September 2015 - galaxy-dev - lists.galaxyproject.org

LDAP Auto register - "username is None"
by Martin Vickers 03 Sep '15

03 Sep '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi All, I've been trying to get the new LDAP module to work. It works fine for existing users but I can't get auto-register to work. In the logs I can see the successful logins look like this; galaxy.webapps.galaxy.controllers.user DEBUG 2015-09-02 13:35:06,130 trans.app.config.auth_config_file: ./config/auth_conf.xml galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP authenticate: email is mjv08(a)aber.ac.uk galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP authenticate: username is mjv08 .... galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,235 LDAP authentication successful and those that are unsuccessful have a username as None, which is why the search filter isn't working; galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP authenticate: email is unreguser(a)aber.ac.uk galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP authenticate: username is None .... galaxy.auth.providers.ldap_ad WARNING 2015-09-02 13:47:14,110 LDAP authenticate: search returned no results My auth_config.xml openldap authenticator looks like this (edited to remove openldap server details); <authenticator> <type>ldap</type> <filter>'{email}'.endswith('@example.com')</filter> <options> <auto-register>True</auto-register> <allow-register>Challenge</allow-register> <server>ldaps://dc1.example.com</server> <search-base>ou=People,dc=dc1,dc=example,dc=com</search-base> <search-user>cn=searchuser,ou=People,dc=dc1,dc=example,dc=com</search-user> <search-password>searchuserpassword</search-password> <search-fields>cn,mail</search-fields> <search-filter>(&(cn={username})(mail={email}))</search-filter> <bind-user>{dn}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{cn}</auto-register-username> <auto-register-email>{mail}</auto-register-email> </options> </authenticator> Are there any settings in galaxy.ini that are required to enable this to work? Many thanks Martin - -- - -- Dr. Martin Vickers Data Manager/HPC Systems Administrator Institute of Biological, Environmental and Rural Sciences IBERS New Building Aberystwyth University w: http://www.martin-vickers.co.uk/ e: mjv08(a)aber.ac.uk t: 01970 62 2807 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJV5vO7AAoJEHa0a8GkKQgIJJQH/20auDZKNYOw0JfXq6y/DpY9 2d7C5e81BepLfi3b715vhuG5qtJUj+fLkI86fgKgloo/y4SqQWeni51buxs3kgSl L0ynVeZC/hIQSSLIEUTfPomT0CIR4GdPwnegbqaWZuy3NBlq2Rj6Boc2V/6EIp1M ARlEKeV/gK64h/cq2guTbPLdgK5vnGFCNKcsLLYCLelBmpXfjRG8z9JIa1nLa/F/ 4p1KaIX+UqCTMZrGAOM2S5Fb3rfmeApcp73w6aM4RDKwdJpsfuhQhFwtkPFjfSyn GrQM6naA/qY8m+Gtl+he6L7XczP4nFyan1JN9AcWEGtzHBappPKMeI/L7ZLoHTw= =Cwa8 -----END PGP SIGNATURE-----

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ActiveDirectory issues with auto register functionality
by Yves Gagnon 03 Sep '15

03 Sep '15

Hello everybody! I try to configure Active Directory authentication on our local instance. So far, I got the authentication to work using direct binding. I have these options in the auth_conf.xml : <allow-register>No</allow-register> <auto-register>Yes</auto-register> <server>ldap:/REDACTED /</server> <bind-user>{username}@REDACTED</bind-user> <bind-password>{password}</bind-password> <continue-on-failure>False</continue-on-failure> <auto-register-username>{sAMAccountName}</auto-register-username> <login-use-username>True</login-use-username> <auto-register-email>{mail}</auto-register-email> Paster.log: galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,158 LDAP authenticate: whoami is u:REDACTED\GagnonY galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,159 LDAP authentication successful However, the authentication module does not seem to be able to fetch information from LDAP to auto register With these settings, I get the debug message in galaxy when I try to log in : URL: http://localhost:8080/user/login?use_panels=False File '/home/galaxy/galaxy_app/galaxy/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/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 482 in login message, status, user, success = self.__validate_login( trans, **kwd ) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 524 in __validate_login autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/__init__.py', line 100 in check_auto_registration auth_result, auto_email, auto_username = provider.authenticate(email, username, password, options) File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', line 177 in authenticate _get_subs(options, 'auto-register-email', params), File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', line 19 in _get_subs return str(d[k]).format(**params) KeyError: 'mail' So for some reason, the module cannot fetch the mail field from AD. If I try to bypass this by putting a harcoded email, same issue occurs with sAMAccountName field. Did anybody encounter this before? Thanks in advance for the help. Yves Gagnon

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discover_datasets
by Sabrina Legoueix Rodriguez 03 Sep '15

03 Sep '15

Hi, I am developing a tool with unknown output dataset number; so, I am trying to use discover_datasets tag. I have tested the following code as explained in the galaxy project documentation: <tool id="sr_discover1" name="Discover"> <command> echo "Hello" > $report; mkdir subdir1; echo "This" > subdir1/this.txt; echo "That" > subdir1/that.txt; mkdir subdir2; echo "1" > subdir2/CUSTOM_1.txt; echo "2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; mkdir subdir3; echo "Foo" > subdir3/Foo; echo "mapped reads" > split_bam_.MAPPED.bam; echo "unmapped reads" > split_bam_.UNMAPPED.bam; echo "1" > sample1.report.tsv; echo "2" > sample2.report.tsv; echo "3" > sample3.report.tsv; </command> <inputs> <param name="num_param" type="integer" value="7" /> <param name="input" type="data" /> </inputs> <outputs> <data format="txt" name="report"> <discover_datasets pattern="__designation_and_ext__" directory="subdir1" visible="true" /> <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" visible="true" /> <discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" /> <discover_datasets pattern="split_bam_\.(?P<designation>([A-Z-])\w+)\.bam" ext="txt" visible="true" /> <discover_datasets pattern="(?P<designation>.+)\.report\.tsv" ext="tabular" visible="true" /> </data> </outputs> </tool> But, when I look at he result, I only obtain a single dataset corresponding to the "report" and the following information: Job Command-Line: echo "Hello" > /path/database/job_working_directory/002/2227/galaxy_dataset_5307.dat; mkdir subdir1; echo "This" > subdir1/this.txt; echo "That" > subdir1/that.txt; mkdir subdir2; echo "1" > subdir2/CUSTOM_1.txt; echo "2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; mkdir subdir3; echo "Foo" > subdir3/Foo; echo "mapped reads" > split_bam_.MAPPED.bam; echo "unmapped reads" > split_bam_.UNMAPPED.bam; echo "1" > sample1.report.tsv; echo "2" > sample2.report.tsv; echo "3" > sample3.report.tsv; and when I check in the job_working_directory, no "subdir(1,2 and 3)" folders have been created and no datasets displayed on galaxy as results. Can someone help me understand how discover_datasets work and why all the supposed multi datasets are not displayed in the galaxy interface? Thanks in advance. Best regards, -- Signature e-mail TWB Sabrina **Sabrina LEGOUEIX RODRIGUEZ** Responsable Plateau Bioinformatique Tél. : +33 (0) 5 61 28 57 92 sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]> www.toulouse-white-biotechnology.com <http://www.toulouse-white-biotechnology.com/> LinkedIn <https://www.linkedin.com/company/2757525h> Twitter <https://twitter.com/TWB_Biotech> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane • 31520 Ramonville Saint-Agne Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.

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Error in installing tool dependencies
by Nuwan Goonasekera 03 Sep '15

03 Sep '15

Hi, We've encountered an error when installing tool dependencies, in particular, with snpEff among others, on the 15.07 branch. We've tracked it down to this particular commit and have commented on the issue there. https://github.com/galaxyproject/galaxy/commit/91bf1d37db59bc69404e9831893b… Should we log a trello issue? cheers, /Nuwan

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Turn your workflow into a tool?
by Alexander Vowinkel 02 Sep '15

02 Sep '15

Hi, this page: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/ToolPanel is linked here: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow but does not exist. How can I put my Workflow for all users into the Tool Panel? Thanks, Alexander

2 3

ProFTPd in CloudMan
by Alexander Vowinkel 02 Sep '15

02 Sep '15

Hi, I get the error "Could not read from socket: ECONNRESET - Connection reset by peer" when connecting with FileZilla to the Cloud Instance. Using launch.usegalaxy.org FileZilla Log: http://pastebin.com/zfACC6wH ProFTP Log: http://pastebin.com/T9JxKVCb With console FTP in linux I can connect, get a listing and upload files. I tried to find out what the reason is, but no solution found. bareFTP is also not able to connect. The ports for PassivePorts are open (checked in AWS) Any idea on this? Thanks, Alexander

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about galaxy
by Dong Liu 02 Sep '15

02 Sep '15

Dear Galaxy I am a new user on Galaxy online service. When I uploaded my data file in fastq form, the utility of Galaxy such as NGS:QC and manipulation, FastQC and Trim sequences can not be availabe. I dont why. can you tell me how to use Galaxy using my data? Dong Liu visiting scholar at the University of Georgia,GA, USA

3 2

PBS Torque 15007: No permission
by Ben Archuleta 02 Sep '15

02 Sep '15

Hello All, I have Galaxy running on the latest version of Biolinux configured to work with PBS/Torque version Version: 4.2.8, all jobs are being submitted as Debian-galaxy (This is a global user in the cluster and a local user on the Biolinux box). Whenever we submit a job we get the error below: galaxy.jobs.runners.pbs ERROR 2015-08-28 11:52:42,608 Connection to PBS server for submit failed: 15007: No permission We are using: /usr/lib/galaxy-server/eggs/pbs_python-4.4.0-py2.7-linux-x86_64-ucs4.egg to interact with the PBS. Below is how the two identical accounts are configured: Debian-galaxy:x:2136:100::/var/lib/galaxy-server/database:/bin/fasle Debian-galaxy:XXXXXXX:2136:100:Debian-galaxy:/var/lib/galaxy-server/database:/bin/bash Is this a PBS Python error or could this be directly related to the PBS? I can submit jobs on that node by hand through Bash but not through Biolinux. Thank You! Ben

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Wiki documentation for tool_dependencies.xml file
by Peter Cock 02 Sep '15

02 Sep '15

Hi all, Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml? What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not? Peter

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PBS Torque 15007: No permission
by Ben Archuleta 02 Sep '15

02 Sep '15

Hello All, I have Galaxy running on the latest version of Biolinux configured to work with PBS/Torque version Version: 4.2.8, all jobs are being submitted as Debian-galaxy (This is a global user in the cluster and a local user on the Biolinux box). Whenever we submit a job we get the error below: galaxy.jobs.runners.pbs ERROR 2015-08-28 11:52:42,608 Connection to PBS server for submit failed: 15007: No permission We are using: /usr/lib/galaxy-server/eggs/pbs_python-4.4.0-py2.7-linux-x86_64-ucs4.egg to interact with the PBS. Below is how the two identical accounts are configured: Debian-galaxy:x:2136:100::/var/lib/galaxy-server/database:/bin/fasle Debian-galaxy:XXXXXXX:2136:100:Debian-galaxy:/var/lib/galaxy-server/database:/bin/bash Is this a PBS Python error or could this be directly related to the PBS? I can submit jobs on that node by hand through Bash but not through Biolinux. Thank You! Ben

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