or output and prevent any arbitrary tabular file from being used as input for a tool) I have a data source tool that declares its output format to be my type (this tool brings the user to a website where they query a database and then sends the data file back to galaxy) when I load data with this tool the format is set to "tabular" by galaxy and not to my custom type. I have a feeling Galaxy is ignoring what the tool .xml says the format of the output is and tries to autodetect, and comes up with tabular. If a data source says the output is a specific type shouldn't galaxy use that as the format rather than autodetect? Also, I have other tools that declare my type as the input type, yet when I go to select an input file it shows me all tabular files in my history, not just those with my custom type. how do I get the format to be correctly set for a file I load from my data_source tool? And how do I limit selections in an input drop down to just my specific file type? I'm guessing I need to extend the Tabular class, but I don't need to add any additional functionality at this point, I just want to limit how the tools can be chained together. This datatype is probably just a place holder for what will probably end up being a binary type, so I'm not going to put much effort in. -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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RPM repository for NGS tools in Galaxy
by Leon Mei 04 Mar '11

04 Mar '11

Dear colleagues, In order to ease administration on our servers running at VIB and NBIC, we will set up an RPM Repository for bioinformatics tools, the primary focus being NGS tools. The purpose is to come to a stable repository of easily installable packages for the common bioinformatics tools that can be used in a local Galaxy server. A list of tools under consideration can be found at https://wiki.nbic.nl/index.php/NBIC_%26_VIB_Bioinformatics_RPM_Repository So are there already similar activities going on? If yes, we would really love to hear your experience and probably work together on this. If you would like to join this effort and contribute into this repository, you are more than welcome to contact us as well! Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

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Galaxy Velvet error: Unknown option -ins_length3
by graham etherington (JIC) 04 Mar '11

04 Mar '11

Hi, I've downloaded the Suite of Velvet assembler tools at http://community.g2.bx.psu.edu/ and installed them as detailed in http://gmod.827538.n3.nabble.com/attachment/868065/0/README?by-user=t I've then run velveth in Galaxy using two files - a file each of corresponding left and right paired-end reads which gives me the following output: 0.000001] Reading FastQ file /opt/galaxy_dist/database/files/002/dataset_2411.dat [0.003878] 1538 reads found. [0.003881] Done [0.003889] Reading FastQ file /opt/galaxy_dist/database/files/002/dataset_2412.dat [0.007500] 1538 reads found. [0.007502] Done [0.007533] Reading read set file /opt/galaxy_dist/database/files/002/dataset_2456_files/Sequences; [0.008571] 3076 sequences found [0.018786] Done [0.018791] 3076 sequences in total. [0.018825] Writing into roadmap file /opt/galaxy_dist/database/files/002/dataset_2456_files/Roadmaps... [0.021716] Inputting sequences... [0.021719] Inputting sequence 0 / 3076 [0.169007] Done inputting sequences [0.169017] Destroying splay table [0.177049] Splay table destroyed I then go to the velvetg tool and select my velveth output file as the input to velvetg, use 'auto' as the -ins_length and -ins_length_sd, and then leave the remaining ins_length fields blank. I leave the final values (from -exp_cov to Minimum Read-Pair Validation) as the default values. When I execute the job it runs and finishes almost instantly and the only output for 'velvetg on data X' is: [0.000001] Unknown option: -ins_length3 The output files Contigs, Contig Stats and Unused Reads are all empty and the LastGraph file has the error: ERROR: /opt/galaxy_dist/database/files/002/dataset_2457_files/LastGraph not found! The version of Velvet that I have installed and that is in the path is velvet_1.0.18. I was wondering if anyone could give me some help here or has any suggestions. Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK

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Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts
by Peter Cock 03 Mar '11

03 Mar '11

Hopefully this will be of interest to some of you... ---------- Forwarded message ---------- From: Nomi Harris <nlharris(a)lbl.gov> Date: Thu, Mar 3, 2011 at 7:37 PM Subject: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts To: bosc-announce(a)lists.open-bio.org, members(a)open-bio.org, GMOD Announcements List <gmod-announce(a)lists.sourceforge.net>, GMOD Developers List <gmod-devel(a)lists.sourceforge.net> Cc: Nomi Harris <nlharris(a)lbl.gov> We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and forgive multiple postings. Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) Dates: July 15-16, 2011 Location: Vienna, Austria Web site: http://www.open-bio.org/wiki/BOSC_2011 Email: bosc(a)open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor _______________________________________________ BOSC mailing list BOSC(a)lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bosc

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QUAL file format(s)
by Peter Cock 03 Mar '11

03 Mar '11

Hi all, Is there any documentation on what Galaxy means by the different qual formats? In particular why is there a qual454 and not a qualsanger (to match fastq)? Historically QUAL files were used back in Sanger/capillary sequencing by PHRED, and just hold PHRED scores as integers. This was followed by the Roche 454 output. Peter

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Shared a value for multiple set-at-runtime workflow parameters
by Peter Cock 02 Mar '11

02 Mar '11

Hi all, I have a multi-step workflow where I've marked some parameters to be set at run time (in this case, a minimum read length, used in two different workflow steps). I want to use the same parameter value in multiple tools, rather than give the user one prompt for each tool. Is this possible? Related to this, it would be nice to specify a default in the workflow (overriding any default in the tool wrapper), and give some caption text to the workflow level parameter. I guess some of this functionality would be related to any enhancement to make a workflow act like a tool (e.g. to combine subworkflows into larger workflows). Thanks, Peter

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requested number of bytes is more than a Python string can hold
by Glen Beane 01 Mar '11

01 Mar '11

one of our users is experiencing this error from the SAM-to-BAM tool: Error extracting alignments from (/hpcdata/galaxy-setup/galaxy-dist/database/files/000/dataset_85.dat), requested number of bytes is more than a Python string can hold The SAM file has 58 million lines of mapped paired end reads. Any suggestions? The galaxy jobs running on our cluster are currently using the version of Python installed with CentOS 5 (python 2.4.3, 64-bit). We have been considering setting up a new python virtualenv for the galaxy user on the cluster that uses a newer version of Python (probably 2.6 so it matches the version on the server running the galaxy web app) -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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