November 2010 - galaxy-dev - lists.galaxyproject.org

Variabels in label elements
by Bossers, Alex 09 Nov '10

09 Nov '10

Hi All, Does someone know how to get the value of a type="select" param_name displayed in the output file label? I know how to do it if its just a non-nested param setup-up using ${input1.value_label} where the input1 is the select_name. But this fails if the select is inside a conditional..... From cheetah script I can call these values like IF $tool.cmd=="something":..... But whatever I try in the <outputs><data> fails (I though it to be ${tool.cmd.value_label} but that complains on cmd not defined.... All possible iteration tried :( Snippet of a generalised tool.xml below. Any suggestions or hints where to get documentation on this syntax is welcomed! Alex <command> /opt/tools/$tool.cmd $cmd_extra $input_delta #if $tool.cmd=="show-aligns": $tool.extra1 $tool.extra2 #end if > $out_tool </command> <inputs> <conditional name="tool"> <param name="cmd" type="select" value="show-snps" label="Select tool" > <option value="show-snps">show snps</option> <option value="show-aligns">show aligns</option> </param> <when value="show-aligns"> <param name="extra1" type="text" size="40" value="" label="IdR" help="FastA header ref sequence" /> <param name="extra2" type="text" size="40" value="" label="IdQ" help="FastA header query sequence" /> </when> <when value="show-snps" /> </conditional> <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" /> <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" /> </inputs> <outputs> <data name="out_tool" format="text" label="tool ${tool.cmd.value_label}" /> </outputs>

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How to implement the button "send query to galaxy" in UCSC Main tool
by Zhe Chen 09 Nov '10

09 Nov '10

Hi, How to implement the button "send query to galaxy" in (Get Data)->(UCSC Main tool) on the second page? Do you have a code example of it? Thanks

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Re: [galaxy-dev] [galaxy-bugs] report the error
by Jeremy Goecks 08 Nov '10

08 Nov '10

Hi Mingquan, Please send your queries to one of our mailing lists -- galaxy-dev or galaxy-user -- rather than to individuals. That way, more people can see and help you with your questions, you'll likely get a more timely response, and the mailing list archive can serve as a useful repository. Your question about GFF to BED is best addressed to galaxy-user (b/c it's about usage of Galaxy), and your question about Tophat is best addressed to galaxy-dev (b/c it's about setting up a local Galaxy instance). Hence, I've cc'd both lists. Ok, on to your questions: > Maybe i can use the tophat anlone. We've got a Galaxy wrapper ready for Tophat version 1.1+ ; it will likely be available in galaxy-central this week. Once you update your version of Galaxy, you'll be able to run Tophat in Galaxy. > But now i have a another question for giff to bed function. > i want to use gff-to-bed function after i run it, it seems that i got the results : > > empty, format: bed, database: ? > Info: 0 lines converted to BED. Skipped 74166 blank/comment/invalid lines starting with line #1. > > i am using gff3 file.and it is the first few lines. > > ##gff-version 3 > ##genome-build MSU Rice Genome Annotation Project osa1r6 > ##species Oryza sativa spp japonica cv Nipponbare > ##sequence-region Chr1 1 43268879 > > Chr1 MSU_osa1r6 gene 1903 9817 . + . ID=13101.t00001;Name=TBC%20domain%20containing%20protein%2C%20expressed;Alias=LOC_Os01g01010 > Chr1 MSU_osa1r6 mRNA 1903 9817 . + . ID=13101.m00001;Parent=13101.t00001;Alias=LOC_Os01g01010.1 > > Chr1 MSU_osa1r6 five_prime_UTR 1903 2268 . + . Parent=13101.m00001 > Chr1 MSU_osa1r6 five_prime_UTR 2354 2448 . + . Parent=13101.m00001 This appears to be a valid GFF3 file and should work fine. We'll look into this and get back to you. Thanks, J.

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Locally cached alignments
by David Hoover 08 Nov '10

08 Nov '10

We have a local copy of MAF files for hg18, and I modified the ~/tool-data/maf_index.loc file to list the full paths to the .maf files. After restarting Galaxy, the MAF Source and Type are listed in the MAF Coverage Stats tool, as expected. However, after trying to run with an interval file, it gives an error "The MAF source specified (17_WAY_MULTIZ_hg18) appears to be invalid". Is there somewhere else I need to edit to get to the locally cached MAF files? David Hoover Helix Systems Staff http://helix.nih.gov

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Integrating tools with variable inputs
by Branden Timm 04 Nov '10

04 Nov '10

Hi All, Is there any documentation on how to integrate tools that take a variable number of input files? We'd like to integrate a tool with the following command line syntax: tool-name <n input files> <n column names> output1 output2 Thanks! -- Branden Timm System Administrator Great Lakes Bioenergy Research Center btimm(a)glbrc.wisc.edu

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Galaxy using PBSPro
by David Hoover 04 Nov '10

04 Nov '10

Has anyone had success with Galaxy using PBSPro? Do you use pbs_python or DRMAA? Does pbs_python work with more recent versions of PBSPro (>=10)? David Hoover Helix Systems Staff http://helix.nih.gov

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Output redirect
by Zhe Chen 03 Nov '10

03 Nov '10

Hi, For general galaxy output, I need to define sth like <outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs> and put $out_file1 as a parameter in the command tag. To my understanding, Galaxy will save the $out_file1 into a file and retrieve and display it on the result panel. I have a *.pl file which takes inputs and generate a file (result.txt) in my local server and return a file path. Can I redirect the galaxy output to this file? Currently, I am reading the file using the file path and push the content in the file into $out_file1. For large files, it is a waste of computing time and resource (since Galaxy will generate another file). Is there a solution for this? Thanks

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how to set PATH variable
by David Hoover 03 Nov '10

03 Nov '10

I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them? David Hoover Helix Systems Staff http://helix.nih.gov

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Number of elements from a REPEAT block
by Branden Timm 03 Nov '10

03 Nov '10

Hi, I'd like to be able to ascertain the length of an array of input files captured by the REPEAT tag. For example: <repeat name="infiles"> <param name="infile" type="data" format"txt" /> </repeat> How can I get the length of $infiles to pass in my command line? Something like $infiles.length ? -- Branden Timm btimm(a)glbrc.wisc.edu

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using local Genome Browser mirror
by David Hoover 03 Nov '10

03 Nov '10

Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else? David Hoover Helix Systems Staff http://helix.nih.gov

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