May 2016 - galaxy-dev - lists.galaxyproject.org

Bug Found: 2 tabs in browser open to different histories confuses tools
by Ryan G 31 May '16

31 May '16

Hi all - I think I found a bug. I have two histories open in two separate tabs in Chrome. When I try to run a tool and select an item from my history, the wrong history items are displayed. Ryan

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Problem running bwa-mem
by C. Ch. 31 May '16

31 May '16

Hi all, When running bwa-mem (installed version 0.7.12.1) I get an empty result with the stderr giving the following error: [main] Version: 0.7.12-r1039 [main] CMD: bwa mem -t 1 -v 1 -I 180 localref.fa /home/galaxy/galaxy/database/files/001/dataset_1958.dat /home/galaxy/galaxy/database/files/001/dataset_1961.dat [main] Real time: 12964.149 sec; CPU: 13152.174 sec [bam_sort_core] merging from 50 files... open: No such file or directory [bam_merge_core] fail to open file /home/galaxy/galaxy/database/files/016/dataset_16712.dat.0000 But the files exist and have the .bam extension (i.e. .../016/dataset_16712.dat.000.bam). How can I solve this? Thanks, Cristian

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SFTP settings
by Durdevic, Marija 30 May '16

30 May '16

Is there anyone who manage to setup SFTP for Glaxay and that can help me please???

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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 26 May '16

26 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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