- galaxy-user - lists.galaxyproject.org

Finding SNP differences between datasets
by Nicola Nadeau 09 Jul '10

09 Jul '10

Hi, I am trying to find SNPs and/or indel variants that differ between two groups of samples. The data are 454 sequence capture results spanning a region of interest for a non-model organism without a complete genome. I have mapped these to my reference sequence of the region and generated BAM and pileup files for them. Does anyone know of a tool or method (either in galaxy or elsewhere) that will allow me to compare datasets and pick out variation between them (as opposed to things that differ from the reference sequence). Many thanks, Nicola

2 1

Is it possible to run processes in parallel?
by Alex Quezada 08 Jul '10

08 Jul '10

Hi, our metagenomics group is experimenting with spliting up assemblies into several chunks, and then combining the outputs. Is it possible to model in Galaxy a process that splits up, and then converges again after all the branches have finished? ************************************************ Alex Quezada Software Developer Genome Science/Joint Genome Institute (B-6) Bioscience Division MS M888 Los Alamos National Laboratory Los Alamos, NM 87545 phone: (505) 606-2153 fax: (505) 665-3024 email: alexq(a)lanl.gov ************************************************

2 1

how to make my data available to a collaborator
by Michael Yourshaw 08 Jul '10

08 Jul '10

I have uploaded some bam files to the public galaxy. I am working with a collaborator who has a Galaxy account. Both of us are new, inexperienced users. How can I give my collaborator access to my data? ॐ Michael Yourshaw UCLA Geffen School of Medicine Department of Human Genetics, Nelson Lab 695 Charles E Young Drive S Gonda 5554 Los Angeles CA 90095-8348 USA myourshaw(a)ucla.edu 970.691.8299 This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.

2 1

asking about allignment figure
by Chandra Trihadi 08 Jul '10

08 Jul '10

Hello, I am sorry, I did not know about the appropriate address ( galaxy-user(a)bx.psu.edu) for asking. I tried to map with Bowtie for my illumina single-read data using the reference genome that I uploaded to the history panel, then filter SAM, then did SAM-to-BAM. However, the final result did not display the allignment figure like on the instruction video. Would you mind to tell me how to obtain the allignment figure or to assembly my illumina data based on my reference genome? Thank you. -Chandra- Quoting Kelly Vincent <kpvincent(a)bx.psu.edu>: [Show Quoted Text - 48 lines][Hide Quoted Text] Hi, Sorry for the delay in response. In the future, please do send queries like this to galaxy-user(a)bx.psu.edu<https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#>instead of galaxy-bugs, since it is about using Galaxy rather than a specific bug in the software. One issue with our screencasts is that Galaxy changes rapidly so they can become slightly out of date. In this case, for Illumina data, there is a tool called "FASTQ Summary Statistics" under Illumina Data under NGS: QC and manipulation. This is like the "Compute quality statistics" tool under AB-SOLiD Data. Then, to draw the boxplot, go to the Graph/Display Data section (not under NGS Toolbox) and choose the "Boxplot of quality statistics" tool. Regarding the results of your Bowtie mapping, could you give more details about what was different from what you were expecting? Did you make sure that you mapped against the correct genome? Regards, Kelly On Jul 1, 2010, at 5:06 PM, Yohanna Gita Chandra wrote: Hello Galaxy Team, I am sorry for asking the same questions for the third time since I haven't gotten any respons from galaxy team about these problem. Could you at least tell me why you do not answer my questions yet? Should I call you? --------------------------------------------------------------------------- I have illumina sequencing data (single reads), and I am trying to analyze it. I listened to the video tutorial on Galaxy about mapping illumina reads (single end read), and tried to analyze my data based on the tutorial. However, I found instructions that I could not find on the Galaxy window. - In the tutorial, after uploading the data, I should "compute quality statistic". The "compute quality statistic" is supposed to be under "GENERIC FASTQ DATA". However, I found it under "AB Solid Data". Since my data is Illumina sequencing data, I could not simply do it. - In the tutorial, if I am done with "compute quality statistic", I have to do "draw quality score boxplot" that is supposed to be under "GENERIC FASTQ DATA". However, it is also under "AB Solid Data". - Then, after uploading my Illumina data, I did FASTQ Groomer, and did mapping with Bowtie for Illumina, but the result was not like the example on the instruction video. Would you mind to tell me what I should do? Thank you very much in advance. -------------------------------------------------------------------------------- Yohanna Gita Chandra University of Arkansas Fayetteville, AR 72701 Email: ytrihadi(a)uark.edu<https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#>& chandratrihadi2(a)yahoo.com<https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#> _______________________________________________ galaxy-bugs mailing list galaxy-bugs(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-bugs

2 1

Indexing Rat genome - Baylor 3.4/rn4 query
by Clokie, Samuel (NIH/NICHD) [F] 07 Jul '10

07 Jul '10

Hi there, I recently started using your amazing NGS tools. They are really amazing! An helping me out enormously. I have some single read rat illumina data and would like to map it to the rat genome. However I see that it isn't yet indexed on the "Map with Bowtie for Illumina" page. I wonder if you have plans in the future to index the rat genome? Many thanks, Sam ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Samuel Clokie, PhD Visiting Fellow PDEGEN/NICHD National Institutes of Health 6A83, building 49 Bethesda Maryland 20892 USA Phone - 301-451-6623 Mobile - 301-760-0454 Fax - 301-480-3526

1 0

Re: [galaxy-user] [galaxy-bugs] asking for the third times
by Yohanna Gita Chandra 06 Jul '10

06 Jul '10

Hello, I am sorry, I did not know about the appropriate address (galaxy-user(a)bx.psu.edu) for asking. I tried to map with Bowtie for my illumina single-read data using the reference genome that I uploaded to the history panel, then filter SAM, then did SAM-to-BAM. However, the final result did not display the allignment figure like on the instruction video. Would you mind to tell me how to obtain the allignment figure or to assembly my illumina data based on my reference genome? Thank you. -Chandra- Quoting Kelly Vincent <kpvincent(a)bx.psu.edu>: > Hi, > > Sorry for the delay in response. In the future, please do send > queries like this to galaxy-user(a)bx.psu.edu instead of galaxy-bugs, > since it is about using Galaxy rather than a specific bug in the > software. > > One issue with our screencasts is that Galaxy changes rapidly so > they can become slightly out of date. In this case, for Illumina > data, there is a tool called "FASTQ Summary Statistics" under > Illumina Data under NGS: QC and manipulation. This is like the > "Compute quality statistics" tool under AB-SOLiD Data. Then, to draw > the boxplot, go to the Graph/Display Data section (not under NGS > Toolbox) and choose the "Boxplot of quality statistics" tool. > > Regarding the results of your Bowtie mapping, could you give more > details about what was different from what you were expecting? Did > you make sure that you mapped against the correct genome? > > Regards, > Kelly > > > On Jul 1, 2010, at 5:06 PM, Yohanna Gita Chandra wrote: > >> >> Hello Galaxy Team, >> >> I am sorry for asking the same questions for the third time since I >> haven't gotten any respons from galaxy team about these problem. >> Could you at least tell me why you do not answer my questions yet? >> Should I call you? >> >> --------------------------------------------------------------------------- >> >> I have illumina sequencing data (single reads), and I am trying to >> analyze it. >> >> I listened to the video tutorial on Galaxy about mapping illumina >> reads (single end read), and tried to analyze my data based on the >> tutorial. However, I found instructions that I could not find on >> the Galaxy window. >> >> - In the tutorial, after uploading the data, I should "compute >> quality statistic". The "compute quality statistic" is supposed to >> be under "GENERIC FASTQ DATA". However, I found it under "AB Solid >> Data". Since my data is Illumina sequencing data, I could not >> simply do it. >> >> - In the tutorial, if I am done with "compute quality statistic", I >> have to do "draw quality score boxplot" that is supposed to be >> under "GENERIC FASTQ DATA". However, it is also under "AB Solid >> Data". >> >> - Then, after uploading my Illumina data, I did FASTQ Groomer, and >> did mapping with Bowtie for Illumina, but the result was not like >> the example on the instruction video. >> >> Would you mind to tell me what I should do? >> >> Thank you very much in advance. >> -------------------------------------------------------------------------------- >> Yohanna Gita Chandra >> University of Arkansas >> Fayetteville, AR 72701 >> Email: ytrihadi(a)uark.edu & chandratrihadi2(a)yahoo.com >> >> _______________________________________________ >> galaxy-bugs mailing list >> galaxy-bugs(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-bugs > >

1 0

Data Libraries Problems
by juan perin 02 Jul '10

02 Jul '10

In my latest pull from the galaxy update server, something has caused my instance to act up. I'm getting an error when trying to upload data into libraries. This is the text based error: URL: http://variome.chop.edu:8082/library_common/upload_library_dataset File '/home/perin/galaxy_dist2/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy_dist2/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/perin/galaxy_dist2/lib/galaxy/web/controllers/library_common.py', line 978 in upload_library_dataset **kwd ) File '/home/perin/galaxy_dist2/lib/galaxy/web/controllers/library_common.py', line 1158 in upload_dataset message=util.sanitize_text( message ), File '/home/perin/galaxy_dist2/lib/galaxy/util/__init__.py', line 138 in sanitize_text for c in text: TypeError: 'NoneType' object is not iterable Strangely, the data gets queued up anyway, if you go back to the library, and you can even see the first few lines of the file in the preview, but it remains queued and never fully becomes available. Not sure what's going on, so was hoping for any suggestions. I just updated to Postgresql as well, but that didn't change the problem. Thanks. Juan

2 1

New Galaxy Community tool sharing site now available
by Greg Von Kuster 02 Jul '10

02 Jul '10

Hello Galaxy community, We have introduced a new Galaxy tool sharing community site at http://usegalaxy.org/community. The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools. We hope that you will find this site useful for hosting tools that you would like to contribute and share. We'll keep you informed as the site's features evolve. Here is the current information about uploading and downloading tools from the site. Uploading Tools Tool File Format A tool file is a tar-format (bzipped or gzipped tar are valid) archive containing all the files necessary to load the tool in Galaxy. At the very least, it must contain a Tool XML File, and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic instructions below, please include a README file which details these steps. If the tool (or parts of it) are written in C, the source code can be included (or put links to the source in the README). Please do not include precompiled binaries without source, since Galaxy is run on a wide variety of platforms. Also, if you are only wrapping or providing a Galaxy config for a tool that is not your own, please be sure the license allows for redistribution before including any part of that tool in the tar archive! There are no requirements about the directory structure inside the tar archive, but for ease of use, it's generally a good idea to put everything inside of a subdirectory, instead of directly at the top level. Tool File Example To package up the LASTZ tool's config file, Galaxy wrapper, and the C source: user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz lastz/ lastz/README lastz/lastz_wrapper.py lastz/lastz_wrapper.xml lastz/lastz-distrib-1.02.00/ lastz/lastz-distrib-1.02.00/src/ lastz/lastz-distrib-1.02.00/src/Makefile lastz/lastz-distrib-1.02.00/src/version.mak lastz/lastz-distrib-1.02.00/src/lastz.c lastz/lastz-distrib-1.02.00/src/lastz.h ... ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. Editing Information, Categories, and Submitting For Approval Simply uploading a tool to the Community will not allow other users to find and download your tool. It will need to be approved by an administrator before it appears in the tool list. After the tool has successfully uploaded, you will be redirected to the Edit Tool page. Please provide a detailed description of what the tool does - this will be used by administrators to understand the tool before approving it for display on the site. Once approved, this information will be displayed to users who view your tool. In addition, the site administrators will have configured a number of categories with which you can associate your tool to make it easily findable by users looking to solve specific problems. Please associate as many categories as are relevant to your tool. You may change the description and associated categories as often as you'd like until you click the "Submit for approval" button. Once submitted, the tool will be approved or rejected by an administrator. Once approved, it will be visible to everyone. At that point, the description and associated categories can only be changed by an administrator. Once the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, clicking the context menu to the right of the tool's name, and selecting "Upload a new version." Downloading and Installing Tools A tool's download link will send you the tool tar archive. Once downloaded, unpack the tool on your local Galaxy instance's server: user@host:~% tar xvf galaxy_tool.tar ... user@host:~% tar zxvf galaxy_tool.tar.gz ... user@host:~% tar jxvf galaxy_tool.tar.bz2 ... If the tar archive includes a README file, consult it for installation instructions. If not, follow these basic steps: Create a directory under galaxy_dist/tools/ to house downloaded tool(s). In the new directory, place the XML and any script file(s) which were contained in the tar archive. If the tool includes binaries, you'll need to copy them to a directory on your $PATH. If the tool depends on C binaries but does not come with them (only source), you'll need to compile the source first. Add the tool to galaxy_dist/tool_conf.xml. Restart the Galaxy server process. We plan to implement a more direct method to install tools via the Galaxy administrator user interface instead of placing files on the filesystem and managing the tool_conf.xml file by hand. In the meantime, this is the process. Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

1 0

New 5' start site, 3' end site and long internal coding exons
by Yanwei Tan 29 Jun '10

29 Jun '10

Deal all, I was wondering if anyone know Galaxy can analyze the New 5' start site, 3' end site and long internal coding exons. Because I just try to run Scripture (http://www.broadinstitute.org/software/scripture/Graph%20building) and got the bed file. Can someone give me some hint? Many thanks in advance! Wei

2 3

hesus RheMac2 genome
by Lakshmanan Iyer 28 Jun '10

28 Jun '10

Hi In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque genome. The web site says: "If your genome of interest is not listed, contact the Galaxy team" Could you please make this reference genome available? Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly -best -Lax

1 0