July 2012 - galaxy-user - lists.galaxyproject.org

Uploading files into local instance! Please help!
by Di Nguyen 24 Jul '12

24 Jul '12

Dear all, I am having a problem uploading my RNA-seq files into my local instance. What would be the easiest way to set this up? I already setup libraries under Admin but cannot upload file directly, perhaps due to the size limit of the browser. 1.FTP? Please give me a step by step instruction. I got no problem setting up Fizilla against Main Galaxy. I looked at the wiki page but not quite clear on what to do 2.Direct upload from local file path (limit by the size of the file << 2Gb, which is not practical? My utmost appreciation, Di Nguyen U of Washington, Seattle, WA

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"Jobs is waiting to run" all day on Main
by Lee Silver 23 Jul '12

23 Jul '12

Since earlier today (at least 6 hours), all of my jobs have been stuck in the "waiting to run" state on the Main Galaxy server. Lee Silver (leemsilver(a)genepeeks.com)

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Re: [galaxy-user] cufflinks eference annotation
by Jennifer Jackson 23 Jul '12

23 Jul '12

Hello Irene, Please see below: On 7/23/12 2:17 AM, i b wrote: > Thanks Jen. > > One thing I still don't get: what if I want to discover novel > tanscripts? Does this have anythign to do with selecting or not a > reference annotation > > Best > I > > On Mon, Jul 23, 2012 at 5:58 AM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: >> Hello Irene, >> >> >> On 7/21/12 5:00 AM, i b wrote: >>> >>> Hello, >>> if I am looking for DE between samples and ran cufflinks without >>> reference annotation, does it mean that when I ran cuffcompare and >>> cuffmerge I DOTN'T HAVE to select a refence annotation in the options? >> >> >> No, you do not have to use a reference annotation, but this will mean that >> some Cuffdiff calculations will be skipped. This is related to the reply I >> just sent to your other question about absent calculations. >> More detail: >> http://cufflinks.cbcb.umd.edu/tutorial.html#differential On this page, the sections titled "Discovering novel genes and transcripts" and "Differential analysis with gene and transcript discovery" cover when to use a reference annotation file during the various stages of analysis for different end purposes. The publication also includes more details. Going forward, please be sure to send questions directly to the mailing list, as this helps us to both track and coordinate replies as a team. Thanks, Jen Galaxy team >> http://cufflinks.cbcb.umd.edu/howitworks.html#hdif >> >> >>> >>> Also,how are my cufflinks fected wheter i use the reference annotation >>> or not?In galaxy tracker, looks like there are alignments missing or >>> added compared to when i ran cufflinks with a reference annotation >> >> >> Reference annotation transcripts can become part of the overall transcript >> dataset. >> More detail: >> http://cufflinks.cbcb.umd.edu/howitworks.html#hrga >> >> >> Sorry to point you back to the tool documentation, but that is the resource >> for these topics. >> >> Full resources are outlined in this wiki link, including the tool author's >> publication that Jeremy recommended: >> http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results >> (see "Tools on the Main server -> Example: unexpected results with RNA-seq >> analysis tools.) >> >> Best, >> >> Jen >> Galaxy team >> >>> >>> Thanks, >>> ib >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at 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/ >>> >> >> -- >> Jennifer Jackson >> http://galaxyproject.org -- Jennifer Jackson http://galaxyproject.org

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cufflinks eference annotation
by i b 23 Jul '12

23 Jul '12

Hello, if I am looking for DE between samples and ran cufflinks without reference annotation, does it mean that when I ran cuffcompare and cuffmerge I DOTN'T HAVE to select a refence annotation in the options? Also,how are my cufflinks fected wheter i use the reference annotation or not?In galaxy tracker, looks like there are alignments missing or added compared to when i ran cufflinks with a reference annotation Thanks, ib

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Re: [galaxy-user] cuffdiff results missing
by Jennifer Jackson 23 Jul '12

23 Jul '12

Hello Irene, This issue is similar to the original. The input GTF for this run (dataset #15) has tss_id populated, but not p_id. The p_id attribute is required for the CDS calculations. http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input (quote) Cuffdiff Input: Attribute Description p_id The ID of the coding sequence this transcript contains. This attribute is attached by Cuffcompare to the .combined.gtf records only when it is run with a reference annotation that include CDS records. Further, differential CDS analysis is only performed when all isoforms of a gene have p_id attributes, because neither Cufflinks nor Cuffcompare attempt to assign an open reading frame to transcripts. Dataset #15 was created from a CuffMerge run (which runs Cuffcompare as a component). Examining the selections used (clicking on the blue arrow "rerun" icon), shows that the option "Use Sequence Data:" was set to "No". Changing this to "Yes" and using "Choose the source for the reference list:" as "Locally cached" (and double checking that all inputs are assigned to hg19) will assign p_id. Note that this will be true only for those transcripts that are associated with reference annotation transcripts containing coding regions (in your data: 'nearest_ref "NM_XXXXX"', not "NR_XXXXX". NR_ human RefSeq transcripts are non-coding). Galaxy's CuffMerge tool form has this option labeled: (quote) Use Sequence Data: Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff. Thanks! Jen Galaxy team On 7/21/12 11:04 PM, i b wrote: > Hi, > I ran again cuffdiff using the cuffmerge as gtf. > The following dataset were empty: > > 128: Cuffdiff on data 12, data 14, and others: CDS FPKM tracking > > 127: Cuffdiff on data 12, data 14, and others: CDS FPKM differential > expression testing > > 126: Cuffdiff on data 12, data 14, and others: CDS overloading > diffential expression testing > > The others have data downloadable as excel. > > any explanation??????? > > Thanks, > ib > > On Fri, Jul 20, 2012 at 12:10 AM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: >> Hello Irene, >> >> Yes, this is can be the result if your source GTF data did not have the full >> compliment of attributes needed by Cuffdiff to perform these calculations. >> >> The primary tool documentation covers this information here: >> http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track >> >> The iGenomes datasets are a popular choice for this reason. A version of >> UCSC RefGenes is available for certain genomes. Please see: >> http://cufflinks.cbcb.umd.edu/igenomes.html (scroll down on page in some >> browsers to find table) >> >> Galaxy has one of these already loaded, mm9 genes.gtf, in the "Shared Data >> -> Shared Libraries" section on the public Main server. More iGenomes .gtf >> files will likely be added here, sometime after the GCC2012 conference. For >> now, locally download to your own system/desktop, uncompress, and just load >> the GTF file to Galaxy. >> Consider FTP for larger datasets: http://wiki.g2.bx.psu.edu/FTPUpload) >> >> More resources include the author supported help email at >> tophat.cufflinks(a)gmail.com and seqanswers.com (where the authors often >> post). >> >> Hopefully this helps, >> >> Jen >> Galaxy team >> >> >> On 7/19/12 1:38 PM, i b wrote: >>> >>> Hi, >>> I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group >>> one has two replicates (treated) and group two only one replicate >>> (untreated). >>> >>> When looking at the outputs the following are empty (1 line): >>> >>> TSS group FPKM tracking >>> TSS groups differential expression testing >>> CDS FPKM tracking >>> CDS FPKM differential expression testing >>> CDS overloading diffential expression testing >>> promoters differential expression testing >>> splicing differential expression testing >>> >>> the other four outputs have data downloadable as excel. >>> >>> Is this normal? >>> >>> thanks, >>> ib >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at 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/ >>> >> >> -- >> Jennifer Jackson >> http://galaxyproject.org -- Jennifer Jackson http://galaxyproject.org

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Galaxy July 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Jul '12

21 Jul '12

Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main Tool Shed/ * *EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * *Tool Shed* now also supports specifying the third party tool dependencies to be automatically installed in new repositories * *Admin Genome Indexing* is now in /BETA/. Download, index, and track progress right from the admin UI! * *Improved Error Handling* that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details. * *TopHat2/Bowtie2* latest support includes option to 'report discordant pairs', updated tests, and more preset options. * *Trackster* new parameter space visualization. /Includes BRAND NEW Features!!/ More details coming soon, but give a test drive now. *http://getgalaxy.org* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ec29ce8e27a1 *Thanks for using Galaxy!* We hope to see everyone in /Chicago/ @ *GCC2012*!! The Galaxy Team

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Cuffconfusion
by i b 21 Jul '12

21 Jul '12

ok, im really confused now about cufflinks and its tools. All I wanted was to look for differentially expressed genes between two samples: treated (2 replicates) and control (one replicate). can anyone give me a workflow for a similar analysis with the various options chosen? I have read a lot of different posts where for cuffdiff they have used cufflinks, cuffcompare, cuffmerge or any gtf file as imput together with the bam file. There must be a difference in using all these different file right??? Also: what is the advantage in using cuffcompare and how we compare them: we give all cufflinks or we separate control from treated? Why do we need cuffmerge?isn't it as well combining the cufflinks? when we use cuffcompare or cuffmerge do we mix all cufflinks no matter is they are control or treated ones? Please don't send me back to the cufflink page (http://cufflinks.cbcb.umd.edu/index.html)...I need more simpler words!!!!! Thanks, ib

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Problem setting up admin in Galaxy local instance!
by Di Nguyen 21 Jul '12

21 Jul '12

Dear all, Please help me figure out what went wrong to set up ADMIN in my local instance using the new retinaMBP! This is what I did 1. I changed universe_wsgi.ini.sample file into universe_wsgi.ini (using Mac TextEdit) 2. Then, I edited universe_wsgi.ini as followed: # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = *dknguyen(a)uw.edu* 3. I shutdown Galaxy, rerun sh run.sh, log back in Galaxy but still no Admin function. 4. The reason that I wanted to ad Admin function is to import my NGS files (bigger than 2Gb fer sure) into Galaxy database. Please give me some tips on this as well. Thank you very much, Di Nguyen, postdoc U of Washington, Seattle, WA

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cuffdiff failed
by i b 20 Jul '12

20 Jul '12

Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuffmerge (all 3 cufflinks) I run cuffdiff with the following options: cuffmerge + tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C. I had the following message: 0 bytes An error occurred running this job: cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.050000 -N -b /galaxy/data/hg19/sam_index/hg19.fa --labels + /galaxy/main_pool/pool4/files/004/645/dataset_4645857.dat /galaxy/main_pool/pool3/files/004/623/dataset_4623286.dat,/galaxy Where did I do wrong? What does it mean? Cheers, ib

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Attempting to use parallelism in BWA
by Kevin C. Dorff 20 Jul '12

20 Jul '12

Hi, I am using Python 2.7. I am running with an hg checked out, up to date version of "https://bitbucket.org/galaxy/galaxy-dist/". I am very new to Galaxy. I have an instance setup *and running* locally. I am able to perform routine actions such as uploading files, processing with Picard, and aligning with BWA. I have been able to make the jobs execute out our SGE cluster. In order to better utilize my cluster, I attempted to enable parallelism of the tasks that support it (such as BWA) by configuring the * universe_wsgi.ini* file with the parameter use_tasked_jobs = True When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I am given the error Result 256 from mv /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 25, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax The alignment failed. If you need the complete error message, contact me and I can supply you with it. It's too large to paste in-line and attachments aren't allowed. Is there more I need to do to enable parallel jobs (splitting of input, align, then merge)? Any suggestions are greatly appreciated. Kevin

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