April 2010 - galaxy-dev - lists.galaxyproject.org

changing "Database/Build" back to 'unspecified'
by Hans-Rudolf Hotz 13 Apr '10

13 Apr '10

Hi I have a small problem with changing the "Database/Build" setting of a dataset: When I create a new history item with the tool 'Upload File from your computer' the "Genome" is unspecified, unless I change the value from 'Click to Search or Select Build' to any of the genomes and/or builds. I can always change it later using the 'pencil' icon. However, once it has changed to any of the genomes and/or builds I can't change it back to "?". This is the case on 'http://main.g2.bx.psu.edu/' as well on our local installation (running changeset 3545). I do have the line "? unspecified (?)" in the file ~/galaxy_dist/tool-data/shared/ucsc/builds.txt Changing back to 'unspecified' was possible before (ie running changeset 2833) when it was a simple drop down menu. Is there a possibility to fix this? Regards, Hans

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Re: [galaxy-dev] Weird problem with importing datasets
by Chris Cole 13 Apr '10

13 Apr '10

On 09/03/10 15:42, Chris Cole wrote: > On 09/03/10 14:53, Nate Coraor wrote: >> Chris Cole wrote: >>> Anyone got any ideas on this? >>> >>> It's still not working (following the most recent updates) and we've >>> got some NGS data to import into Galaxy. >> >> Hi Chris, >> >> To use this feature, the contents of library_import_dir should >> themselves be directories (or symlinks to the same). Selecting that >> directory from the dropdown in the library upload form will then import >> the contents of those directories. > > Ah, right. That's not clear in the docs. > > How come it works with locally symlinked files, then? Just checked it again (sorry I shouldn't have sent the previous email) with a directory and it still isn't working. www-galaxy@ge-002: tmp> cd ~/data_import/ www-galaxy@ge-002: data_import> ls README www-galaxy@ge-002: data_import> ln -s /homes/pschofield/data/TOH www-galaxy@ge-002: data_import> ls TOH/ 0min_1.txt 30m_1.txt 60min_1.txt Cd_inuc_1.txt Cmono_1.txt Dd_inuc_1.txt Dmono_1.txt processed 0min_2.txt 30m_2.txt 60min_2.txt Cd_inuc_2.txt Cmono_2.txt Dd_inuc_2.txt Dmono_2.txt www-galaxy@ge-002: data_import> ls -l total 96 -rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README lrwxrwxrwx 1 www-galaxy barton 26 Mar 9 15:59 TOH -> /homes/pschofield/data/TOH I got the TOH option in the 'Upload directory of files', which I selected, but the upload failed. Again, this is the error I get when selecting one of the filenames in the dataset: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error Thanks for help. Chris

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Automated deployment of Galaxy associated data files
by Brad Chapman 12 Apr '10

12 Apr '10

Galaxy folks; We recently moved our local Galaxy instance to a new server, and in the process developed an automated script to install and integrate associated data libraries and programs. I thought this might be of interest to other developers on the list and is available at: http://github.com/chapmanb/bcbb/blob/master/galaxy/galaxy_fabfile.py This uses Fabric (http://docs.fabfile.org) to: - Install 3rd party tools, focused around next-gen analysis: bowtie, bwa, maq, samtools, fastx-toolkit, UCSC programs - Download and index genome builds. There are provided classes to handle UCSC, Ensembl and NCBI downloads. - Update associated tool-data files with links to the builds and indexes. It works incrementally, skipping programs and libraries that are already installed, so you can use it to keep data files synchronized across multiple installations. We do this internally with a test and deployment Galaxy, and find it useful to have the exact same genome builds on all of our machines for running off-Galaxy alignments. Happy to hear thoughts and suggestions. My long term goal is to get this to the point that it could be used alongside existing Galaxy egg scrambling automation to automate deploying Galaxy on a bare bones machine, like Amazon EC2 instances. Hope others find this useful, Brad

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sharing histories with a group
by Edward Kirton 09 Apr '10

09 Apr '10

Hello, I'd like to be able to share histories with an entire group at a time, rather than by user. I see this issue has been submitted as a ticket here: http://bitbucket.org/galaxy/galaxy-central/issue/45/data-sharing However, I only see a button to "Share with a user" in the "Share or Publish" history menu. Is a "Share with a group" button planned? Thanks, Ed

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cleanup of old userless histories
by Matthew Eldridge 09 Apr '10

09 Apr '10

Hi, I noticed that the update timestamp for history objects gets "updated" when these are deleted or purged using the cleanup_datasets.py script. When userless histories older than 30 days, for example, are deleted with this script, they cannot then be purged immediately (along with associated datasets) unless the --days 0 option is used. However, I think this would also purge histories that have been recently deleted through the web interface by a user. It seems that to prevent that happening I'd need to wait another 30 days before really freeing up disk space associated with files from the old userless histories. Perhaps I've misunderstood something about the way is supposed to work? Thanks Matt

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removing the "view in GeneTrack" link
by Hotz, Hans-Rudolf 08 Apr '10

08 Apr '10

Hi I fully appreciate the fact that the visualization module is still in development - although, I am looking very much forward to use it. In the meantime, is there a way to remove the link "view in GeneTrack" you get for all the BED files in your history? I am running changeset 3545 and I have the following lines commented in my 'universe_wsgi.ini' file: # Uncomment following line below to enable visualization module #enable_tracks = True # Comma separated list of UCSC / gbrowse browsers to use for viewing #ucsc_display_sites = main #gbrowse_display_sites = main # Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = Nevertheless, I get a link like: http://galaxy-dev.fmi.ch/display_application/d12c5c8ceaef53e4/genetrack_inte rval/genetrack which (if clicked on) results in an Error with the following message: "Exception: A data display parameter is in the error state: genetrack_file" I am running another course next week promoting the use of our local galaxy server, and people will probably stumble across this broken link Thank you very much for your help Hans

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Having Problems with DRMAA_python
by vill 08 Apr '10

08 Apr '10

L.S. I'm having trouble getting Sun Grid Engine and galaxy to work. The steps I did: #hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist #cd galaxy_dist #sh setup.sh #SGE_ROOT=/usr/local/gridengine python scripts/scramble.py DRMAA_python I'm getting this error when building the DRMAA egg. Can you help me getting this egg build. There is a .egg verion downloadable from : http://code.google.com/p/drmaa-python/downloads/list When placing this one in the eggs dir it does not work. The SGE 6u4 is installed and working correctly. ##################################################################### # SGE_ROOT=/usr/local/gridengine python scripts/scramble.py DRMAA_python fetch_one(): Trying to fetch: http://eggs.g2.bx.psu.edu/new/DRMAA_python/DRMAA_python-0.2.tar.gz fetch_one(): Fetched to: /usr/local/galaxy_dist/scripts/scramble/archives/DRMAA_python-0.2.tar.gz unpack_source(): Unpacked to: /usr/local/galaxy_dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/DRMAA_python copy_build_script(): Using build script /usr/local/galaxy_dist/scripts/scramble/scripts/DRMAA_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /usr/local/galaxy_dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/DRMAA_python: /usr/bin/python -ES scramble.py --------------------------------------------------------------------------- This script requires setuptools version 0.6c11 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.6/s/setuptools/) but you may need to enable firewall access for this script first. I will start the download in 8 seconds. (Note: if this machine does not have network access, please obtain the file http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg and place it in this directory before rerunning this script.) --------------------------------------------------------------------------- Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg Traceback (most recent call last): File "scramble.py", line 14, in <module> from scramble_lib import * File "../../../lib/scramble_lib.py", line 146, in <module> use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) File "/usr/local/galaxy_dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/DRMAA_python/ez_setup.py", line 119, in use_setuptools return do_download() File "/usr/local/galaxy_dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/DRMAA_python/ez_setup.py", line 99, in do_download import setuptools; setuptools.bootstrap_install_from = egg File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/setuptools/__init__.py", line 2, in <module> File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/setuptools/extension.py", line 2, in <module> File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/setuptools/dist.py", line 5, in <module> File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/setuptools/command/install.py", line 2, in <module> File "/usr/lib/python2.6/distutils/command/install.py", line 21, in <module> from site import USER_BASE File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/site.py", line 73, in <module> # Enable per user site-packages directory File "/usr/local/galaxy_dist/scripts/scramble/lib/setuptools-0.6c11-py2.6.egg/site.py", line 38, in __boot configuration files, foo.pth and bar.pth. Assume foo.pth contains the ImportError: Couldn't find the real 'site' module Traceback (most recent call last): File "scripts/scramble.py", line 44, in <module> egg.scramble() File "/usr/local/galaxy_dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/usr/local/galaxy_dist/lib/galaxy/eggs/scramble.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for DRMAA_python 0.2 ##################################################################### Thanks, //Michel

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sharing tools?
by Edward Kirton 07 Apr '10

07 Apr '10

Hi, I've wondering what's the best way to share tools with other galaxy site sysops? I've got tool config xml files and associated datatype config files for many popular programs, like newbler, velvet, vmatch, mummer, lucy, uclust, cd-hit, more. Plus I've written several small but useful tools/utilities. I'd like to support Galaxy by making them available to others (and am interested in getting tools other have created as well). Ed Kirton US DOE JGI

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funny bug: a tool with a variable named "type" causes exception in workflows
by Assaf Gordon 07 Apr '10

07 Apr '10

Hi, I have a tool which have a variable named "type" (see example XML file below). This tool works fine when running it manually, but when adding this tool to a workflow *and* changing the default options from "typeA" to "typeB" - an exception is thrown when trying to save the workflow, and the "saving workflow" progress bar hangs forever. XML: ========================== <tool id="dummy_tool" name="Test tool"> <description>with a variable named 'type'</description> <command>echo $type > '$output'</command> <inputs> <param name="type" type="select" label="Type variable"> <option value="typeA">Type A</option> <option value="typeB">Type B</option> <option value="typeC">Type C</option> </param> </inputs> <outputs> <data format="txt" name="output" /> </outputs> </tool> ========================== The exception: ===== URL: http://tango.cshl.edu/galaxy/workflow/editor_form_post File '/home/gordon/projects/galaxy_devel/eggs/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/gordon/projects/galaxy_devel/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/gordon/projects/galaxy_devel/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/gordon/projects/galaxy_devel/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/gordon/projects/galaxy_devel/lib/galaxy/web/framework/middleware/remoteuser.py', line 103 in __call__ return self.app( environ, start_response ) File '/home/gordon/projects/galaxy_devel/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/gordon/projects/galaxy_devel/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/gordon/projects/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 62 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/home/gordon/projects/galaxy_devel/lib/galaxy/web/controllers/workflow.py', line 519 in editor_form_post 'tool_state': incoming.pop("tool_state") File '/home/gordon/projects/galaxy_devel/lib/galaxy/workflow/modules.py', line 286 in from_dict assert type in self.module_types AssertionError: ===== It seems like somehow the tool variable "type" overwrote the value of the python variable 'type' in that module (see attached screenshot). Maybe there is such a thing as 'too much' of a dynamic language ;) The obvious workaround is not to name my XML variables with a name that might conflict with galaxy's internals. -gordon P.S. My galaxy version is based on 3545:2590120aed68 .

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problem getting Galaxy to run on web
by nsfox＠uwaterloo.ca 06 Apr '10

06 Apr '10

Hi, I have a Galaxy Instance that is up and running. I started running it locally on my computer. There I can access it using my web browser (firefox) but of course I can't use the Galaxy instance from a different computer. So I then moved a copy of the Galaxy instance to a web server. Galaxy runs on the web server but I cannot access the Galaxy instance through my web browser on my computer. However I can use the Galaxy instance by starting firefox from the command line on the web server. Access through the firewall on the web server was granted but is there another firewall or something I may need to change to allow web access? Any help is greatly appreciated. Thanks, Natalie

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