- galaxy-dev - lists.galaxyproject.org

BEDtools wrapper development - help needed
by Björn Grüning 19 Jun '14

19 Jun '14

Hi, if you are interested in wrapper development you can help to improve the current BEDtools in Galaxy. We have wrapped nearly all available BEDtools from version 2.19. A test repository is located here: https://testtoolshed.g2.bx.psu.edu/view/bgruening/bedtools_test_bag and the development github repository is here: https://github.com/bgruening/galaxytools/tree/master/bedtools If you would like to learn how to write wrappers, improve the documentation or the unit-test, if you are a BEDtools expert or just want to speed up the upload to the Tool Shed ... please drop me a mail or clone the repository and go crazy. Thanks, Bjoern

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Can' Start the Galaxy instance!
by xlwang 19 Jun '14

19 Jun '14

Hello, I got an error when I installed and started a new galaxy instance just now. And I have an old version galaxy instance, it can be started and runs well, but when I updated it, the old one will get the same error like the following picture: please help me and tell me how to fix it, thank you very much!

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specifying default file by name in workflows
by Evan Bollig 19 Jun '14

19 Jun '14

I don't know all the subtleties of the galaxy workflow syntax. My goal is to specify the default input file names for a number of tools in a workflow. Is this possible, or am I limited to only providing the file type or extension? If possible, can you provide an example? Thanks, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Import of Capsules failing on local toolshed instance
by Will Holtz 18 Jun '14

18 Jun '14

I am now able to export capsules from the main/test toolsheds -- thanks Dave! When attempting to import these capsules into my local toolshed (latest_2014.06.02 for changeset fb68af9a775a) I receive the following error: URL: https://galaxy.lygos.com:99/repository/import_capsule File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py', line 74 in __call__ return self.app( environ, start_response ) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 1992 in import_capsule import_util.check_status_and_reset_downloadable( trans, import_results_tups ) File '/home/galaxy/galaxy-dist/lib/tool_shed/util/import_util.py', line 34 in check_status_and_reset_downloadable tip_changeset_revision = repository.tip( trans.app ) AttributeError: 'NoneType' object has no attribute 'tip' I have seen the same behavior for capsules based on the following repositories from the test toolshed: package_biopython_1_62, package_vienna_rna_2_1, and package_bowtie_0_12_7. I am logged in as an admin user for the import process. thanks, -Will

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Postgresql database time wrong...
by Neil.Burdett＠csiro.au 18 Jun '14

18 Jun '14

Hi I have quite a strange issue. I have a local install of Galaxy setup. When I type 'date' on my Ubuntu machine I get something like: Wed Jun 18 09:25:22 EST 2014 When i then execute a job and look in the database at the create_time i.e. # select create_time from job order by create_time; I get 2014-06-17 23:20:00.133828 So about 10 hours different. Is there some configuration I need to set as Brisbane is 10hrs ahead of GMT (coincidence?) Thanks Neil

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How Galaxy prevents security attacks?
by Neil.Burdett＠csiro.au 18 Jun '14

18 Jun '14

Hi, we'd like to host a version of Galaxy, but our security team have identified some potential areas that could be subjected to attack. I was wondering if Galaxy had mechanism in place to avoid the following issues: Cross site scripting Description Cross site scripting (also referred to as XSS) is a vulnerability that allows an attacker to send malicious code (usually in the form of Javascript) to another user. Because a browser cannot know if the script should be trusted or not, it will execute the script in the user context allowing the attacker to access any cookies or session tokens retained by the browser Impact Malicious users may inject JavaScript, VBScript, ActiveX, HTML or Flash into a vulnerable application to fool a user in order to gather data from them. An attacker can steal the session cookie and take over the account, impersonating the user. It is also possible to modify the content of the page presented to the user Affected URLS and parameters: * /capaibl/visualization/list o update_time param * /capaibl/history/delete_current o purge * /capaibl/history/list o F-deleted o F-name * /capaibl/user/edit_address o Address_id o User_id * /capaibl/edit_info o Username o User_id * Capaibl/user/logout o Referrer * /capaibl/user/manage_user_info o Change_password_button o Cntrller o Current o Email o Id o Message o Status o Username o User_id * /capaibl/user/reset_password o Message * /caibl/user/set_default_permissions o cntrller Denial of Service Description of attack During security testing we used two different types of crawlers and both caused the system to crash. Without access to the backend it is hard to document the reason, however, an educated guess would be that there is limited memory available to sessions. When crawlers ask for multiple sessions, this could cause the webserver to allocate all its memory and crash. Attack scenario 1. Open burpsuite and start the proxy function 2. Open a browser and set burpsuite as the proxy 3. Navigate to the milxcloud homepage 4. Turn on the spider function within burpsuite The website will crash within seconds. There is an entry in universe_wsgi.ini # Galaxy encodes various internal values when these values will be output in # some format (for example, in a URL or cookie). You should set a key to be # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. #id_secret = USING THE DEFAULT IS NOT SECURE! Would this help address the XSS issue? Thanks for any information Neil

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Gzipped input to functional tests with multiple="true"
by Peter Cock 18 Jun '14

18 Jun '14

Hi all, I think I've found a bug in the Galaxy test framework :( With most file inputs, a gzipped input file works fine (Galaxy's upload code handles unzipping it). However, with multiple="true" this seems to break (with the Twill backend, the API test framework is OK), e.g. <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> Fails: <param name="filenames" value="SRR639755_mito_pairs_sample.fastq.gz" ftype="fastqsanger" /> e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426318 Excerpt from log: ====================================================================== FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_mira_4_0_de_novo) MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 108, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 32, in do_it data_list = galaxy_interactor.run_tool( testdef, test_history ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py", line 449, in run_tool self.twill_test_case.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py", line 1789, in run_tool self.submit_form( **kwd ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py", line 1999, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'read_group_0|filenames' to value '['SRR639755_mito_pairs_sample.fastq.gz']' in form 'tool_form' threw exception: id=None name=None label='SRR639755_mito_pairs_sample.fastq.gz' control: <SelectControl(read_group_0|filenames=[80])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. This works, <param name="filenames" value="SRR639755_mito_pairs_sample.fastq" ftype="fastqsanger" /> e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426336 See: https://github.com/peterjc/pico_galaxy/commit/e6967767535ca29debcdc19d7f050… Regards, Peter

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What is the correct place under Galaxy for a database that's created by a tool?
by Melissa Cline 17 Jun '14

17 Jun '14

Hi folks, Hopefully this is a quick question. I'm working on a set of tools that will fire off a VM from within Galaxy and will then communicate with the VM. The VM will create a local database. The vision is that this won't be a shared database; in a shared Galaxy instance, each user will have his or her own database. What is the best place to create this database under the Galaxy file system? Thanks! Melissa

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R bioconductor dependencies when creating toolshed installation
by Stef van Lieshout 17 Jun '14

17 Jun '14

Hi all, I'm running into some difficulties on how to setup the installation procedure for a galaxy tool which executes an R script and has certain dependencies (mainly bioconductor packages). R can deal with dependencies, packages can be installed with install.packages (has a "dependencies" argument) or biocLite() for bioconductor packages. Yet, now I want my tool to be available at toolsheds. To do this I see several options: 1) setting up tool_dependencies.xml with "R CMD INSTALL" for all packages. BUT: need to download all dependencies before install, and can older versions still be downloaded? Maybe need to upload them to toolshed too.. 2) setting up tool_dependencies.xml to call an installation script with Rscript (where I could use install.packages), BUT: Dependencies are taken care of. But how do I select specific (older) versions, because if I dont, installing at different time can give different version. 3) creating a repository for each package and have all of them as requirement in my galaxy tool. BUT: a lot of work for a lot of dependencies All have pros and cons, how do people deal with this? Stef

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R version 3.1.0
by Stef van Lieshout 17 Jun '14

17 Jun '14

Any plans to create a R 3.1.0 repository? Thanks, Stef

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