- galaxy-user - lists.galaxyproject.org

How can I get back a permanently deleted history?
by Enklaar, Thorsten 14 Feb '14

14 Feb '14

Dear All, I'm working on Main and just deleted my history with all actual datasets and analyses instead of purging the deleted datasets. Is there a way to get it back? Is there a kind of backup? There were more than 1000 datasets in the history, a lot of workflows produced datasets that were further analysed and had to be purged to save diskplace. Then I unfortunatly clicked on delete permanently instead of purge deleted... Thanks, Thorsten

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Bisulfite seq
by Mathew Bunj 14 Feb '14

14 Feb '14

Do we have any tool which can be used for analyzing and QC check for bisulfite sequencing. I have FASTq files. Thanks Mathew

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Re: [galaxy-user] galaxy-user Digest, Vol 91, Issue 21
by Gang Wang 13 Feb '14

13 Feb '14

Hi, I just notice that NGS FASTQ Trimmer<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2F…>by column can't detect the fastq file I loaded. Anyone knows why. thanks a lot. On Fri, Jan 24, 2014 at 11:00 AM, <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: Creating a Trackster visualisation from a reference in > your history (Jeremy Goecks) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 23 Jan 2014 15:49:44 -0500 > From: Jeremy Goecks <jgoecks(a)email.gwu.edu> > To: graham etherington (TSL) > <graham.etherington(a)sainsbury-laboratory.ac.uk> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Creating a Trackster visualisation from a > reference in your history > Message-ID: <C3382F38-D243-4979-B6A7-BA13EF161EE5(a)email.gwu.edu> > Content-Type: text/plain; charset="windows-1252" > > > Is it possible to create a custom build and use it to view a SAM file > without adding the .len and .2bit files in to the Galaxy file system as an > administrator? > > Yes, it definitely is. > > > If so, what am I doing wrong? > > > This is a Galaxy bug which has been fixed in this commit: > > > https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd23151… > > We have a release coming up, so this fix will be included in the release > and will make it to our public server soon. In the meantime, note that you > can use the genome fasta file rather than the len file to create a custom > build and everything should work. > > Thanks, > J. > >

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cuffmerge
by Janice Patterson 12 Feb '14

12 Feb '14

I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guide, with bias correction using the genome.fa as a reference. When I subsequently attempt to run cuffmerge on my assembled transcript files, however, I get the following errors, and cuffmerge fails. Error: duplicate GFF ID 'CUFF.1.1' encountered! [FAILED] Error: could not execute gtf_to_sam I am using the same genes.gtf file I used for cufflinks. It is the genes.gtf file attained from the Data Libraries provided by galaxy. I ran Cufflinks on the same data set without bias correction (and therefore a genome.fa file was unnecessary) and no multi-read correct, and subsequent cuffmerge with the same genes.gtf file provided ran just fine. Why did turning on bias correction and providing cufflinks with a fasta reference file making cuffmerge fail? Thanks. Janice Patterson

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Error running the Picard tool?
by Dottorini, Tania 12 Feb '14

12 Feb '14

Hi, I am trying to determine the mean inner distance between mate pairs, but encountered odd results. Briefly, to calculate the mean inner distance I mapped PE data with 2x100bp read length with Bowtie against the reference transcriptome, and used the Picard InsertSize Metrics to calculate the Mean insert size. I then, subtracted the combined insert size (2*100) from the Mean insert size value, thus obtaining the mean inner distance between mate pairs. In all the cases studied, 4 samples and 4 controls, I have always obtained negative mean inner distance between mate pairs values. In addition, in some cases I had the following error running the Picard Tool: "Unable to find expected pdf file /galaxy/main/jobdir/006/471/.…../InsertSizeHist.pdf …This always happens if single ended data was provided to this tool" But in all cases I can confirm I provided paired-end NGS data. For same of the runs that gave me this failure log, I rerun them again but mapping to the genome instead of the transcriptome, and in this case it did work but always giving me negative distance values. I would like to know if this is the correct procedure to be followed or if there are other approaches I can use to find these distance values and if I can eventually use such negative distance values in Tophat Thank you for your help Tania

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Depth of coverage error
by Sandrine Imbeaud 12 Feb '14

12 Feb '14

Hi, I am using the "Depth of coverage on BAM files" tool from the NGS: GATK Tools but encounter problem. While part of the BAM files proceed successfully, some BAM files end proceeding with a systematic error (see below). The entire BAM file dataset was generated with the same deepseq analysis pipeline (MiSeq Reporter, PCR amplicon Workflow) => alignemnent is done on Hs. hg19 and manifest is focused on specific regions. Does someone know how to solve this problem? Also, the chromosome X and Y appear to be exclude from the calculation. Is there any settings to select in order to include both sexual chromosomes? Is it expected? Kind Regards / Sandrine -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes Génomique Fonctionnelle des tumeurs solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/ Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp [Mon Feb 10 07:08:03 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-hPNp7B/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-hPNp7B/dict1033574942916796988.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Feb 10 07:08:03 CST 2014] Executing as g2main(a)roundup49.tacc.utexas.edu on Linux 2.6.32-431.1.2.0.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057) [Mon Feb 10 07:08:04 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2025324544 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found. ##### ERROR reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY] ##### ERROR reference contigs = [c1_27022371-27108741, c1_65310990-65312594, c1_103341958-103574198, c1_115256193-115258963, c11_533546-534529, c11_108093339-108239879, c12_25379959-25398502, c12_46123245-46302016, c12_49412540-49449288, c12_70910587-71031382, c12_121416337-121440487, c13_77618564-77901349, c16_337220-402825, c16_2097254-2138873, c17_7571510-7591038, c17_40474813-40500706, c19_10596592-10614570, c2_21224182-21267085, c2_178098515-178099162, c20_57484200-57484647, c3_41240709-41282027, c3_41265294-41266864, c3_47057688-47205620, c3_178928002-178948337, c4_74269729-74287296, c4_185308648-185395907, c5_1253083-1294978, c5_1294819-1295755, c5_55251637-55260189, c5_71402848-71505569, c6_36644019-36655290, c7_135242597-135333692, c7_140452856-140453348, c9_21967531-21994664, c9_135766517-135820181] ##### ERROR ------------------------------------------------------------------------------------------ mv: cannot stat `/galaxy-repl/main/files/007/581/dataset_7581988.dat.sample_summary': No such file or directory

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Picrust upload
by Ines 12 Feb '14

12 Feb '14

Hello, I was trying to run a dataset through Picrust on the web-based Galaxy. I did the OTU table in Qiime as explained in http://picrust.github.com/picrust/tutorials/otu_picking.html#otu-picking-tu…, with the command line: pick_closed_reference_otus.py -i $path/file.fasta -r $path/rep-set/97_otus.fasta -o $path/OTU_Table.biom. I uploaded the file in Get Data, and I want to run the Normalize by Copy Number step, but I get the following message History does not include a dataset of the required format / build. I am not sure if when I generate the OTU Table I need to specify a particular format, or what the problem is. I would really appreciate some advice. I attach the biom file generated in case you need to take a look. Thank you very much in advance.

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Questions regarding Circster visualization
by Friederike Dündar 12 Feb '14

12 Feb '14

Hi, I just noticed that Circos plots are now incorporated into Galaxy's visualization methods which is awesome! However, I'm a bit lost as to what kinds of data I can load into Circos and I cannot find much documentation, so I hope you guys can help out. 1. I tested it using a bigWig and a BED file. Both were loaded nicely in Circos, but I was surprised to see that the visualization of both files looked exactly the same, i.e. both file types seemed to be interpreted as histograms/coverage data. From the Circos plots I've seen in publications, I assumed that BED files should be visualized as straight lines, indicating genome regions (rather than a coverage). Am I doing anything wrong? Or, rather, how should I modify the BED file so that its content is simply interpreted as genomic regions? 2. In the Galaxy publication (www.biomedcentral.com/1471-2164/14/397) "line data" is mentioned for displaying connecting lines in the center of the circle - could you give me an example line of how this kind of data needs to be formated? It would be great to make much more use of Circster! Thanks a lot! Best wishes, Friederike

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Re: [galaxy-user] Help with Cuffdiff
by Jennifer Jackson 11 Feb '14

11 Feb '14

Hi Maria, I didn't notice any obvious problematic usage, format, or content issues with the Tuxedo pipeline execution in your history. Your protocol is right on track. This leaves data and parameter inputs to consider. I did notice that you are mainly using defaults and omitting the use of reference annotation that Cuffdiff uses to generate the full compliment of statistics. The "NOTEST" result indicates that the coverage is too shallow. You could follow the advice here, by adjusting "-c" to be lower. This is "Min Alignment Count:" and is set to "10" in your runs. http://cufflinks.cbcb.umd.edu/faq.html#notest Adding in a reference annotation file could also potentially help. Aligned sequences may be falsely fragmenting without a reference transcript to help bind them together. But, this is just a guess - I didn't examine any assembly regions. This is however something that you could do. The UCSC Table Browser is one source for a GTF file. Experimenting with other parameters as you are doing also is worth it. The manual and such cover these in detail, and there is always the tool author's google group for detailed questions/advice. Good luck with your project, Jen Galaxy team On 2/6/14 12:38 PM, Maria Hoffman wrote: > Hello, > > Thank you for your help. I have found that wiki page very helpful and > actually us it very often (I was using it this AM too before I emailed > you). In looking at the wiki again, nothing is really standing out to > me ( my chromosome notation matches up etc). I am going to keep > looking etc but I did send you my history too. I did try running > another cuffdiff playing with the dispersion estimation method too out > of curiosity. > > Thank you so much for your help! This is my first real data set doing > this and we have abstracts due soon, so the pressure is on! > > Thanks! > Maria -- Jennifer Hillman-Jackson http://galaxyproject.org

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Feb 10, 2014 Galaxy Distribution & News Brief
by Jennifer Jackson 11 Feb '14

11 Feb '14

Feb 10, 2014 Galaxy Distribution & News Brief <https://wiki.galaxyproject.org/News/2014_02_10_Galaxy_Distribution> // *CompleteNews Brief <https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10>* *Highlights:* * Visualization upgrades, including Trackster CSS styling * Multiple Tools migrated to the Tool Shed for a leaner distribution * Redesign of UI rendering: new icons, new font, history pane updates * API functionality upgrades featuring a new master admin API key and * Tool Shed updates a focus on repository metadata, displays, installs, and tests * Over 35 new community contributions added http://getgalaxy.org <http://getgalaxy.org/> http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/> new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2014.02.10 /Thanks for using Galaxy!/ The Galaxy Team <https://wiki.galaxyproject.org/Galaxy%20Team>

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