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EdgeR returning empty output
by Anto Praveen Rajkumar Rajamani 19 Dec '13

19 Dec '13

Hi, I have used http://galaxy.nbic.nl/ server to run edgeR on my RNA-seq data to identify differentially expressed genes successfully in August 2013. However, while trying with another digital expression matrix at present, I get only empty output repeatedly. Has anyone used edgeR wrapper recently? What could be the problem? Best wishes, Anto

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GCC2014 Training Day: Topic Nomination is now open
by Dave Clements 19 Dec '13

19 Dec '13

Hello all, Training Day topics are nominated by you <http://bit.ly/gcc2014tdnom>, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> , - what topics were nominated in 2013 <http://bit.ly/1i2j1gN>, and - the Events <http://wiki.galaxyproject.org/Events> and the Events Archive<http://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day<http://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! <http://bit.ly/gcc2014tdnom> Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. See you in Baltimore! GCC2014 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2014/Organizers> --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)<http://galaxyproject.org/gcc2014>will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> of Johns Hopkins University <http://jhu.edu/>, inBaltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Error running CCAT test
by Nicolas Lapalu 19 Dec '13

19 Dec '13

Hi, I tried to run CCAT functionnal test, but I get an exception (same problem via web form) Data are well associated with the hg18 build, which is available in test-data/chrom/hg18.len Error running CCAT. Traceback (most recent call last): File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 41, in <module> if __name__ == "__main__": main() File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 38, in main return stop_err( tmp_dir, e ) File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 13, in stop_err raise exception AssertionError: The required chromosome length file does not exist. Any Idea ? Thanks, Nicolas -- ------------------------------------------------------------------- Nicolas Lapalu INRA - URGI, Bat. 18 Route de Saint Cyr 78000 Versailles Tel: +33 (0)1 30 83 38 10 - Fax: +33 (0)1 30 83 38 99 nicolas.lapalu(a)versailles.inra.fr http://urgi.versailles.inra.fr/ http://www.versailles-grignon.inra.fr/bioger -------------------------------------------------------------------

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problem reimporting histories
by Alessandro Ogier 19 Dec '13

19 Dec '13

Dear galaxy users, here at European Institute of Oncology we're deploying a brand new galaxy install, but facing problems with history (re)importing. We have configured a galaxy running on one node where users took a "sneek peek" on features while developing a real deployment on nfs and cluster integration. Now I have to migrate histories to new galaxy install, I'm doing that on behalf my users because we choose to integrate with an apache proxy that does reverse proxying and ldap authentication. Yesterday I produced four tar.gz for a user, placed on a temporary webserver and then proceeded with reimport on new instance: two where reimported, two not. All those files are relatively small (from 1MB to 13MB), and no clues from galaxy debug log: SUCCESSFUL ONE: galaxy.jobs DEBUG 2013-12-18 13:29:32,718 (354) Working directory for job is: /srv/galaxy/galaxy-dist/database/job_working_directory/000/354 galaxy.jobs.handler DEBUG 2013-12-18 13:29:32,738 (354) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 13:29:32,826 (354) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2013-12-18 13:29:32,864 (354) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:33,151 (354) executing: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-37.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url galaxy.jobs DEBUG 2013-12-18 13:29:33,326 (354) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:34,451 execution finished: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-37.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url galaxy.jobs DEBUG 2013-12-18 13:29:34,644 job 354 ended galaxy.datatypes.metadata DEBUG 2013-12-18 13:29:34,644 Cleaning up external metadata files UNSUCCESSFUL ONE: galaxy.jobs DEBUG 2013-12-18 13:30:42,824 (392) Working directory for job is: /srv/galaxy/galaxy-dist/database/job_working_directory/000/392 galaxy.jobs.handler DEBUG 2013-12-18 13:30:42,844 (392) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 13:30:42,934 (392) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2013-12-18 13:30:42,963 (392) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:43,236 (392) executing: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-138.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url galaxy.jobs DEBUG 2013-12-18 13:30:43,400 (392) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:47,524 execution finished: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-138.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url galaxy.jobs DEBUG 2013-12-18 13:30:47,711 job 392 ended galaxy.datatypes.metadata DEBUG 2013-12-18 13:30:47,712 Cleaning up external metadata files sorry for line wraps, I also attached logs. I cloned your repository on my development machine to try to recreate/debug this issue but unfortunately this time I'm unable to import successfully any history (plain galaxy instance, sqlite, no ext user, no job_conf, either default and stable branches). I'm attaching the new galaxy instance universe_wsgi.ini and job_conf.xml, as you can see they are pretty straight-forward. What I'm asking to you : which is the correct way for debugging this sort of things ? No luck putting some debugging code in * lib/galaxy/tools/actions/history_imp_exp.py * lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py maybe I'm missing something ... also, I'd like to contribute some patch on a couple of minor glitches I found, but I'll write to -dev list for that Thank you, and thanks for this great tool :) ciao -- Alessandro Ogier Specialista Reti e Sistemi - Area Ricerca Direzione ICT Gruppo IEO/CCM Istituto Europeo di Oncologia Via Serio, 15 - 20139 Milan, Italy P +39 02 94375269 M +39 334 6841627 (9am-6am CET) E alessandro.ogier(a)ieo.eu W http://www.ieo.it

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Velvet-galaxy
by Jorge Braun 18 Dec '13

18 Dec '13

Hello mates, I'm new working with velvet and these days have several questions, if anyone knows solution ... It is a great help! Try using the galaxy velvet web platform but there are problems: a) Velveth Velveth and functional? Because galaxy appears when running in error: Unable to run Velveth: No file exists b) there worflow to install velvet in galaxy? thank you very much

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Assembly of Paired and Unpaired sequences
by Prash 17 Dec '13

17 Dec '13

Dear All Greetings! I am analysing a genome of ca. 3.4Mb where I have paired.fa and unpaired.fa files as of now. The sequences have been trimmed before that. Now when I assemble these reads using 'ssake -f paired -g unpaired ...', it takes hell lot of time. Perhaps, I am running out of memory in analyzing the sequence reads. I could use galaxy platform, but would like to stick with ssake. Few questions: What if I concatenate these two files, would I be able to peruse this for blasting against my reference? At this point, how do I know whether or not paired or single-end reads are better? How do I know the two chromosomal sequences? Help appreciated for stupid questions :) Thank you in advance Prash Prashanth Suravajhala, PhD. Homepage: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio <http://dk.linkedin.com/in/prashbio> “What counts in life is not the mere fact that we have lived. It is what difference we have made to the lives of others that will determine the significance of the life we lead.” — Nelson Mandela On 15 December 2013 18:00, <galaxy-user-request(a)lists.bx.psu.edu> wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." > to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: fastqc and blast? trinity? (Peter Cock) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Dec 2013 21:18:29 +0000 > From: Peter Cock <p.j.a.cock(a)googlemail.com> > To: Jorge Braun <braun_bio(a)hotmail.com> > Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] fastqc and blast? trinity? > Message-ID: > <CAKVJ-_4BKUgtb37EYF_FsAAj= > YC+eT5ZuRvFgZk0pUySKdmsxg(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <braun_bio(a)hotmail.com> > wrote: > > > > Hello, of course, Jennifer is right for the first question . For > > the second question about blast ... I wonder if running after > > blast in galaxy I can remove sequences that can contaminate > > the data. It's possible? > > > > The BLAST suite is not available on the public Galaxy > server at http://usegalaxy.org but is available from the > Galaxy Tool Shed if you have a local Galaxy instance: > > http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ > > One way to filter your FASTA file based on BLAST hits > would be to use the tabular output from BLAST with > this sequence filtering tool: > > http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id > > e.g. If you want to remove transcripts which seem > to be mitochondria, you could BLAST against a > mitochondrial database, and take only the sequence > with no hits. > > Regards, > > Peter > > > ------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > End of galaxy-user Digest, Vol 90, Issue 13 > ******************************************* >

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fastqc and blast?
by Jorge Braun 17 Dec '13

17 Dec '13

Hello mates, I have two doubts galaxy: a) I have rna-seq data from Illumina and do fastqc ... the results are good but when I fastgroomer to Sanger format and then fastqc ... the results are bad. Does anyone know the cause? I do not understand why. b) With the same sequences can know if they are different Rna and eliminate those that do not want to examine? merry christmas :)

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CEAS/Transcription Factor Binding sites
by Benjamin Osei-agyeman 17 Dec '13

17 Dec '13

Hi List, I am performing a chip seq experiment using CEAS in galaxy, i obtained the following output in pdf form: http://www.datafilehost.com/d/a9d75211 Could some one explain what the output from CEAS tells about the location of the binding sites for the dataset? Thanks in advance Benjy

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Estimated Fragment Lenghth/FDR
by Benjamin Osei-agyeman 17 Dec '13

17 Dec '13

Hi List, Could someone explain the Estimated Fragment length? How is it used in Peak detection? Again what files are used in calculating for the False Discovery Rate (FDR)? Thanks in advance Benjy

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Re: [galaxy-user] fastqc and blast?
by Jennifer Jackson 14 Dec '13

14 Dec '13

Hello Mark, Correct - not needed. Any Illumina data that results from a CASAVA 1.8 or higher pipeline is already has quality scores scaled to Sanger Phred with an ASCII offset of 33. This translates to the ".fastqsanger" format in Galaxy, so no grooming is required, you can just assign the datatype. How to do that is in the first link below. And all the details, including how to read a FastQC report to determine this is in the screencast. Thanks! Jen Galaxy team On 12/13/13 8:58 AM, Mark Lindsay wrote: > Hi James > > do you need to run the Groomer on the latest Illumina data? > > BW > > Mark > > > > On 13 Dec 2013, at 16:53, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > >> Hello, >> >> For the first question, make sure that you are running the groomer >> with the correction options. In almost all cases for Illumina data >> this will mean leaving all but one setting at default. The setting to >> change is "Input FASTQ quality scores type:". The results of FastQC >> will inform you about how to set this. An example is in this wiki >> section's screencast plus the first bullet point: >> https://wiki.galaxyproject.org/Support#Dataset_special_cases >> http://vimeo.com/galaxyproject/fastqprep >> >> For the second, I am not sure what you mean by 'different'. Do you >> mean the data may have contamination from another species? Or that >> the the data content may be different with respect to quality? >> >> In short, to filter based on quality as reported in the FastQC >> report, try tools in the same tool group such as "FASTQ Trimmer" or >> "FASTQ Quality Trimmer". >> >> The protocols included in our RNA-seq pipeline help start out with >> some quality steps: >> https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq >> >> And many from our community have contributed RNA-seq tutorials: >> https://wiki.galaxyproject.org/Learn#Other_Tutorials >> >> Hopefully this helps! >> >> Jen >> Galaxy team >> >> On 12/13/13 7:05 AM, Jorge Braun wrote: >>> Hello mates, >>> >>> I have two doubts galaxy: >>> >>> a) I have rna-seq data from Illumina and do fastqc ... the results >>> are good but when I fastgroomer to Sanger format and then fastqc ... >>> the results are bad. Does anyone know the cause? I do not understand >>> why. >>> >>> b) With the same sequences can know if they are different Rna and >>> eliminate those that do not want to examine? >>> >>> merry christmas :) >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> atusegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on >> the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- Jennifer Hillman-Jackson http://galaxyproject.org

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