galaxy-dev July 2010

galaxy-dev@lists.galaxyproject.org

48 participants
66 discussions

Re: [galaxy-dev] Fwd: Enabling User Pages
by Jeremy Goecks 07 Jul '10

07 Jul '10

> Huh. I've updated to the latest galaxy-central, added enable_pages = > True to my universe_wsgi.ini (didn't see a sample in either this file > or the .sample) and restarted Galaxy. I can see the parameter check > in the base_panels template and can access the page list and editor by > manually using the URL, but the link isn't showing up for me under the > User menu. > > Did I miss something? That's weird. The Pages link works fine on my local instance, on our Test server, and on our main server. Are you using remote_user or other upstream config? This could be causing some trouble. The new universe_wsgi.ini.sample does seem to be missing documentation for enable_pages - I'll add it momentarily. Thanks, J.

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SNP effect prediction
by Pablo Cingolani 06 Jul '10

06 Jul '10

I had to predict the effect of a few thousand SNP that we found in our re-sequencing project. I tried using ENSEMBL's tool (http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations), but it was kind of painful (it only admits 700 SNPs, takes a long time, etc.). So I decided to write a java program (snpEff). I noticed that Galaxy does not have a tool for SNP prediction (see http://bitbucket.org/galaxy/galaxy-central/issue/156/synonymous-and-non-syn…). So I integrated snpEff it with Galaxy. Here is a link to a tar file which includes the jar files, databases, configuration files for Galaxy, etc. http://www.mcb.mcgill.ca/~pcingola/snpEff.tgz YOu'll find the databases for hg37 and mm37, but I'll be happy to create and update the tool for the genome of your choice. The program first loads the database for a genome (it takes 20 secs in my computer) and then calculates the effect for all SNPs (I used an Interval-Tree structure, so it's very fast). I hope you find it useful. Yours Pablo Cingolani P.S.: Needless to say, the code is open source (I'll post it on sourceforge as soon as possible). In the mean time you can download it here http://www.mcb.mcgill.ca/~pcingola/SnpEffect_eclipse_project.tgz P.S.2: I've attached an image of a demo run in my Galaxy server

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Data Library Uploading Issue
by juan perin 06 Jul '10

06 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. Thanks. Juan

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Re: [galaxy-dev] [galaxy-user] Data Libraries Problems
by Greg Von Kuster 06 Jul '10

06 Jul '10

Galaxy works with Python 2.4 or higher ( but not Python 3 ). On Jul 2, 2010, at 3:15 PM, Juan Perin wrote: > No changes at all. I seem to get this with a new installation as well. Both using postgres and mysql. Is there a new python requirement perhaps? I may be running and older version. > > ~ juan > > On Jul 2, 2010, at 14:13, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > >> Hello Juan, >> >> We're not able to reproduce this error. Have you made any changes to the code in your instance? >> >> Greg >> >> On Jul 2, 2010, at 12:16 PM, juan perin wrote: >> >>> 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 >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Enabling User Pages
by Jesse Erdmann 06 Jul '10

06 Jul '10

My Google/grep fu is failing me. How do I enable user pages in my local galaxy server? Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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handling multiple output files on galaxy.
by Vipin TS 04 Jul '10

04 Jul '10

Hi Galaxy team, I would like to create output files of my tool based on the input request. I referred to the contents at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput. Here it doesn't mention how I can handle if I have more conditional statements. <tool id="example_tool" name="Multiple output" description="example"> <command>example_tool.sh </command> <inputs> ... <conditional name="condition1"> ... <conditional name="condition2"> ..... <param name="format" type="select" label="Output format"> <option value="bed">BED format</option> <option value="sam">SAM format</option> </param> </condition> ... </condition> ... </inputs> ... <outputs> <data format="bed" name="output1" > <filter>condition1 condition2['format'] == "bed"</filter> ## How I can give multiple conditions. </data> <data format="sam" name="output2" > <filter>condition1 condition2['format'] == "sam"</filter> </data> </outputs> </tool> Many thanks in advance, Vipin T S

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Recently used tools options
by Assaf Gordon 03 Jul '10

03 Jul '10

Again, very nice feature. And of course, some comments: 1. The search is too general (IMHO). If I search for "rna", I get (among other tools) the "lastz" tool, because it has the following line in the help section: === 3. RNAME Reference sequence NAME === (Note the "RNA" in "RNAME"...) To be useful, the basic search has to include the tool name and possibly the description, and preferably some keywords (specified manually in the XML). An advanced search might offer a global text search. 2. The "recently used tools" is not updated after running a new tool. One has to reload the page (and then the list is hidden by default). 3. a small bug: 1. reload galaxy (for a clean start) 2. click "options->Search Tools" (search box is shown) 3. click "options->Show recently used" (recently-used menu is shown) 4. Search for a tool which is NOT in the recently used menu (e.g. search for "foobar") 5. The "recently used" menu is forever gone, no way to get it back: the "options" menu still says "hide", but even clicking multiple times on hide/show does not bring it back. 4. not necessarily a bug: All workflows in the "workflow" menu (i.e. workflows that were configured to be on the user's tools menu) are always displayed, regardless of the active search. This is probably by design, but it's conceptually confusing (because you encourage users to use workflows as regular tools in that menu). -gordon

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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

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sge & pbs job dependency
by Andrey Tovchigrechko 01 Jul '10

01 Jul '10

I am looking at the code inside lib/galaxy/jobs. It appears that the dependency tracking between jobs is done entirely by Galaxy. In other words, the option of e.g. SGE to submit a job with a dependency on previously submitted jobs is not used. Galaxy simply waits until the dependency jobs have finished, and then it submits the dependent job. It seems like inefficient to me on a busy cluster. E.g. if a user has one "reducer" job in a workflow that depends on a 100 "mapper" jobs, and all are submitted at once with an SGE dependency of the mapper on the reducer, then the mapper can be at the top of the SGE queue by the time all mappers have finished, and run immediately. In the current Galaxy implementation, the reducer will only be submitted to SGE queue after all mappers have finished, and have to wait for all the jobs in front of it (assuming a simple FIFO policy on the SGE side). Why is such design necessary?

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TopHat with FASTA and Illumina FASTQ
by Assaf Gordon 01 Jul '10

01 Jul '10

Hi all, Similar to the previous Bowtie patch, this one allows the TopHat wrapper to use FASTA and Illumina FASTQ files. Also available here: http://cancan.cshl.edu/labmembers/gordon/files/galaxy_tophat_wrapper_fasta_… Comments are welcomed, -gordon

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galaxy-dev July 2010