- galaxy-user - lists.galaxyproject.org

Adding new tools in Galaxy
by Makis Ladoukakis 06 Oct '11

06 Oct '11

Dear Galaxy developers, Currently I am adding new tools to my galaxy instance as scripts written in Perl language. I was wandering if there is a way to add tools either as .bin or .exe format or if only scripts are supported. I couldn't find anything about it in the wiki or in the FAQ. Thank you, Makis Ladoukakis

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Re: [galaxy-user] How to count reads in 200bp windows and save the output per chromosome?
by Jennifer Jackson 06 Oct '11

06 Oct '11

Hello Di, Yes, the 200 bp windows should be for the reference genome, apologies if that was not clear. The idea is to create a simple text file of the chrom-start-stop (one line per chromosome), upload, convert to BED, then create windows. Or better and less manually, you can extract the "chromInfo" table from the UCSC Table Browser (since you are using mm9, sourced from UCSC), do a few text edits to format, and use that as the BED file to create windows. Once you have the 200 bp windows as the "target ranges" for the regional variation tool, compare your "query alignments" (BAM/SAM->Interval dataset) to get coverage. Group per window, per chrom, or however you wish with the tools I mentioned. If using "Group", the other data points are the numbers that can be graphed or manipulated. But that is just one suggestions, once you have the data in the right format (tabular), trying out different tools should be quick to do and tune/evaluate. Good luck with the project, Jen Galaxy team On 10/5/11 3:19 PM, Di Nguyen wrote: > Hi Jen, > > Why is that when I made 200bp windows using "gro-seq.bed" file (my data > file), it came up empty? Did I think about this the wrong way, my 200bp > window supposes to be my reference genome, in this case mm9? > > Secondly, when using regional variation, can I use a reference genome > such as mouse, and how do I created interval file for mm9, for example? > > Thank you, > > Di -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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How to count reads in 200bp windows and save the output per chromosome?
by Di Nguyen 05 Oct '11

05 Oct '11

Hi all, I recently have some Gro-seq data. What I want to do is this: 1. Workflow Counting how many reads per 200bp windows per chromosome. For this, my work flow is as followed: fasq -> fasq groomer -> bowtie -> BAM to SAM -> interval BED -> 200 bp windows regional variation -> feature 2. Questions: how do I sort and save per chromosome? For example, I would like to compare X chromosome versus autosomes or X versus chromosome 1? Please accept my appreciation, Di Nguyen, U of Washington, WA

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data libraries
by Hilary Morrison 05 Oct '11

05 Oct '11

How does one get admin privileges to make datasets available to multiple users? Or is that only available for local installations? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hilary G. Morrison, Ph.D. Senior Research Scientist Josephine Bay Paul Center Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 508-289-7339 508-457-4727 (fax) morrison(a)mbl.edu https://jbpc.mbl.edu/labs-morrison.html

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Galaxy-Condor Permission Denied
by Oren Livne 05 Oct '11

05 Oct '11

Dear All, I am using Galaxy with condor as the scheduler via the DRMAA Job Runner. on Debian 6. Jobs are submitted to COndor but they are held because of permissions: condor@vm-debian:~$ condor_q -analyze 10.0 -- Submitter: vm-debian.uchad.uchospitals.edu : <165.68.219.43:40312> : vm-debian.uchad.uchospitals.edu --- 010.000: Request is held. Hold reason: Error from vm-debian.uchad.uchospitals.edu: Failed to open '/home/galaxy/galaxy-dist/database/pbs/19.o' as standard output: Permission denied (errno 13) condor@vm-debian:~$ ls -l /home/galaxy/galaxy-dist/database/pbs/19.o -rw-r--r-- 1 galaxy galaxy 0 Oct 4 16:40 /home/galaxy/galaxy-dist/database/pbs/19.o I am running galaxy as the galaxy user. I also have a condor user. How to ensure that jobs are submitted as the proper user? Thanks so much, Oren

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Re: [galaxy-user] [galaxy-bugs] loading data
by Peng, Tao 05 Oct '11

05 Oct '11

Hi Jen, I have RNA-seq data for 2 biologial samples loaded in to galaxy. The samples are from human skin biopsies from genital herpes reactivation. Using Tophat I will align the reads to human genome. But I am NOT how to build genital herpes genome (HSV-2) and aligh reads to HSV-2 genome? Any suggestion is greatly appreciated! Thanks, tao -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 12, 2011 11:54 AM To: Peng, Tao; galaxy-bugs(a)bx.psu.edu Subject: Re: [galaxy-bugs] loading data Hello, Glad to hear that you were able to load your data. When logged in, FTP loaded data will initially be in the FTP upload area under the "Get Data -> Upload" tool (in the center pane). From here, load data into the history that you wish to work with. If you are not sure where this is exactly, please note the graphics in the FTP wiki and screencast. As a reminder, please send all new and followup questions with a to or cc to the mailing list, not to individual team members. This is important for our team to be able to track and answer questions. We would appreciate your helping out with this going forward. Hopefully this helps. Jen Galaxy team On 8/12/11 11:39 AM, Peng, Tao wrote: > Hi jen, I just finished FTP of R4 data set with 8.4 GB. Why can't I see > the data on the right panel of galaxy after loggin in? > > Tao > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Tuesday, August 09, 2011 3:26 PM > To: Peng, Tao > Cc: galaxy-bugs(a)bx.psu.edu > Subject: Re: [galaxy-bugs] loading data > > Hello Tao, > > It sounds like the load works with an uncompressed file but is failing > when compressed? Perhaps there is a problem with the compression itself. > > We can't really help with this part of the process except to note which > compression types we accept. The help wiki link again is: > http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP > > The final goal would be to have all of the data compressed and then load > > using FTP in a batch. If this takes too long to run, then the next > option is to run either a local or cloud install. Help can be found at: > http://getgalaxy.org > http://galaxyproject.org/Admin/Cloud > > Please send all questions related to local or cloud installations to the > > galaxy-dev(a)bx.psu.edu mailing list and not to individual team members or > > to the galaxy-bugs(a)bs.psu.edu mailing list. > > Best wishes for your project, > > Jen > Galaxy team > > On 8/9/11 2:25 PM, Peng, Tao wrote: >> If I up-load one file (uncompressed) at one time, I will have 4x8=32 >> files to up-load. Each file takes about 1 hour to load. This is >> untenable. Any suggestion? >> >> Thanks, >> >> >> tao >> >> -----Original Message----- >> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >> Sent: Tuesday, August 09, 2011 2:04 PM >> To: Peng, Tao; galaxy-bugs(a)bx.psu.edu >> Subject: Re: [galaxy-bugs] loading data >> >> >> >> On 8/9/11 1:55 PM, Peng, Tao wrote: >>> Hi Jen, if I have 8 fastq.gz files for each of my 4 samples, how >> should >>> I load the data for analysis in galaxy? >>> >>> Thanks, >>> >>> tao >>> >>> -----Original Message----- >>> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >>> Sent: Tuesday, August 09, 2011 1:31 PM >>> To: Peng, Tao >>> Cc: galaxy-bugs(a)bx.psu.edu >>> Subject: Re: [galaxy-bugs] loading data >>> >>> Hello Tao, >>> >>> For your other question sent to me directly, Galaxy will accept only >> one >>> >>> file per archive, so sending a multi-file .gz will result in only the >>> first file in the archive loaded into the "Get Data -> Upload" FTP >> area. >>> >>> Given the current issues, please try a restart. Log out of Galaxy and >>> FileZilla (and restart your computer if possible). Then begin again, >>> testing with a single, uncompressed file. You do not have to be > logged >>> into your Galaxy account to load with FileZilla, but you will need to >> be >>> >>> logged in to access the files on the "Get Data -> Upload" form > after >>> upload is complete. >>> >>> If this fails, perhaps try reinstalling FileZilla or even a different >>> FTP client. This tutorial covers an alternative that can also be used >>> from the desktop: >>> http://galaxyproject.org/Learn/Upload via FTP >>> >>> If you do have more questions, please leave galaxy-bugs(a)bx.psu.edu on >>> the cc list so that our entire team can help contribute to replies. >> This >>> >>> may also be a question that you want to ask the larger user community >> at >>> >>> galaxy-user(a)bx.psu.edu, as this sounds like an external issue. > Another >>> user may have encountered this problem using a PC and have >> suggestions. >>> >>> Thanks! >>> >>> Jen >>> Galaxy team >>> >>> On 8/9/11 1:16 PM, Peng, Tao wrote: >>>> Hi jen, I attached a screen shot of FileZilla. Do you know why the >> top >>>> panel says "disconnected from server" while the bottom panel >> indicates >>>> it is transferring the data? >>>> >>>> Thanks, >>>> >>>> >>>> tao >>>> >>>> -----Original Message----- >>>> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >>>> Sent: Monday, August 08, 2011 4:55 PM >>>> To: Peng, Tao >>>> Cc: galaxy-bugs(a)bx.psu.edu >>>> Subject: Re: [galaxy-bugs] loading data >>>> >>>> Hello Tao, >>>> >>>> The loading times do seem to be long for the size of the files, >>> perhaps >>>> the internet connection is the problem. That said, FileZilla can >>> restart >>>> >>>> an FTP if it is interrupted and a message would be reported. I > didn't >>>> see any restarts reported in the log in the screenshot you sent. >>>> >>>> The compression is another place to look for a problem. You might > try >>> to >>>> >>>> use an alternate compression or no compression and load that way. > Try >>>> one file, through FileZilla, as a test to see if that performs >> better. >>>> Winzip can compress in a few different formats, .bz2 is also > accepted >>> by >>>> >>>> Galaxy. >>>> >>>> Hopefully one of these will work. Please keep galaxy-bugs in the cc >>> for >>>> any follow-up so that our team can help contribute to replies, >>>> >>>> Thanks, >>>> >>>> Jen >>>> >>>> On 8/8/11 4:04 PM, Peng, Tao wrote: >>>>> Hi jen, when I FTP 9 of the fasq.gz files (each about 350 MB) for >>>>> sample, the FTP program (FileZilla) keep coping the files again and >>>>> again, this is strange to me. Do you know what went wrong here. >>>>> >>>>> I attached a powerpoint slide that is the screen shot of FileZila >>>>> (R1_002.fasq.gz has been copied 3x so far??) >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> tao >>>>> >>>>> -----Original Message----- >>>>> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >>>>> Sent: Friday, July 29, 2011 1:20 PM >>>>> To: Peng, Tao >>>>> Cc: galaxy-bugs(a)bx.psu.edu >>>>> Subject: Re: [galaxy-bugs] loading data >>>>> >>>>> Hello Tao, >>>>> >>>>> Our apologies, the public Galaxy instance at http://usegalaxy.org >> has >>>>> been experiencing higher than usual usage the last few days. This >>>> should >>>>> >>>>> now be improved. Please try your FTP load again - it is the best > way >>>> to >>>>> load files and the sizes you mention are well within the accepted >>>>> limits. >>>>> >>>>> Thank you for your patience, >>>>> >>>>> Best, >>>>> >>>>> Jen >>>>> Galaxy team >>>>> >>>>> >>>>> On 7/29/11 9:47 AM, Peng, Tao wrote: >>>>>> Hi I work at FHCRC in Seattle. I am trying to load the FASQ data >>> from >>>>>> Illumina HySeq. I have 4 samples with 2.4 GB of seq data per >> sample. >>>>> For >>>>>> the overnight FTP, I can't even finish loading half of one sample. >>> Is >>>>>> there any faster way to load the data? Can GALAXY do the analysis >>> for >>>>>> this type of large data? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> tao >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Does Cuffdiff support multiple groups analysis
by An, Hongyan 05 Oct '11

05 Oct '11

I have 3 groups of accepted hits, each group has 3 replicates. When I add 3 groups with corresponding replicates, the cuffdiff output only gave 2 groups comparison of differential expression, Please help me here ------ Hongyan An, Ph.D. Research Associate Genomics Core of Yale Stem Cell Center Yale University School of Medicine 10 Amistad Street Room 203 New Haven, CT 06520 phone: (203)-737-6203 Fax: (203) 785-4305 hongyan.an(a)yale.edu<mailto:hongyan.an@yale.edu>

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1000 genome variant calls
by Jennifer Jackson 05 Oct '11

05 Oct '11

Repost -------- Original Message, Please send all replies to "all" -------- Hello Jennifer, I am a new to Linux and have no programming skills and hence galaxy is the only rescuer for me. I have nextgen dna seq data. I finished analysis and now have a list of variants. I want to see if these variants are already in 1000 genome data released in Aug 2011. I want to upload list of my chromosome locations and see if they are any matches with 1000 genome data. IS there a way we can do it in galaxy...instead of writing scripts to do it. Like I said, I have no programming skills. Thanks.

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aligning long reads
by Shalabh Sharma 05 Oct '11

05 Oct '11

Hi, I am new to mapping. I have reads ranging from 150-300bp, i am not sure which is the best suitable program for that in Galaxy. I already tried bwa but i am not sure if thats the best choice for long reads. Thanks Shalabh

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Macs
by Keith Giles 05 Oct '11

05 Oct '11

To add to my post, I reread the macs documentation and it seems that the fdr is calculated based on the p value of negative peaks, regardless of their location. That is to say, a strong peak on one chromosome could be associated with a high fdr bc of an even stronger negative peak, anywhere in the genome. So, is the fdr then the percent of negative peaks relative to total peaks (pos + neg) at or below a certain p value ? Sent from my iPhone

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