- galaxy-user - lists.galaxyproject.org

All I want is a question answered please!
by Jennifer Jackson 26 Jul '12

26 Jul '12

Hi Crystal, The galaxy-user(a)galaxy.bx.psu.edu mailing list would be the best for this question. All lists are described here: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists http://wiki.g2.bx.psu.edu/Mailing%20Lists Grey jobs are scheduled to run the and aere in the queue. While they are waiting to run, it is important to not start and restart, as this effectively movest them to the end of the line@ Hopefully this helps, Jen Galaxy team On 7/26/12 8:57 AM, Crystal Marconett wrote: > Hello, > > I am trying desperately to get an answer to a question. I've been over the help area for an hour trying to find an email address to ask questions to, and the only one is the tophat people's email... which is not helpful, because the problem is starting the tool in Galaxy, not getting TopHat errors yet because the job is simply stuck on grey (waiting......) > > The question: > I am trying to start running tophat on my history in the Galaxy main wed interface. I started the job last night at 10pm. It's now 9am. The job is still "waiting to run", ie. grey. How long does it take the Tophat web interface to start? is there a data limit that above which Tophat can no longer run? I don't think this is right, I've run TopHat before on Galaxy with the Illumina whole body tissue data and it took a while, but not this long.... > > My username is: cmarcone(a)usc.edu > the History's name is: Per-RNAseq > The job is : #32, 33, 34, 35 (all grey Tophat for Illumina). > The history has 65.7GB in it, and says it is using 21% (I assume the amount of allocated space left on the server). > > Please help! And if this is not the right e-mail address can you forward this along to the correct one, please!!! or at least let me know the correct email to mail this too. > Thanks! > C -- Jennifer Jackson http://galaxyproject.org

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CloudMan - Can't start nodes
by mailing list 25 Jul '12

25 Jul '12

Hi guys, I created a new Galaxy instance (probably around early July) with the web launcher (https://biocloudcentral.herokuapp.com/launch) I've been coming back and re-using it since then. However for the past week at least I haven't been able to launch new nodes. They show up as red on the indicators, and below I've pasted the error messages. (Could this be related to a new version of cloudman being released?) Thanks, Greg This is the cluster status log from my last attempt: 15:55:02 - Retrieved file 'persistent_data.yaml' from bucket 'cm-[redacted]' to 'pd.yaml'. 15:55:02 - Master starting 15:55:05 - Completed initial cluster configuration. 15:55:25 - Prerequisites OK; starting service 'SGE' 15:55:37 - Configuring SGE... 15:55:37 - Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '1' and following stderr: '' 15:55:57 - Saved file 'persistent_data.yaml' to bucket 'cm-[redacted]' 15:55:57 - Trouble comparing local (/mnt/cm/post_start_script) and remote (post_start_script) file modified times: [Errno 2] No such file or directory: '/mnt/cm/post_start_script' 15:55:58 - Adding 2 instance(s)... 15:57:32 - Instance 'i-56ba942e' reported alive 15:57:33 - Successfully generated root user's public key. 15:57:33 - Sent master public key to worker instance 'i-56ba942e'. 15:57:47 - Adding instance 'i-56ba942e' as SGE administrative host. 15:57:47 - Process encountered problems adding instance 'i-56ba942e' as administrative host. Process returned code 2 15:57:47 - Adding instance 'i-56ba942e' to SGE execution host list. 15:57:47 - Process encountered problems adding instance 'i-56ba942e' as execution host. Process returned code 2 15:57:47 - Problems updating @allhosts aimed at adding 'i-56ba942e', running command 'export SGE_ROOT=/opt/sge;. $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -Mhgrp /tmp/ah_add_15_57_47' returned code '2' and following stderr: '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' 15:57:47 - Waiting on worker instance 'i-56ba942e' to configure itself... 15:57:47 - Instance 'i-54ba942c' reported alive 15:57:47 - Sent master public key to worker instance 'i-54ba942c'. 15:58:01 - Adding instance 'i-54ba942c' as SGE administrative host. 15:58:01 - Process encountered problems adding instance 'i-54ba942c' as administrative host. Process returned code 2 15:58:01 - Adding instance 'i-54ba942c' to SGE execution host list. 15:58:01 - Process encountered problems adding instance 'i-54ba942c' as execution host. Process returned code 2 15:58:01 - Problems updating @allhosts aimed at adding 'i-54ba942c', running command 'export SGE_ROOT=/opt/sge;. $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -Mhgrp /tmp/ah_add_15_58_01' returned code '2' and following stderr: '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' 15:58:01 - Waiting on worker instance 'i-54ba942c' to configure itself...

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Re: [galaxy-user] "Jobs is waiting to run" all day on Main
by Lu, Mengmeng 24 Jul '12

24 Jul '12

Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng ----- Original Message ----- From: "Mengmeng Lu" <mira0501(a)neo.tamu.edu> To: "Lee Silver" <lsilver(a)genepeeks.com> Sent: Sunday, July 22, 2012 2:45:52 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng ----- Original Message ----- From: "Lee Silver" <lsilver(a)genepeeks.com> To: galaxy-user(a)bx.psu.edu Cc: "Lee Silver" <lsilver(a)genepeeks.com> Sent: Saturday, July 21, 2012 5:20:19 PM Subject: [galaxy-user] "Jobs is waiting to run" all day on Main 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) ___________________________________________________________ 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/

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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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