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Re. RNA-Seq
by Songyan Liu 23 Nov '12

23 Nov '12

I was using Cufflinks to analyze Clip-Seq data. The results as 'gene expression' and 'transcript expression' gave me almost same results (No. of genes ? No. of transcripts). I guess the number of genes should be relatively smaller than that in transcripts. I wonder if I need to get a special format for the annotation? I used '62: UCSC Main on Human: refGene (genome)'. Thanks, Songyan Liu

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help
by Magriet Van Der Nest 23 Nov '12

23 Nov '12

Dear Galaxy help-centre I want to use Tophat and Clifflinks to do an expression analysis. However, the reference genome for Heterobasidion annosum (it is available at JGI) is not listed. You have posted on your website that we can contact you if 'your genome of interest' is not listed. Is it possible that you can included the H. annosum genome on the list? Thank you very much Magriet

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piping two scripts in the same xml tool wrapper
by Christophe Antoniewski 22 Nov '12

22 Nov '12

Hi, Is there a way to pipe in the same xml wrapper two scripts in different languages, the output of the first script becoming the input of the second ? I know that the spirit of galaxy would be to make a workflow, but the intermediate output in the present case is not interesting at all and may confuse the user. I am testing something like : <command interpreter="python">plotter.py $input $minsize $maxsize $factor $output</command> <command interpreter="bash">r_wrapper.sh $Rplotter</command> <inputs> <param name="input" type="data" format="tabular" label="Compute Plot table from this bowtie standard output"/> <param name="minsize" type="integer" size="3" value="20" label="Min size of small RNA to plot" help="'20' = 20 nucleotides"/> <param name="maxsize" type="integer" size="3" value="22" label="Max size of small RNA to plot" help="'22' = 22 nucleotides"/> <param name="factor" type="float" size="6" value="1.00" label="Normalization factort" help="leave at 1.00 for no normalization"/> <param name="title" type="text" size="15" value="Main Title" label="Main Titles"/> <param name="xlabel" type="text" size="15" value="Coordinates (nt)" label="x axis label"/> <param name="ylabel" type="text" size="15" value="Normalized number of reads" label="y axis label"/> <param name="yrange" type="integer" size="6" value="400" label="y axis range"/> </inputs> <configfiles> <configfile name="Rplotter"> ## Setup R error handling to go to stderr options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) tab = read.delim("${output}", header=TRUE) ## Open output PDF file pdf( "${outputFinal}" ) #determining y and x axis ranges MAXcoord = max(tab[,1]) + 100 MINcoord = min(tab[,1]) MMAX = ${yrange} plot(tab[,1], tab[,2], type="h", xaxt="n", xlim=c(MINcoord , MAXcoord), ylim=c(-MMAX , MMAX), frame.plot=FALSE, lwd=2, las=2, xlab= "${xlabel}", ylab="${ylabel}", main = "${title}") lines(tab[,1], tab[,3], type="h", lwd=2) axis(1) ## Close the PDF file devname = dev.off() </configfile> </configfiles> <outputs> <data name="output" format="tabular" label= "Data Frame"/> <data name="outputFinal" format="pdf" label= "PDF plot"/> </outputs> but the second script output is empty. I suspect that the second script is launched when the output of the first script is not available yet. Thanks for the help Chris

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Bug when using data_column
by aristos aristodemou 22 Nov '12

22 Nov '12

Dear galaxy developers and users, When using the data_column type for a tool in galaxy, there is a bug that gives the message "An invalid option was selected, please verify". The problem occurs when for example you had selected a dataset with 6 columns in it and selected as a choice the 6th column and then changed your mind and selected another dataset with 5 columns. This happens because when it checks in basic.py if the value selected is in the accepted values of the selection list, the value it uses is the one that was selected on the previous dataset. Does anyone know how this issue could be solved so that the check is not performed when the dataset is selected or if there is a way to reset the value when a new dataset is selected? Regards, Aris

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History will not refresh after workflow submission via the API
by MSc. Sascha Kastens 22 Nov '12

22 Nov '12

Hi devs! After updating my local instance to changeset 19cbbaf566216cb46ecc6a6d17e0f1e0ab52978e my tool which submits a workflow via the API and set force_history_refresh to TRUE does not refresh the history anymore. The job is submit via DRMAA to SGE. Unfortunately the job seems to run forever because it is still in yellow state (even after SGE tells Galaxy that the job has finished. As soon as I refresh the history manually the according history entries get green and all entries for the submitted workflow are shown. I have no idea where I can have a look at. If you need any further information let me know! Thanks for your help in advance! Cheers, Sascha

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Where is the eye icon for datasets in error state?
by MSc. Sascha Kastens 22 Nov '12

22 Nov '12

Hey devs! It seems that many things related to history datasets has changed since I have updated my local Galaxy instance and the current version. Unfortunately it seems that one cannot "Display data in browser" (eye icon) if the dataset is in error state. Where can I get that feature back? Some of my tools write logging information to a separate logfile which will be in error state if the tool fails but contain useful information. Thanks, Sascha

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Re: [galaxy-dev] [galaxy-user] help
by Jeremy Goecks 21 Nov '12

21 Nov '12

Because your questions are about a local installation of Galaxy, your email is best suited to the galaxy-dev mailing list, so I've moved it there. > 1. FastQC not running . gives an error and doesn’t run on groomed or un-groomed FastQ file. The error message shows in the below pic. I don't see the pic, you probably need to install FastQC: (a) download the tool (b) put the fastqc script in the <galaxy_home>/tool-data/shared/jars/FastQC directory (c) make the script executable: %chmod 777 <galaxy_home>/tool-data/shared/jars/FastQC/fastqc > 2. No reference genomein the drop down list in TOPHAT for illumine tool and TOPHAt2. See the section 'Setting Up the Reference Genomes for NGS Tools' on this page for help setting up genomes/indices: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J.

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Failed to run display.py
by Tom Hait 21 Nov '12

21 Nov '12

Hello, I'm new with Galaxy api. I'm following the ReadMe file in script/api. I'm trying to run: python display.py ff76834f42d18414b4aaed577466ef35 http://0.0.0.0:8080/api/libraries and it doesn't work, it says: HTTP Error 503: Service Unavailable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" " http://www.w3.org/TR/html4/loose.dtd"> <HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"> <TITLE>ERROR: The requested URL could not be retrieved</TITLE> <STYLE type="text/css"></STYLE> </HEAD><BODY> <H1>ERROR</H1> <H2>The requested URL could not be retrieved</H2> <HR noshade size="1px"> <P> While trying to retrieve the URL: <A HREF=" http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35"> http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35</A> <P> The following error was encountered: <UL> <LI> <STRONG> Connection to 0.0.0.0 Failed </STRONG> </UL> <P> The system returned: <PRE><I> (111) Connection refused</I></PRE> <P> The remote host or network may be down. Please try the request again. <P>Your cache administrator is <A HREF="mailto:root">root</A>. <BR clear="all"> <HR noshade s so I tried to change the URL to: http://localhost:8080, http://127.0.0.1:8080 ... It also didn't work. Any Ideas about could go wrong? Thanks, Tom.

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Multiple language in one tool
by Philipe Moncuquet 20 Nov '12

20 Nov '12

Hi dev, I was wondering if the following is possible or not. What if I want to build a tool that that uses Perl and R at the same time ? If I had to do it on my local machine I would create a pipeline but wouldn't it be cool if a wrapper could use different languages. Philippe

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Direct access the fastq files stored in galaxy server local storage
by Fenglou Mao 20 Nov '12

20 Nov '12

We have a local galaxy server. I know I can get data by ftp, upload directly from browser, or by a URL. If I have some fastq files in the Galaxy server local storage, is it possible to let Galaxy use it directly? Thanks, Fenglou

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