June 2013 - galaxy-dev - lists.galaxyproject.org

how to access galaxy model in the tool wrapper
by BingXin Lu 08 Jun '13

08 Jun '13

Hi all, Do you know any way to access galaxy model (like 'HistoryDatasetAssociation') in the tool wrapper python file for a newly added tool, without overriding 'exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr)'? Thank you very much. Best Regards, -Bingxin

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disk space usage
by Katie Kathrein 07 Jun '13

07 Jun '13

Hi, I am having an issue with disk space. I had some problems with loading datasets and ended up deleting a few that had errors. Now things are fine, except that my disk space says 90% is being used, yet I only have about 70 GB of data right now. Please help! Thanks! Katie Katie Kathrein, Ph.D. Zon Lab Children's Hospital Boston Karp Research Laboratories, 7005H 1 Blackfan Circle Boston, MA 02115 kkathrein(a)enders.tch.harvard.edu

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Error in getting updates from server
by Mather Ali Khan 07 Jun '13

07 Jun '13

Hi, Two days earlier i have executed my file for tophat, since then it is still in gey color and not getting any updates from server. Should i delete the executed file and run again? Please help me out. Thanks Mather -- *Mather Ali Khan, Ph.D.* *247, Bond Life Sciences Center* *1201 Rollins Street* *University of Missouri-Columbia* *Columbia, MO, 65211, USA * Think Green - don't print this email unless really needed

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Can I use javascript in the xml to select a date on a calender?
by Ramon Tiburski 07 Jun '13

07 Jun '13

Hi, I want to select a date from a calender in my tool, but I think that it's not possible in the xml. I was looking for some examples with xml, javascript and jquery but I could not do what I wanted. My code is: <tool id="idPlot" name="Plot"> <command interpreter="bash">r_wrapper.sh $script_file</command> <inputs> <param name="arg1" type="text" value="" label="Data 1"/> <param name="arg2" type="text" value="" label="Data 2"/> </inputs> <configfiles> <configfile name="script_file"> pv1 = "$arg1" pv2 = "$arg2" pdf("${out_file1}") source("/home/ramao/Galaxy-ES/tools/my_tools/modelo.R") devname=dev.off() </configfile> </configfiles> <outputs> <data format="pdf" name="out_file1"/> </outputs> </tool> I want that when I click in the input area the tool, it shows a calender to me select the date. Is this possible? With javascript? Or what? Thanks

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bug in galaxy-central security
by Robert Baertsch 07 Jun '13

07 Jun '13

James, I upgraded to the latest galaxy-central and starting with a blank database. When I add more than 20 users, the security group admin screen doesn't populate. mako is pulling the correct data but there is some jquery code for autocomplete or search that seems to be having trouble. Here is a screen shot. Let me know if you want admin access to this server and I'll setup a user for you. -Robert

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Basic setup question
by Malcolm Tobias 07 Jun '13

07 Jun '13

All, I manage a cluster and have been asked to set up a local instance of galaxy. I'm neither a galaxy user nor a biologist, so apologies in advance if my terminology is off. I have a basic setup running now, but have been asked to include the option to "display at UCSC Main" when a user uploads a bam and clicks on the dataset. Currently I have the options of "display in IGB Local Web". I've tried this at a few of the other Galaxy sites, and the behavior seems unpredictable. Uploading the same data set to some sites gives me this option, while others don't. I'm assuming this is determined by the option in the universe_wsgi.ini file: # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt ucsc_display_sites = main,test,archaea,ucla but uncommenting this option and restarting the server doesn't help. Increasing the log_level to DEBUG doesn't provide any insight. Any suggestions about how to proceed? Could there be any firewall-related issues? I ask because of this in the configuration file: # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to # bypass security to display datasets. Please be aware that there are security # implications if this is allowed. More details (including required changes to # the proxy server config) are available in the Apache proxy documentation on # the wiki. Thanks in advance, Malcolm -- Malcolm Tobias 314.362.1594

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galaxy cloud ftp
by Mallon, Eamonn B. (Dr.) 07 Jun '13

07 Jun '13

Hi I started a cloud instance using cloud man (very easy by the way). The ftp instructions say use localhost. I'm assuming that's the webpage http://184.73.86.130/ (in my case). When I try and connect using cyberduck it says connection reset. Any ideas? Thanks Eamonn Dr Eamonn Mallon Lecturer in Evolutionary Biology Adrian 220 Biology Department University of Leicester http://www2.le.ac.uk/departments/biology/people/mallon

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Problems running functional tests
by Ira Cooke 06 Jun '13

06 Jun '13

Hi All, I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies. The tool I'm considering is xtandem http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3(a)protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat --var-mods=' 57.021464__at__C ' --fix-mods=' 15.994915__at__M ' /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///) Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine. When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails. On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs). (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ). Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3(a)protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' 15.994915__at__M , ' --fix-mods=' 57.021464__at__C ' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3(a)protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' 15.994915__at__M ,' --fix-mods=' 57.021464__at__C ' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files ... galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR Is there something wrong with the way I've defined my tool dependencies for this tool? Or perhaps it's a bug in the testing framework. Cheers Ira

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Bypassing the proxy server when using the API, without breaking the automatic update of the history in the web interface
by Anthonius deBoer 06 Jun '13

06 Jun '13

Hi, I am trying desperately to setup my GALAXY system so that if you enter the website, you need to authenticate yourself using the proxy setup... I also would like to be able to BYPASS the proxy server when an API call is made... In the example proxy setting I have setup in the following way: ReWriteRule ^(/api/histories/.*) http://localhost:8080$1 [P,L] ReWriteRule ^(/api/.*) http://localhost:8081$1 [P,L] RewriteRule ^(.*) http://localhost:8080$1 [P] I then setup a <PROXY setting in the apache galaxy.d in /etc/httpd/conf.d/galaxy.d to require authentication when a user is re-directed to the localhost:8080 and allow the calls to localhost:8081 to pass unhindered... This works brilliantly EXCEPT for when you want to make an API call that involves some histories.... The call fails, since /api/histories calls are routed through the proxy server and require authentication, which I want to avoid... It seems that histories are "special" so they have their own line in the configuration file above... I tried to change ReWriteRule ^(/api/histories/.*) http://localhost:8080$1 [P,L] to ReWriteRule ^(/api/histories/.*) http://localhost:8081$1 [L] Which DOES work, but it also breaks the automatic update of the history in the webbrowser... I have to reload the page manually to update the history... Is there anyway I can get the automatic update to work again, but don't require autentication? Thanks Thon

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local install problem
by Andrew Krohn 06 Jun '13

06 Jun '13

I looked through others' problems, but this seems unique. I just did a clean install of Ubuntu 12.04 and wanted to add Galaxy to integrate our various pipelines (16S rRNA via qiime, RADseq data, small genome assemblies). However, I seem to be stuck at the beginning of the install. Followed instructions from this page explicitly ( http://wiki.galaxyproject.org/Admin/Get%20Galaxy) When I run sh run.sh, I get the below output, and the server cannot be accessed via web browser. I am using python 2.7.3. I opened a python instance and ran import bz2, but then I get the same error (ImportError: No module named bz2). enggen@OptimusPrime:~/galaxy-dist$ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/enggen/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/enggen/galaxy-dist/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/home/enggen/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 17, in <module> import galaxy.model File "/home/enggen/galaxy-dist/lib/galaxy/model/__init__.py", line 23, in <module> import galaxy.datatypes.registry File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 14, in <module> from galaxy.datatypes.checkers import is_gzip File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/checkers.py", line 1, in <module> import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr ImportError: No module named bz2 Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

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