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

ldap module not present
by Will Holtz 18 May '15

18 May '15

I'm trying out the new LDAP auth features in v15.05. I'm getting the following error in my logs: galaxy.auth.providers.ldap_ad DEBUG 2015-05-15 08:53:43,886 LDAP authenticate: could not load ldap module this is from 'import ldap' failing in lib/galaxy/auth/providers/ldap_ad.py Should there be some egg magic that takes care of this dependency for me? thanks, -Will -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.

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Can a tool retrieve a user's API KEY?
by Ryan G 18 May '15

18 May '15

I'm trying to create a tool that user's can use that will interact with Galaxy 's API, however the tool needs to be able to determine the user's API key. Is this possible? Can a tool determine what the user's API key is when the user actually runs the tool?

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alternative solution to logout ldap users
by Pablo Escobar 18 May '15

18 May '15

Hi, I have configured apache as reverse proxy for galaxy and I also configured apache to access my openldap for authentication. It's working fine but I was getting some trouble to logout the users as explained in the documentation here https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth#Logging_out_Ba… So I tried a different approach by adding this mod_rewrite lines to my apache vhost and it seems to work fine to logout users RewriteEngine on RewriteRule "^/user/logout$" "https://logout@%{HTTP_HOST}" [R,L] It took me some time to figure out this workaround so I send it to the list in case it's useful for anyone else. It would be nice if someone can update the docs. I have verified it works with latest chrome and firefox. It doesn't work with internet explorer 11 regards Pablo.

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difficulty creating composite data type
by Brian Haas 16 May '15

16 May '15

I'm having some trouble creating a composite data type in galaxy. The composite type is created but is always empty. I've tried to put together a very simple test for the system. Attached are my input files as well as a screenshot of what I'm experiencing. I've registered my new data type in 'config/datatypes_conf.xml' <datatype extension="compositeDatatypeTest" type="galaxy.datatypes.composite_datatype_test:CompositeDataTest" display_in_upload="True" /> and I've added the attached module 'composite_datatype_test.py' to the 'lib/galaxy/datatypes/' area. The module is being parsed properly on start-up (log from the galaxy/run.sh) galaxy.datatypes.registry DEBUG 2015-05-16 11:13:51,869 Loading datatypes from ./config/datatypes_conf.xml galaxy.datatypes.registry DEBUG 2015-05-16 11:13:51,872 Retrieved datatype module galaxy.datatypes.composite_datatype_test from the datatype registry. galaxy.datatypes.composite_datatype_test DEBUG 2015-05-16 11:13:51,872 ######### Composite Data Test ############ I've tried running the system with my composite type set to 'basic' as well as 'auto_primary_file' and neither work. Under 'auto_primary_file', the html file isn't generated. Thanks in advance for any help! ~brian -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

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missing auth_conf.xml.sample
by Tony Kusalik 15 May '15

15 May '15

Hi This morning I did a hg pull -u This took me from changeset: 17103 to changeset: 17121:7a4e3a661a76 However, when trying to restart the galaxy server, I get IOError: [Errno 2] No such file or directory: './config/auth_conf.xml.sample' Checking the config subdirectory, I can confirm that this .xml.sample file is not present. Where can I get a copy of config/auth_conf.xml.sample? (I'd rather just grab this file rather than doing something as drastic as a re-install.) Why did the update not pull down a copy of config/auth_conf.xml.sample? Did I do something wrong? Thanks.

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Issue with latest run of automated tool shed testing?
by Christy Shafer 15 May '15

15 May '15

Hi Galaxy Developers, Was there a bug with the last round of automated tool testing within the public tool shed? All of my tools failed due to installation errors; one per tool (one tool per repo), error message for all being “An entry for the repository was not found in the database.” I looked a few other tools from the devteam and found that same error from the test done on 5/7/2015, hence my wondering whether there was an issue with the testing itself. If there was a bug or something, when will re-testing be performed? (FWIW, I do plan to use planemo for testing future tools prior to public tool shed upload) Thanks, Christy ———————— Christina Shafer, Ph.D. Bioinformatics Analyst Regenerative Biology Laboratory Morgridge Institute for Research cshafer(a)morgridge.org

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May 2015 Galaxy Release (v 15.05)
by Jennifer Hillman-Jackson 14 May '15

14 May '15

*The May 2015 Galaxy Release is out!* Release Notes v 15.05 <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html> Release Highlights - *Authentication Plugins* - Galaxy now has native support for LDAP and Active Directory via a new community developed authentication plugin system. - *Tool Sections* - Tool parameters may now be groupped into collapsable sections. - *Collection Creators* - New widgets have been added that allow much more flexibility when creating simple dataset pair and list collections. - And *much more <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html>* The release notes have a new home at Read the Docs <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html>. We hope that you like the new format as much as we do! *Thanks for using Galaxy! * The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Registration for the 2015 Galaxy Community Conference is OPEN! http://gcc2015.tsl.ac.uk *Love* *Galaxy*? We are inviting Galaxy power end-users as well as scientists and bioinformatics support researchers to *join us for the inaugural* *Galaxy Data Wrangling Hackathon* preceding the 2015 Galaxy Community Conference conference this July. http://gcc2015.tsl.ac.uk/data-hackathon

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user data in home folder and SGE integration
by Pablo Escobar 14 May '15

14 May '15

Hi, We have a test galaxy instance integrated with our SGE cluster. The filesystem is shared in the galaxy server and all the cluster compute nodes. Now we are submitting all the jobs as galaxy user and all the data is stored in the home folder for galaxy user. We plan to configure galaxy to submit the jobs to SGE as the real user as explained in docs https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_… and we would like that each user store their galaxy data in their personal home folder and not in the galaxy user home folder so each user can keep their private data not accesible to other users in the cluster and also to be able to do proper accounting of how much storage each user is using. Our main concern is about users keeping their data private, the storage usage accounting is something that would be nice but it's not so critical. Is this setup possible? Any advice or documentation about how to achieve this setup? thanks in advance for any help or suggestion. regards, Pablo.

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Installing DAVID Functional Annotation 1.0.0 in local instance
by Gabriele Zoppoli 14 May '15

14 May '15

Dear Dev group, I can't find a way to install the DAVID Functional Annotation tool on our local instance of Galaxy. I have tried on both the Main and the test Tool Sheds, and all I come up to, if I look for DAVID 1.0.0 on the Main one, is a repository named "sharplabtool", with a dead link: toolshed.g2.bx.psu.edu/repos/xuebing/sharplabtool/hgv_david/1.0.0 Can anybody help me to solve this problem? Thanks in advance! -- Gabriele Zoppoli, MD Ph.D., Clinical and Experimental Oncology and Hematology Internal Medicine Specialist Assistant Professor, DiMI, IRCCS AOU San Martino IST, Genova, IT Member of the Board of Directors, Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC) ---------------------------------------------------------- Ζεῦ πάτερ ἀλλὰ σὺ ῥῦσαι ὑπ' ἠέρος υἷας Ἀχαιῶν, ποίησον δ' αἴθρην, δὸς δ' ὀφθαλμοῖσιν ἰδέσθαι: ἐν δὲ φάει καὶ ὄλεσσον, ἐπεί νύ τοι εὔαδεν οὕτως. *Father Zeus, at least deliver the sons of Acheans from the gloom,* *And make clear the air, and give it to our eyes to see.* *In the light destroy us, since to do thus pleases you. (Il. 17, 645-7)*

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Planemo test fail if sys.error writen to
by Christian Brenninkmeijer 14 May '15

14 May '15

Hi, I have noticed that Planemo (0.11.1) causes tests to fail if anything is written to sys.error. For example if I test the following simple python: import sys if __name__ == '__main__': #sys.stderr.write("This is a test") print "Done" My test pass; But if I remove the comment: import sys if __name__ == '__main__': sys.stderr.write("This is a test") print "Done" The test fails! Is there a way to tell planemo that it is ok if the program writes to sys.error? Assuming of course a normal 0 exit as above. Without this it wuld be impossible to test any tool that wraps code that writes to sys.error such things as warning message up %done. Thanks in advance Christian Brenninkmeijer University of Manchester

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