July 2011 - galaxy-dev - lists.galaxyproject.org

Conditional and where tags
by SHAUN WEBB 13 Jul '11

13 Jul '11

Hi, I am creating a tool that provides the user with different input options based on the format of the input file. I have a conditional statement: <conditional name="fType"> <param name="file_type" type="select" label="Input File Type"> <option value="1">Type1</option> <option value="2">Type2</option> <option value="3">Type3</option> </param> <when value="1"> etc..... There is overlap between the options available for each file type and type1 and type 2 have identical options. Is there a way to avoid repetition under each <when> tag? For instance, I tried <when value="1,2"> but this doesn't work. I also want to send the file type to the program "--ftype $fType.file_type" so I want the values in each option tag to be unique. Thanks for any help Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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cleanups for cleanup scripts
by Assaf Gordon 13 Jul '11

13 Jul '11

Hi Greg, Another small patch for cleanup_datasets.py, that makes the output messages slightly more informative. The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed. The main goal is for the "delete_datasets.sh" script (with "-i" or without) to display exactly what's going on. comments are welcomed, -gordon Example of items 1,2: Without patch: ===== ... ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ====== Which shows that dataset 1782 seems to be processed three times, but still not deleted, without giving a reason. With this patch, the output will be: ====== ######### Processing dataset id: 1782 Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted) ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ====== Example of item 3: Without patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' have been purged: /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) ========== With patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' will be marked as deleted (without 'info_only' mode): /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) =========== Example of item 4: Without patch: ==== Examined 606 datasets, marked 589 as deleted and purged 595 dataset instances ==== With patch: === Examined 606 datasets, marked 589 datasets and 595 dataset instances (HDA) as deleted ===

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Error in running
by Dayananda Sagar 13 Jul '11

13 Jul '11

Hello, My name is Dayananda Sagar Gangadharaiah and I am a computational biology research associate at the University of Nebraska, Lincoln. We have been trying to install Galaxy for running a software tool called KIRMES. We are encountering the following errors when we run Galaxy using sh ./run.sh command *ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared * */ucsc/builds.txt'* *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt * *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/gbrowse/gbrowse_build_sites.t * *xt* *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/genetrack/genetrack_sites.txt * *python path is: /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/* *pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/nfs/software/pkgs/* *TFBS/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-li * *nux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkg* *s/TFBS/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/ga* *laxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /mnt/nfs/software/pkgs/TFB* *S/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /mnt/nfs/softwar* *e/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /* *mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6. * *egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /mnt/* *nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2 * *.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.* *6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib, /arch/lib/python2.6/site-pack* *ages/setuptools-0.6c11-py2.6.egg, /arch/lib/python2.6/site-packages/pip-1.0.1-py2.6.egg, /arch/lib/python26.zip, /arch/lib/python2.6, /arch/lib/python2.6/plat-li* *nux2, /arch/lib/python2.6/lib-tk, /arch/lib/python2.6/lib-old, /arch/lib/python2.6/lib-dynload, /mnt/nfs/software/software/64-bit/lib/python2.6/site-packages* *Traceback (most recent call last):* * File "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory* * app = UniverseApplication( global_conf = global_conf, **kwargs )* * File "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/app.py", line 20, in __init__* * self.config.check()* * File "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/config.py", line 174, in check* * raise ConfigurationError("Directory does not exist: %s" % path )* *ConfigurationError: Directory does not exist: /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/tool-data* Since we do not work on Python we are not able to rectify these problems. Please help us in fixing these errors. Regards, Dayananda Sagar Gangadharaiah E115, Beadle Center University of Nebraska- Lincoln 1901 Vine St., Lincoln, NE 68588-0665 Phone: (402) 472-8236

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how to purge histories/datasets not accessed/updated for a certain time
by Chaolin Zhang 13 Jul '11

13 Jul '11

Hi, We have a local mirror of the galaxy system and the disk is occupied really quickly. Is there a way to purge histories/datasets not accessed/updated for a certain period of time, no matter if they are deleted by the user? It looks like the current scripts for clean up only purges deleted histories/datasets. Thanks! Chaolin

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Galaxy Events Page and Google Calendar
by Dave Clements 13 Jul '11

13 Jul '11

Hello all, The new Galaxy wiki includes a Galaxy Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) that lists upcoming events (such as ISMB/ECCB 2011 <http://wiki.g2.bx.psu.edu/Events/ISMB-ECCB-BOSC%202011> and the Workshop on Comparative Genomics<http://www.molecularevolution.org/workshops/WCG#wcgna>) that have Galaxy related content. The page also contains a link to the new Galaxy Events Google Calendar<https://www.google.com/calendar/embed?src=mq93blfvdoosh5unpmivu4kh1c%40grou…>, that lists events and deadlines that may be of interest to the Galaxy community. For example, this week there are 5+ events going on and these 5 deadlines as well: <http://psb.stanford.edu/> - PSB 2012 <http://psb.stanford.edu/> abstracts (were due Monday) - Beyond the Genome <http://www.beyond-the-genome.com/program.html>abstract and early registration (Friday) - GIW 2011 <http://www.kobic.re.kr/giw2011/> abstracts (Friday) <http://meetings.cshl.edu/courses/c-ecg11.shtml> - Computational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml>application (Friday) <http://meetings.cshl.edu/courses/c-seqtech11.shtml> - Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml>application (Friday) If you know of events that either have significant Galaxy content, or are of interest to the overall community, please send them to outreach(a)galaxyproject.org and they will be added to the Events<http://wiki.g2.bx.psu.edu/Events>page and the calendar. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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plotting/statistics tools suggestion
by Marshall Hampton 12 Jul '11

12 Jul '11

I've just started seriously looking at Galaxy, and I already have a suggestion (everyone's a critic...): switch from using rpy or even rpy2 to scipy/numpy/matplotlib for basic statistics and plots. I wrestled a bit with getting rpy to work on my local setup and decided it would be quicker to write my own plotting tool extensions, which indeed turned out to be the case. Since you already require python it seems much more natural to use python-native tools. To give some positive feedback, learning to write an extension was surprisingly easy and encourages me to work on more. I use currently use Sage (http://www.sagemath.org/) to both analyze next-generation sequence data (454 and Illumina) and create interactive tools for the biologists I collaborate with. The Sage project involves many of the same issues and challenges facing Galaxy. Sage is based on python, but includes R. I realize that there are many things you would want to do with R that aren't included in scipy/biopython, so it might be worthwhile to look at how Sage wraps R. Its far from perfect, but I prefer it to rpy2. In the Sage source tree the interface is at: $SAGE_ROOT/devel/sage/sage/interfaces/r.py. (Ugly online copy at: http://hg.sagemath.org/sage-main/file/361a4ad7d52c/sage/interfaces/r.py) -Marshall Hampton Department of Mathematics and Statistics and the Integrated Biosciences Program University of Minnesota Duluth

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How to download data from History
by colin molter 12 Jul '11

12 Jul '11

Hello all, I have two related questions about getting data from the Galaxy History. I installed `galaxy in my server, I did some data analyses and now i want the resulting data back. But I am facing two problems: 1/ I just try to use the download button. If i do it with the button (or with curl or wget), i get the following error: <h1>Proxy Error</h1> <p>The proxy server received an invalid response from an upstream server.<br /> The proxy server could not handle the request <em><a href="/galaxy/datasets/b701da857886499b/display">GET /galaxy/datasets/b701da857886499b/display</a></em>.<p> Reason: <strong>Error reading from remote server</strong></p></p> </body></html> any ideas? Does I am suppose to modify the universe_wsgi.ini? 2/ In fact, i would prefer to just copy the result on the same server (no need to use the network). Something similar that what is used to add data to the datalibrary. Is it a way to just copy data from within galaxy to some given place in the same server? thank you colin -- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/

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Galaxy @ ISMB/ECCB, 3DSIG, and BOSC
by Dave Clements 12 Jul '11

12 Jul '11

Hello all, Galaxy will have a large presence at ISMB/ECCB, 3DSIG, and BOSC, all of which start this week in Vienna. Galaxy related content includes (at least): 1 Galaxy organized workshop on "Genomics for Non-Model Organisms" featuring 4 talks, 7 additional talks at ISMB/ECCB and BOSC, and 3 Posters at ISMB/ECCB and 3DSIG That's enough to fill a wiki page and a flier (and so it has :-). See http://wiki.g2.bx.psu.edu/Events/ISMB-ECCB-BOSC%202011 for a listing of all known Galaxy-related content and a flyer you can print out and take with you. Watch Twitter (@galaxyproject, #usegalaxy) during the conference for updates and reminders. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Tool Shed Problem
by SHAUN WEBB 12 Jul '11

12 Jul '11

Hi Galaxy team, I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error. When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs. Apologies if I broke it... On a side note, I did not see an option to delete a created repository. Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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how to reduce Load of galaxy in standalone system by python
by shashi shekhar 11 Jul '11

11 Jul '11

Hi All, i have system with single cpu . and have installed galaxy .while running galaxy it will create high load on system. how are you reducing the load of galaxy in system by using the python . Regards shashi

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