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joining two FASTq files with overlap reads
by shamsher jagat 09 Jan '13

09 Jan '13

I have a data generated from Miseq 2X250 bp these reads are overlap, before aligning to a my custom bacterial genome, I have to join these two mate pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH can be used. I am looking for if there are similar tool or any way I can join two Fastq files which i can use for alignment. Just to clarify further with overlapping reads as such BWA is not aligning the reads. I have used both as mate pair or used only forward reads to align to genome. The idea is to find SNPs in different samples. Thanks Kanwar

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Download data using FTP-access?
by Karen Margrethe Jessen 08 Jan '13

08 Jan '13

Is there any way of downloading processed files at galaxyproject.org by e.g. FTP, instead of “Save as” in the web browser? I have some large (~50Gb) BAM files to download, and downloading it via the browser is not stable. Thanks, Karen.

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Trackster custom builds wrong
by Jennifer Hillman-Jackson 08 Jan '13

08 Jan '13

Repost to Galaxy-user ----------- When using Trackster on Galaxy( https://main.g2.bx.psu.edu/root ), as the Galaxy Wiki of Trackster (http://wiki.galaxyproject.org/Learn/Visualization) recommend , I need to build a track browsers for soybean because that it isn't installed for all users. But after I enter the all the request information on the webpage(new build name, key and definition) and submit, but I get an server error information, it says "an error occurred. see the error logs for more information.(Turn debug on to display exception reports here)" Since I find there is also someboby encounter this problem in the mail list, but did't find any useful solution. So, I want to know why it happend and how to fix it. Is there something wrong in my maniputation? Any replay will be appreciated. Thank you very much! Yours sincerely, Yanting Shen

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Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul
by Sarah Maman 08 Jan '13

08 Jan '13

Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that we have to install your version or thaht we just need to rename some files? Your error message when running ruby run_chiphorde4.rb is : LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage <motif_template> <ChIPHorde-engine-params> LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Thanks in advance, Sarah Support a écrit : > Bonjour, > > Voilà ce que j'obtiens quand je lance la commande qu'il demande: > > ruby run_chiphorde4.rb > LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory > /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts > LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage <motif_template> > <ChIPHorde-engine-params> > LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb > > Je n'obtiens donc pas l'erreur dont il parle. > Par ailleurs voici le chemin de la librairie: > /usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver. > > Je continue à chercher avec ce que tu m'as envoyé. > Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils > aient renommé les fichiers > > > Cordialement, > > Marie-Stephane Trotard > > Génopole - Plateforme bio-informatique > Centre INRA de Toulouse - Unité de BIA > Chemin de Borde-Rouge - AUZEVILLE > BP 52627 - 31326 CASTANET-TOLOSAN CEDEX > tél. : +33 (0)5 61 28 54 27 > Support : support.genopole(a)toulouse.inra.fr > 08.01.2013 09:05 - Sarah Maman a écrit: > > >> Bonjour Marie-Stephane, >> >> A priori, il manquerait une librairie : >> >> I think that there's some ruby libraries missing. >> >> Please try to run ChIPMunk externally this way: >> >> ruby /path/to/ChIPMunk/run_chiphorde.rb >> >> If you receive this kind of error message, it means that it missed one library >> > to work: > >> ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- >> > rexml/formatters/pretty (LoadError) > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in >> > `require' > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in >> > `require' > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 >> >> I already had the problem and the missing library was this one: >> >> http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pre… >> >> >> Merci d'avance, >> Sarah >> >> >> Support a écrit : >> >>> Bonjour, >>> >>> Il me semble que je l'avais installé en même temps que FindPeaks: >>> >>> /usr/local/bioinfo/src/ChIPMunk/current >>> >>> Parles-tu d'un autre logiciel? D'un version? >>> >>> >>> Cordialement, >>> >>> Marie-Stephane Trotard >>> >>> Génopole - Plateforme bio-informatique >>> Centre INRA de Toulouse - Unité de BIA >>> Chemin de Borde-Rouge - AUZEVILLE >>> BP 52627 - 31326 CASTANET-TOLOSAN CEDEX >>> tél. : +33 (0)5 61 28 54 27 >>> Support : support.genopole(a)toulouse.inra.fr >>> 07.01.2013 14:35 - sarah.maman(a)toulouse.inra.fr a écrit: >>> >>> >>> >>>> A user filled out the contact form on bioinfo.genotoul.fr. >>>> >>>> >>>> ###master_email-line-plain_mailsubject## >>>> >>>> E-Mail: sarah.maman(a)toulouse.inra.fr >>>> >>>> >>>> Priority: Very low >>>> >>>> >>>> Your Message: Bonjour, >>>> >>>> Il me semble, sauf erreur de ma part, que ChipMunk n est pas installÃ© sur >>>> > Genotoul. > >>>> Est-il possible, s il vous plaÃ®t, de l installer. >>>> >>>> TrÃšs cordialement, >>>> Sarah Maman >>>> >>>> >>>> >>>> ---------------------------------- This message was created automatically. >>>> >>>> >>> -------------------------------- >>> >>> >>> >>> >>> >>> >>> >> > > > > > >

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gene names from cuffdiff data
by Elwood Linney 08 Jan '13

08 Jan '13

How does one get gene names when using cuffdiff when looking at "gene differential expression testing" results? I am doing some +/- exposure studies with zebrafish embryos and then processing the 50bp single-ended fastq files through Galaxy with particular interest in the cuffdiff readout of differential gene expression. It seems to be working well but my readout is only giving me gene ID's. It would by more efficient if I could get gene names from the output. I suspect I may be able to do this through selection of options from the UCSC TABLE BROWSER when I use its Zv9 danRer7 assembly as a reference genome. I see a place for selected genes but not for all the identified genes. Is this something that could be done directly or is there just a "beyond Galaxy" method of gene gene lists from a list of gene ID's. Thanks, el linney Duke University Medical Center

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Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements 08 Jan '13

08 Jan '13

Hello all, Nominations are now open <http://bit.ly/gcc2013nom> for Training Day topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Any topic of interest to the Galaxy Community can be nominated<http://bit.ly/gcc2013nom>(see what was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January. Topic nomination closes 11 January. Thanks, Dave Clements, on behalf of the GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee> Links: http://bit.ly/gcc2013nom - nominate a topic http://bit.ly/gcc2013td - Training Day page http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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nebula suite / _chiphorde.log not found
by Sarah Maman 07 Jan '13

07 Jan '13

Hello, I 've integrated nebula suite in my local instance of galaxy but here is the error message received when running ChipMunk analysis : Galaxy cannot stat a file "_chiphorde.log" in the job working directory. Do you have any idea ? Thanks in advance, Sarah

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(no subject)
by Eric Guo 07 Jan '13

07 Jan '13

http://hard-mobile.com/fkjbgs.php?ffij=ffij

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Add new page server error
by Aaron Stonestrom 05 Jan '13

05 Jan '13

When logged into main trying to create a new shared page under "Add new page" in Saved Pages, entering any page title and selecting Submit gives me: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Thanks for any help,

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Error Running CuffCompare on Galaxy Server
by Samit Watve 04 Jan '13

04 Jan '13

Hi, I'm attempting RNA-seq data analysis on *Vibrio cholerae* samples, at galaxy main https://main.g2.bx.psu.edu/. I was able to align transcripts using Ion Torrent's TMAP aligner. I uploaded the BAM files and used the cufflinks tool, which gave me FPKM scores for various transcripts. Now I want to extract the relevant gene_id for each mapped transcript using a reference genome. I tried using CuffCompare for this purpose using a reference file from the UCSC archaea database or using a FASTA file from history. In either case, cuffcompare gives me an error. Error1: (When using a reference genome from the UCSC archaea database) An error occurred running this job:*cuffcompare v2.0.2 (3522) No sequence data found for dbkey vibrChol1, so sequence data cannot be used. cp: cannot stat `/galaxy/main_pool/pool4/tmp/job_working_directory/004/846/4846005/cc_output.input1.refmap': No such file or directory cp: cannot stat `* * * Error 2: (When using a reference genome from history) An error occurred running this job:*cuffcompare v2.0.2 (3522) cuffcompare -o cc_output -r /galaxy/main_pool/pool1/files/005/515/dataset_5515739.dat -s ref.fa ./input1 Error running cuffcompare. You are using Cufflinks v2.0.2, which is the most recent release. No fasta index found for ref* * * Could you help me figure out what's going on? Thanks, -Samit Regards, Samit Watve Graduate Teaching Assistant, School of Biology, Georgia Institute of Technology PhD Student at the Hammer Lab, Office: Cherry Emerson, 218-E, 310 Ferst Drive Atlanta GA School of Biology, Georgia Institute of Technology Lab Page: http://www.hammerlab.biology.gatech.edu/

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