- galaxy-dev - lists.galaxyproject.org

PLINK 1.90 wrapper
by Jochen Bick 30 May '16

30 May '16

Hi all, I just found the plink tool in two version 1.9 and 1.7. It looks like that it has no wrapper yet? Is it possible that the owner gives a feedback about this? We are are very interested in that tool. Cheers Jochen

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Error in Deleting datasets
by nazeer＠ibe.med.uni-muenchen.de 30 May '16

30 May '16

Hello, We are using galaxy 15.10 in our production machine. I had to delete several intermediate datasets from many histories in order to save some space. The command I used is as follows, ''' #EVERYTHING WORKED FINE BEFORE I DID THE FOLLOWING #SHOULDN'T HAVE DONE IT! ''' requests.put(gi._make_url(gi.histories, module_id=module_id, contents=True) + "/" + dataset_id, data=json.dumps({"deleted": True, "purged" : True}), params=gi.default_params) Once I used this, the galaxy interface showed an error message (attached with this email) I did a temporary fix by placing empty files of those datasets which were deleted (eg: touch dataset_1.dat) But, after using the python command, any dataset which are deleted permanently(from galaxy interface or commandline) resulted in this same error. I even tried THE microsoft solution("restarting"). Didn't help. I apologize for my long email. Kindly let me know if anyone faced this issue. Any info would be of great help! Thank you all in advance, Aarif

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Problems using LDAP authentification
by Fahrenholz, Jan-Nikolas 26 May '16

26 May '16

Dear list, I have some problems using the LDAP module for registering users... User which have been previously created by the admin user can login without any problems, but Galaxy won't create new ones for first-time users. Here's my auth.conf: <?xml version="1.0"?> <auth> <authenticator> <type>ldap</type> <filter>'{email}'.endswith('@gwdg.de')</filter> <options> <allow-register>False</allow-register> <auto-register>True</auto-register> <allow-password-change>False</allow-password-change> <server>ldap://ldap.gwdg.de</server> <login-use-username>True</login-use-username> <search-fields>dn,mailAddresses,uid</search-fields> <search-base>ou=Users,dc=gwdg,dc=de</search-base> <search-filter>(&(uid={username})(platforms=*HPC*))</search-filter> <search-user>cn=searchuser,ou=gwdgadm,dc=gwdg,dc=de</search-user> <search-password>supersecretpassword</search-password> <bind-user>{dn}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{uid}</auto-register-username> <auto-register-email>{email}</auto-register-email> </options> </authenticator> I already tried several different combinations of <bind-user>, <search-filter> and <auto-register-username>, but still get the following error: galaxy.auth.providers.ldap_ad DEBUG 2016-05-26 10:30:39,675 LDAP authenticate: email is glxytest(a)gwdg.de galaxy.auth.providers.ldap_ad DEBUG 2016-05-26 10:30:39,675 LDAP authenticate: username is None galaxy.auth.providers.ldap_ad DEBUG 2016-05-26 10:30:39,675 LDAP authenticate: options are {'bind-user': '{dn}', 'search-fields': 'dn,mailAddresses,uid', 'login-use-username': 'True', 'allow-register': 'Challenge', 'auto-register-email': '{email}', 'server': 'ldap://ldap.gwdg.de', 'auto-register': 'True', 'search-base': 'ou=Users,dc=gwdg,dc=de', 'search-filter': '(uid={username})', 'continue-on-failure': 'False', 'auto-register-username': '{uid}', 'search-password': 'supersecretpassword', 'search-user': 'cn=searchuser,ou=gwdgadm,dc=gwdg,dc=de', 'bind-password': '{password}', 'allow-password-change': 'False'} galaxy.auth.providers.ldap_ad DEBUG 2016-05-26 10:30:39,675 LDAP authenticate: username must be used to login, cannot be None galaxy.auth DEBUG 2016-05-26 10:30:39,675 Email: , Username , stopping due to failed non-continue I entered "glxytest" as user on the frontend (as I only want to use the username to log in) and it seems that the module converts that to {email} field and misses the {username} field?! Do I have to change my galaxy.ini (mailing is not configured and user_activation_on = False) or am I missing something simple? Thanks for any recommendations! Jan-N. Fahrenholz-------------------GWDG------------- Arbeitsgruppe "Nutzerservice und Betriebsdienste" Tel. +49(0)551/201-1791 Raum C2 E-Mail: jfahren1(a)gwdg.de<mailto:jfahren1@gwdg.de> ------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG), Am Fassberg 11, 37077 Göttingen URL: http://www.gwdg.de<http://www.gwdg.de/> E-Mail: gwdg(a)gwdg.de<mailto:gwdg@gwdg.de> Tel. +49 (0)551 201-1510 Fax +49 (0)551 201-2150 Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Christian Griesinger Sitz der Gesellschaft: Göttingen Registergericht: Göttingen Handelsregister-Nr. B 598 Zertifiziert nach ISO 9001 -----------------------------------------------------------

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Unsorted BAM file --> Galaxy crash?
by Raymond Wan 25 May '16

25 May '16

Dear all, We are experiencing a crash of our Galaxy instance (latest git log is early January 2016) and it seems unable to restart. The last entries in paster.log says the following: galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,622 Enabling 'history_contents' API controller, class: HistoryContentsController [bam_index_core] the alignment is not sorted (XXX): 21-th chr > 11-th chr [bam_index_build2] fail to index the BAM file. galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,632 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController [bam_index_core] the alignment is not sorted (XXX): 24-th chr > 9-th chr [bam_index_build2] fail to index the BAM file. galaxy.datatypes.metadata DEBUG 2016-05-24 17:46:42,638 setting metadata externally failed for HistoryDatasetAssociation 442: External set_meta() not called galaxy.jobs.runners.slurm WARNING 2016-05-24 17:46:42,642 (313/189770) Job not found, assuming job check exceeded MinJobAge and completing as successful So, the system cannot start and if we visit the site, it says "503 Service Temporarily Unavailable". The log file seems to indicate some problem with the sorting of the BAM file. The problem looks a bit like something from 9 months ago (https://www.biostars.org/p/159336/) but the messages I've seen do not indicate that the problem prevents Galaxy from starting up. I would have thought if there is a problem with the input file, the job would have failed, but not affect Galaxy from starting up again. So, I'm wondering if that is the problem or maybe it's the line after about, "setting metadata externally failed" Has anyone seen this problem before or might have an idea about what to do about it? Thank you in advance! Ray

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Question: How to limit the number of dispatched jobs in Galaxy?
by George Weingart 25 May '16

25 May '16

Hi Is there a way to control the demand that Galaxy is putting on the server by limiting the number of jobs that will dispatch at a time ? Thanks! George Weingart PhD Huttenhower Lab Harvard School of Public Health

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setting up a local galaxy instance - need sftp help
by Jessica Grant 25 May '16

25 May '16

Hello, I have a local instance running - I see the page with instructions for setting up an ftp server, but my institution prefers I use sftp, which is already installed. Can I get help/info about configuring galaxy to accept this? Thanks! Jessica -- Jessica Grant Research Associate, Williams Lab 205C Ford Hall Smith College Northampton, MA 413-585-4341

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Current history via the REST API (or blend4j)
by Suderman Keith 25 May '16

25 May '16

I have been looking at the JavaDoc for Blend4J [1] and the REST API [2], but I don’t see any way to obtain the “current” history as selected by the user in the Galaxy UI. I see `/api/histories/most_recently_used`, but it seems that simply selecting a history as the current history in the UI does not make it the “most recently used” (MRU) history; I guess the user has to actually _do_ something with before it becomes the MRU history. Am I missing something? Failing the above, is there some way to get the history ID from the UI? Thanks, Keith REFERENCES 1.http://jmchilton.github.io/blend4j/apidocs/ 2. https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#… ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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sftp over proftpd and postgresql
by Durdevic Marija 25 May '16

25 May '16

Dear all, I am trying to setup sftp connection for my new Galaxy server. I managed to configure sftp_module and I am able to connect to the server as an system user. The problem is that I am not able to login there as Galaxy user. I guess that the problem is with settings for backend and postgresql, but I don't know how to solve it. My configuration for sql is: # Do not authenticate against real (system) users AuthPAM off # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 SQLLogFile /home/galaxy/galaxy/log_files/sqlLog.txt SQLPasswordEngine on SQLPasswordEncoding hex # Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy@localhost:5432 galaxy SQLAuthTypes SHA1 SQLAuthenticate users # An empty directory in case chroot fails SQLDefaultUID 1001 SQLDefaultGID 1001 SQLDefaultHomedir /var/lib/proftpd/empty # Define a custom query for lookup that returns a passwd-like entry. UID and GID should match your Galaxy user. SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,'1001','1001','/home/data/galaxy_ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" Db name is galaxy, user is galaxy, no pass. Any recommendation, please? Regards, Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)medunigraz.at Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

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wheels.galaxyproject.org
by Patrice Dehais 24 May '16

24 May '16

Hello Since yesterday I've the following warning at Galaxy () start-up : Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x3149390>, 'Connection to wheels.galaxyproject.org timed out. (connect timeout=15)')': /simple/pip For running instances, it's not a problem, but I'm trying to install a fresh one today, and of course, I can't go further ... Is it a local problem on my side, or a more general problem on the server side (wheels.galaxyproject.org) ? Thanks Patrice -- Patrice Dehais : INRA - GenPhySE - SIGENAE, 24, chemin de Borde-Rouge Auzeville Tolosane CS 52627 31326 Castanet Tolosan cedex France tel: +33(0)5.61.28.57.08 fax: +33(0)5.61.28.53.08 http://www.sigenae.org

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It 's possible to purge deleted datasets with last galaxy code ?
by Sarah Maman 24 May '16

24 May '16

Hello, I have a local instance of Galaxy with the latest code version. In 2015's code, it was possible to purge deleted datasets. With the lastest code, in history menu, we do not find the possibility to purge deleted datasets. Could you please explain us how to purge dataset and not only hidde these datasets ? Thanks in advance, Sarah Maman -- Sarah Maman INRA - GenPhySE - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

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