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Help need in troubleshooting cufflinks
by Vijay T 14 Dec '11

14 Dec '11

Hi Team, This is Vijay from ELogic Technologies Pvt Ltd, Bangalore, India. 1. Using Galaxy local 2. NA 3. Galaxy was downloaded using the tar files 4. NA 5. When i tried to install Cufflinks into my system i am getting the following error. In file included from hits.h:21:0, from abundances.h:20, from differential.cpp:17: common.h: At global scope: common.h:25:25: error: ‘boost::BOOST_FOREACH’ has not been declared In file included from differential.h:29:0, from differential.cpp:18: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’: replicates.h:141:50: warning: unused variable ‘s2’ [-Wunused-variable] differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’: differential.cpp:111:31: warning: unused variable ‘s2’ [-Wunused-variable] differential.cpp: In function ‘void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)’: differential.cpp:704:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] make[2]: *** [differential.o] Error 1 make[2]: Leaving directory `/home/binet/Downloads/cufflinks-1.2.0/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/binet/Downloads/cufflinks-1.2.0' make: *** [all] Error 2 Even i have tried with various versions of cufflinks but i am getting the same error. Please kindly help me in getting out of this error. Thanks and Regards Vijay

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enabling regular users to upload large data volumes to a local Galaxy server
by Yury V Bukhman 13 Dec '11

13 Dec '11

Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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Help
by Giuseppe Petrosino 13 Dec '11

13 Dec '11

Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file". Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datasets (text manipulation) and then use MACS for the peaks calling? Thank you so much. Giuseppe

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EMBOSS fuzzpro tool pattern is not read correctly from the input
by domantas.motiejunas＠cropdesign.com 12 Dec '11

12 Dec '11

Hello, I'm trying to run EMBOSS fuzzpro tool, however, I get Illegal character error '_', aparently from the fuzzpro tool itself. One of the input parameters is amino acid sequence pattern, for instance I submit AV[RL]E, but somehow it get's converted and passed to the fuzzpro as AV__ob__RL__cb__E, and then apparently these '_' are causing the error. I tested the tool on command line and it works fine. Also it works on Galaxy if I submit AVRE (just amino acid letters no special characters for pattern) So basically seems that in my input pattern string AV[RL]E the character [ is somehow converted into __ob__ and character ] is converted into __cb__ Any ideas how to fix this? Thanks, Domantas

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Genomic interval file for GATK
by Praveen Raj Somarajan 12 Dec '11

12 Dec '11

All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that "Genomic Interval" option can accept in beta version. It produced an error when I provided an (enrichment coords) bed file? DepthOfCoverage had also produced error when I used bed files. Would beta release (v1.3) accept bed file as input for genomic intervals? 2) SAMtool index is seem to be missing in Galaxy. Is this true or any other module (say SAM->BAM) incorporates this functionality? Looking forward to your comments. Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Re: [galaxy-user] Text Editing
by Dave Clements 09 Dec '11

09 Dec '11

Hi Luce, I'm forwarding this question to the Galaxy-User mailing list, as I think this is a pretty common situation. Here's how I replace text in a column. It's a two step process for each dataset. First go to Text Manipulation -> Compute. In the Add expression text box enter columnNum.replace("oldVal", "newVal") In your case I think this is c4.replace("MACS_peak_", "treatment1_peak_", 1) "replace" is a Python character string operation, and c4 is the character string column we are working on. I added the 1 out of paranoia. This tells galaxy to only replace the first occurrence of the old string, in each line. Care must be taken to avoid more replacement than you want. Executing this will create a dataset with a new column at the end. Now, use the Text Manipulation -> Cut operation to substitute the new column in place of the old column. Does that do the trick? Thanks, Dave C. On Thu, Dec 8, 2011 at 4:24 PM, las2017 <las2017(a)med.cornell.edu> wrote: > I have two ChIPSeq datasets, and I am trying to find the common and > distinct peaks between them and visualize them. I end up with a MACS bed > file for each (listing a bunch of MACS_peaks). I then use the Intersect and > Subtract tools from the Genomic Intervals tab and end up with the peaks I > want. However, because of the way that MACS names its peaks, there can end > up being some peaks named the same way in both files (because, for example, > peak 20 in file1 is from position 300,000-300,500 but peak 20 in file 2 is > from position 320,000-320,500). So, I can end up with multiple peaks with > the same name. Because all the peak names have the same form, it can also > be difficult to tell them apart when visualizing them in the UCSC Genome > Browser. > > What I would like to do is to be able to edit the bed file to change the > text MACS_peak_<number> to, say, treatment1_peak_<number> so that peak 20 > would now still be numbered 20 in both files, but would have a different > label. This would be pretty easy to do using regular expressions and sed. > > I know there have been a few posts about text manipulation, and I know > that there is a text manipulation tab, but I can't seem to find an easy way > to do what I want to do. > > Any advice? > > Thanks, luce > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Text Editing
by Jennifer Jackson 09 Dec '11

09 Dec '11

Hello Luce, I can explain the use of the tools "Text Manipulation". For each file independently, the following steps will rename the "name" identifier in column 4. I don't believe that there a more direct method, but you may discover one. This type of customization is why the tools are distinct - so they can be used in sequence to do many of the same text manipulations as on the unix line command. There is a biosed command as part of EMBOSS, but that tool works on sequence text, not text files in general. To save time in the future, these steps can be put into a workflow, with a edit of step 2 to customize the new ID text as needed when run. Starting with a 5 column MACS BED file: 1 - Save the track header line with the tool "Select first lines from a dataset" with the option to save the line 1. 2 - Create the working dataset that does not include the first line with the tool "Remove beginning of a file" with the option "Remove first: 1" lines. 3 - Split of up the existing ID with the tool 'Convert delimiters to TAB" using the "Underscores" option. This will split the fourth "name" column into three distinct columns, the last new column will be using to create the new ID. 4 - Create a column in your file named "treatment1_peak_" with the tool "Add column to an existing dataset" This will create an extra column at the end of the BED file, to be used in the new ID. The file should now be: c1 - chrom c2 - start c3 - end c4 - the text "MACS" c5 - the text "peak" c6 - the text will be a number, second part of the new ID c7 - score c8 - the text "treatment1_peak_" (or "treatment2_peak_" if the second file) 5 - Merge the two ID portions with the tool "Merge Columns together" using the option of merging column c8 with c6. This will create a new field, c9, with the text "treatment2_peak_N" where "N" is whatever the number in c6 was, per row. 6 - Create the new BED file, putting the new "name" column in the correct order and omitting the columns not needed, using the tool "Cut columns from a table" and pasting into the "Cut columns:" box the this text (no quotes): c1,c2,c3,c9,c7 7 - Add in back the track line (removed in step 1) with the tool "Concatenate datasets tail-to-head" with the options set to concatenate the output of step#1 as the first file and the output of step 6 as a second file. 8 - Use the Edit Attributes form to change the file type back to BED and assign all five columns to the proper attribute (click on pencil icon to reach form). Hopefully this is will work (it did for my test) or is enough information for you to worked out the exact steps for your particular datasets. Next time, please send data/tool questions directly "to" the galaxy-user(a)bx.psu.edu mailing list. Replies should be send "reply-all". The outreach account is for other purposes. las2017(a)med.cornell.edu wrote: > I have two ChIPSeq datasets, and I am trying to find the common and distinct peaks between them and visualize them. I end up with a MACS bed file for each (listing a bunch of MACS_peaks). I then use the Intersect and Subtract tools from the Genomic Intervals tab and end up with the peaks I want. However, because of the way that MACS names its peaks, there can end up being some peaks named the same way in both files (because, for example, peak 20 in file1 is from position 300,000-300,500 but peak 20 in file 2 is from position 320,000-320,500). So, I can end up with multiple peaks with the same name. Because all the peak names have the same form, it can also be difficult to tell them apart when visualizing them in the UCSC Genome Browser. > > What I would like to do is to be able to edit the bed file to change the text MACS_peak_<number> to, say, treatment1_peak_<number> so that peak 20 would now still be numbered 20 in both files, but would have a different label. This would be pretty easy to do using regular expressions and sed. > > I know there have been a few posts about text manipulation, and I know that there is a text manipulation tab, but I can't seem to find an easy way to do what I want to do. > > Any advice? > > Thanks, luce -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Cucumber genome
by changlong wen 09 Dec '11

09 Dec '11

Hi, In the NGS mapping option with "lastz" I cannot find the Cucumber genome.* *Could you please make this reference genome available? Or we have the reference sequence. How to add them in in the local server? Many thanks. Have a good day. Best regards changlong

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Cucumber genome
by changlong wen 09 Dec '11

09 Dec '11

Hi, In the NGS mapping option with "lastz" I cannot find the Cucumber genome.* *Could you please make this reference genome available? or we have the reference sequence. How to add them in the list? Many thanks. Have a good day. Best regards changlong

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January 2012 Galaxy Events: Dec 15 Deadline for Czech Republic Workshop
by Dave Clements 08 Dec '11

08 Dec '11

Hello all, The January Events <http://wiki.g2.bx.psu.edu/Events> email is going out a little early this month, mainly because of a *December 15 deadline for the Galaxy Developer Workshop in the Czech Republic<http://evomics.org/workshops/galaxy-developer-workshop/> *. There are Galaxy-related events on (at least) 3 continents next month: * Date * * Topic/Event * * Venue/Location * * Contact * January 8-21 *2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> * Features Galaxy and much more. Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 *Galaxy Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper2350.html>@ GMOD Workshop<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1123.html> *, and *The Galaxy Platform: Running Analyses in the Cloud<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper4623.html>@ Cloud Computing Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1139.html> * PAG 2012 <http://wiki.g2.bx.psu.edu/Events/PAG2012>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> Dannon Baker January 17 *Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> * Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> January 23 *Galaxy Developer Workshop<http://evomics.org/workshops/galaxy-developer-workshop/> Application deadline is December 15.* Český Krumlov, Czech Republic <http://www.ckrumlov.info/php/>, immediately following the Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…>, (which also features Galaxy content) James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 26 *今回の講習会では，「Next-Generation Sequencer(NGS) 微生物解析と Galaxy ツール」を中心に講義と実習を行ないます。講義内容をよりよく理解して頂くために，PC を使用した実習を行ないます。<http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ> * (Next-Generation Sequencing (NGS) and microbiological analysis with Galaxy) DNA Data Bank of Japan (DDBJ), National Institute of Genetics<http://www.ddbj.nig.ac.jp/> DDBJ <http://www.ddbj.nig.ac.jp/addresses-j.html> And I apologize in advance if I messed up the translation of the event at DDBJ <http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ>! Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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