Re: [galaxy-dev] divide fq into 2
On Tue, Mar 08, 2011 at 11:15:44PM -0500, Musa A. Hassan wrote: Yes I can't get the file into galaxy at all. Am uploading from a file path. the file is 35mb. When you say uploading from a filepath are you using the administrator-only functionality explained here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles _not_ the 'Get Data' - 'Upload File' selection from the 'Tools' menu? People work with files _much_ larger than that in Galaxy all the time. Musa From: Ry4an Brase [ry4an+gal...@msi.umn.edu] Sent: Tuesday, March 08, 2011 11:06 PM To: Musa A. Hassan Subject: Re: [galaxy-dev] divide fq into 2 On Tue, Mar 08, 2011 at 10:44:51PM -0500, Musa A. Hassan wrote: Hi Ry4an, I'd like to do this in galaxy, but the problem is it wont load into galaxy. As for using split, the file generated from this returns a length mismatch in say Tophat, maybe in the process of splitting the file some changes happen to the format. So you can't get the file into galaxy at all? Are you trying to upload it through your browser (suitable only for non-huge files) or are you using 'upload from file path'? How big (bytes) is the file. Also, you should try to keep your replies on the mailing list so that other searching in the future find the same help. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] setup.sh missing
Hi Curtis, setup.sh has been removed from the installation process, as discussed in this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004588.html On Wed, Mar 9, 2011 at 2:12 PM, Curt Palm cp...@stanford.edu wrote: I just cloned the current release version of galaxy: hg clone http://bitbucket.org/galaxy/galaxy-dist and can not run setup.sh because it is not present in the /galaxy-dist/ directory. setup.sh is also not listed on the https://bitbucket.org/galaxy/galaxy-dist/src page, is this an error or has the installation process changed? thanks *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] irc channel for galaxy
Hi George, Thanks to your suggestion and work by Nate Coraor, Galaxy now has an IRC channel: Server: irc.freenode.net Channel: #galaxyproject This is an informal online gathering place for the Galaxy community to post questions and help each other out. Note that while IRC is conducive to quick discussion, it doesn't work so well as an official support channel (and therefore IRC is not an official Galaxy support channel). If you have a question, bug, or feature suggestion that you want to make sure the Galaxy team knows about, please continue to send these to the mailing lists. Please reply to this thread if you have any questions, or you can post them on the IRC. Thanks, Dave C. On Mon, Mar 7, 2011 at 1:57 PM, George Marselis george.marse...@kaust.edu.sa wrote: Hey guys, Is there an irc channel for galaxy? I googled for galaxy irc but all I see in the first fifty results are entries for the samsung galaxy (which is an excellent phone ;) Best Regards, George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a ___ 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/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] galaxy-cloud display data in browser broken
Uploaded data from Biomart and the data is displayed correctly in the middle pane. I deleted all datasets in the history except the first one (a fastq file), and it now displays correctly too! I upload a fasta file: it does not display. Could this be a bug with fasta data? Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 -Original Message- From: Isabelle Phan Sent: Wednesday, March 09, 2011 6:21 PM To: 'galaxy-dev@lists.bx.psu.edu' Cc: Andy Leonard; Gowthaman Ramasamy Subject: galaxy-cloud display data in browser broken Hello, Running galaxy-cloud latest release on amazon EC2, configuration out of the box except for: host = 0.0.0.0 I can upload data, run tools, but when I click on the 'eye' icon to view the data , the middle panel is empty (accessing galaxy cloud from Firefox and Chrome on CentOS linux). I tried creating a simple fasta file. It shows fine on the right panel, but won't display in the middle panel. View parameters displays correctly. Only the actual data is not displayed. The log shows no error: 146.129.249.238 - - [10/Mar/2011:02:19:52 +] GET /datasets/5969b1f7201f12ae/display/?preview=True HTTP/1.1 200 - http://ec2- xx.compute-1.amazonaws.com:8080/history?show_deleted=False Mozilla/5.0 (X11; Linux i686 (x86_64)) AppleWebKit/534.24 (KHTML, like Gecko) Chrome/11.0.697.0 Safari/534.24 Our local instance of Galaxy does not have this issue, only the cloud instance. Since this is a total blocker, any hint is *very* gratefully received, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Enabling iterative test-driven development of tools
Hello, The current tool testing options provided by Galaxy are excellent for verifying that Galaxy is functioning properly and that tools provide reproducible results. However, I believe there are two related shortcomings to the current Galaxy approach, and I would like to propose a solution for these shortcomings. The first is that the workflow for the tool developer is very clunky, especially if the developer is building up a tool incrementally with a test-driven development (TDD) approach. For each parameter addition a whole new output file must be created externally, manually verified by the developer, possibly converted to a regular expression, and placed in the test data directory. Put another way, it is easy to iteratively build up a tool, but not to iteratively build a test case. The second point is a bit pedantic. The current approach only verifies that the output is the same as the supplied output, not that the output is actually correct. The typical workflow I described above relies on manual inspection of the expected output file to verify it is correct. I believe it is better to programmatically state assertions about what makes an output correct than to rely on manual verification, this serves both to reduce human error and act as documentation about what makes an output correct. To address these two points, I propose an extensible addition to the Galaxy tool syntax (and provide an implementation) to declaratively make assertions about output files. The syntax change is to the output child element of test elements. With this change, the output element may have a child element named assert_contents, which in turn may have any number of child elements each of which describes an assertion about the contents of the referenced output file. The file attribute on the output element is still required if an assert_contents element is not found, but it is optional if an assert_contents element is found. The whole file check described by the file attribute will be executed in addition to the listed assertions if both are present. As an example, the following fragment assserts that an output file contains the text 'chr7', does not contain the text 'chr8', and has a line matching the regular expression '.*\s+127489808\s+127494553'. test param name=input value=maf_stats_interval_in.dat / output name=out_file1 assert_contents has_text text=chr7 / not_has_text text=chr8 / has_line_matching expression=.*\s+127489808\s+127494553 / /assert_contents /output /test Each potential child element of assert_contents corresponds to a simple python function. These functions are broken out into modules which are dynamically (mostly) loaded at test time. The extensibility of this approach comes from how trivial it is to add new assertion functions to a module and whole new modules of such functions. I have started work on three modules of assertion functions, these are for text, tabular, and XML output files respectively. has_text, not_has_text, and has_line_matching above are examples of three such assertion functions from the text module. To see how it works, here is a function from the file test/base/asserts/text.py defining the has_line_matching element: def assert_has_line_matching(output, expression): Asserts the specified output contains a line matching the regular expression specified by the argument expression. match = re.search(^%s$ % expression, output, flags = re.MULTILINE) assert match != None, No line matching expression '%s' was found in output file. % expression As demonstrated, the function name corresponding to the element element_name is just assert_element_name. The code that calls these assertion functions, automatically matches XML attributes with function arguments by names, and matches an argument named output with a string containing the contents of the output file resulting from the test run. Matching function arguments this way gracefully allows for multiple arguments and optional arguments. There is additional information about the implementation at the end of this e-mail. This approach should really aide iterative development of tools. Each new parameter you add to a tool is going to change the output in some way, hopefully you will be able to describe how it affects the output as an assertion. As you add new parameters, the previous parameters will hopefully affect the output in the same way and the old assertion will not need to change, you will just need to add new ones. Obviously this won't always be the case, but hopefully changes to previous assertions will be minimal over time. I believe this process will be faster over time than repeatedly producing output files or interactive GUI based testing, and the final product will be a richer test case. I have attached two patches. The first patch (implementation.patch) is the patch that I propose merging into galaxy-central. It modifies the tool parser to parse these new elements,
