- galaxy-dev - lists.galaxyproject.org

Developer Events in Europe this Fall: Swiss-German Galaxy Tour
by Dave Clements 26 Aug '14

26 Aug '14

Hello all, The *2014 Swiss-German Galaxy Tour <https://wiki.galaxyproject.org/Events/SG2014>* is happening from 30 September through 2 October. The tour features 3 events and they will all be great ways to meet fellow developers, and learn more about defining tools and deploying and administering Galaxy. Space is limited at all these events, so if you are interested, *you are strongly encouraged to register now*. The tour is organized (and hosted) by Hans-Rudolf Hotz and Björn Grüning. The events are: *Galaxy Training and Demo Day <https://wiki.galaxyproject.org/Events/Switzerland2014/trainingday>* 30 September Bern, Switzerland *(second Swiss) Galaxy Workshop <https://wiki.galaxyproject.org/Events/Switzerland2014> * 1 October Bern, Switzerland *German Galaxy Developers Day <https://wiki.galaxyproject.org/Events/Germany2014> * 2 October Freiburg, Germany There are also several events for Galaxy Users planned this fall. See the Galaxy Events page <https://wiki.galaxyproject.org/Events> for more. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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problems with database migration 119 -> 120
by Hans-Rudolf Hotz 26 Aug '14

26 Aug '14

Hi all I am in the process of updating our galaxy servers (from "release_2014.04.14" to "latest_2014.08.11"). when I execute ~/lib/galaxy/model/migrate/versions/0120_dataset_collections.py as part of the 'manage_db.sh upgrade' I run into a bizarre error: First, it produces 10 "Mysql 1050 Error 'Table already exists' ", I have encountered this before, and usually everything is fine. The table gets created and for whatever reason, the command get's executed a second time - no big deal. However, this time for two of those ten table the situation has been different. As usual, I have checked all the tables (where I got the errors) with the MySQL command describe <table>. For two tables: history_dataset_collection_association library_dataset_collection_association the order of the columns was wrong (ie did not correspond to the order in the create statement) - see below for example. I have dropped the tables and executed the create statements manually, everything seems fine, eg mysql> describe library_dataset_collection_association; +---------------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +---------------+--------------+------+-----+---------+----------------+ | id | int(11) | NO | PRI | NULL | auto_increment | | collection_id | int(11) | YES | MUL | NULL | | | folder_id | int(11) | YES | MUL | NULL | | | name | varchar(255) | YES | | NULL | | | deleted | tinyint(1) | YES | | NULL | | +---------------+--------------+------+-----+---------+----------------+ 5 rows in set (0.00 sec) mysql> drop table library_dataset_collection_association; Query OK, 0 rows affected (0.02 sec) mysql> CREATE TABLE library_dataset_collection_association ( -> id INTEGER NOT NULL AUTO_INCREMENT, -> collection_id INTEGER, -> name VARCHAR(255), -> deleted BOOL, -> folder_id INTEGER, -> PRIMARY KEY (id), -> FOREIGN KEY(collection_id) REFERENCES dataset_collection (id), -> CHECK (deleted IN (0, 1)), -> FOREIGN KEY(folder_id) REFERENCES library_folder (id) -> ); Query OK, 0 rows affected (0.01 sec) mysql> describe library_dataset_collection_association; +---------------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +---------------+--------------+------+-----+---------+----------------+ | id | int(11) | NO | PRI | NULL | auto_increment | | collection_id | int(11) | YES | MUL | NULL | | | name | varchar(255) | YES | | NULL | | | deleted | tinyint(1) | YES | | NULL | | | folder_id | int(11) | YES | MUL | NULL | | +---------------+--------------+------+-----+---------+----------------+ 5 rows in set (0.00 sec) mysql> Has anyone else (among those few who are still using MySQL) seen something similar? Regards, Hans-Rudolf PS: Please don't make any comments about the fact, that I should change to PostgreSQL. I am more than aware of that, and eventually, I will do it. ;) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Galaxy and object stores
by Raknes Inge Alexander 26 Aug '14

26 Aug '14

?I have a few questions about object stores in Galaxy: 1: Can all Galaxy data sets be stored in an object store? 2: If so, does Galaxy still need to maintain a local copy of the data? 3: Is LWR or Pulsar able to get the data directly from the object store, or does it still have to go through Galaxy? We are planning to let users of our Galaxy installation handle large input/output files (~30G) and we expect that the VM containing our Galaxy installation will become a bottleneck if all data needs to travel through that node. - Inge Alexander Raknes

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Re: [galaxy-dev] ssl proxy
by Eric Rasche 26 Aug '14

26 Aug '14

> is just an apache page Is it an error page/the default index.html/other? Next: Are you doing the proxying with mod_proxy or with mod_rewrite? mod_rewrite looks like RewriteRule ^(.*) https://144.174.51.187:8080$1 [P] while mod_proxy looks like ProxyPass / http://localhost:8080/ ProxyPassReverse / http://localhost:8080/ Cheers, Eric On 08/26/2014 09:39 AM, Shrum, Donald C wrote: > If I go directly to https://galaxy.rcc.fsu.edu what I get is just an apache page. It's not doing the proxy to galaxy. > > The debug shows... > [Tue Aug 26 10:36:45 2014] [debug] proxy_util.c(1837): proxy: worker proxy:reverse already initialized > [Tue Aug 26 10:36:45 2014] [debug] proxy_util.c(1934): proxy: initialized single connection worker 0 in child 21513 for (*) > [Tue Aug 26 10:36:46 2014] [debug] proxy_util.c(1818): proxy: grabbed scoreboard slot 0 in child 21514 for worker proxy:reverse > [Tue Aug 26 10:36:46 2014] [debug] proxy_util.c(1837): proxy: worker proxy:reverse already initialized > > -----Original Message----- > From: Eric Rasche [mailto:rasche.eric@yandex.ru] > Sent: Tuesday, August 26, 2014 10:34 AM > To: Shrum, Donald C > Subject: Re: [galaxy-dev] ssl proxy > >> not forwarded to the galaxy server > > hmm. (technically it shouldn't be forwarding, once you hit https, it should display galaxy directly). Is it just a blank white screen or a proper error code? > > Why don't you increase the log level and see if anything shows up in the logs? Add > >> LogLevel debug > > and then tail all of your apache logs. What do those look like when you request https://your-domain/ ? > > Cheers, > Eric > > On 08/26/2014 09:25 AM, Shrum, Donald C wrote: >> I get a redirect from http to https but then I'm not forwarded to the galaxy server. >> >> If you have a suggestion I'll take it and thanks for the help with this. >> >> -----Original Message----- >> From: Eric Rasche [mailto:rasche.eric@yandex.ru] >> Sent: Tuesday, August 26, 2014 10:19 AM >> To: Shrum, Donald C; Kandalaft, Iyad >> Cc: galaxy-dev(a)lists.bx.psu.edu >> Subject: Re: [galaxy-dev] ssl proxy >> >> What issues are you still seeing? How is it non-functional? >> >> >> On 08/26/2014 08:32 AM, Shrum, Donald C wrote: >>> I think I'd also need to change the proxy config to include the https >>> >>> <Proxy *> >>> AddDefaultCharset off >>> Order Deny,Allow >>> Allow from all >>> </Proxy> >>> >>> <Proxy https://144.174.51.187:8080> >>> Order deny,allow >>> Allow from all >>> </Proxy> >>> >>> >>> Even with that and your change... no luck. I'll keep tinkering. >>> >>> -----Original Message----- >>> From: Kandalaft, Iyad [mailto:Iyad.Kandalaft@AGR.GC.CA] >>> Sent: Tuesday, August 26, 2014 8:44 AM >>> To: Shrum, Donald C; Eric Rasche >>> Cc: galaxy-dev(a)lists.bx.psu.edu >>> Subject: RE: [galaxy-dev] ssl proxy >>> >>> Sorry Don, I forgot the http"s" in the proxy line: >>> RewriteRule ^(.*) https://144.174.51.187:8080$1 [P] >>> >>> That should do it :) >>> >>> >>> >>> Iyad Kandalaft >>> >>> >>> -----Original Message----- >>> From: Shrum, Donald C [mailto:DCShrum@admin.fsu.edu] >>> Sent: Monday, August 25, 2014 9:27 PM >>> To: Kandalaft, Iyad; Eric Rasche >>> Cc: galaxy-dev(a)lists.bx.psu.edu >>> Subject: RE: [galaxy-dev] ssl proxy >>> >>> I'm not using a virtual host. Apache is just there as a proxy. I tried the rewrite rules below... >>> >>> I get a redirect from 80 to 443 as expected for the ldap authentication. After authenticating I do not get redirected to 8080 for galaxy. I've tried a few different ways and always get that. I'll dig in tomorrow morning and after some coffee to see if I can figure it out. >>> >>> It's probably worth posting the solution in the docs. >>> >>> -----Original Message----- >>> From: Kandalaft, Iyad [mailto:Iyad.Kandalaft@AGR.GC.CA] >>> Sent: Monday, August 25, 2014 8:42 PM >>> To: Eric Rasche; Shrum, Donald C >>> Cc: galaxy-dev(a)lists.bx.psu.edu >>> Subject: RE: [galaxy-dev] ssl proxy >>> >>> Hi Eric >>> >>> I'm not sure that he is using a virtual host on 443. I suppose that a "redirect permanent" would work in either case, but I was thinking along the lines of: >>> >>> >>> RewriteEngine On >>> >>> RewriteCond %{HTTPS} !=on >>> >>> RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L] >>> >>> RewriteRule ^/static/style/(.*) >>> /panfs/storage.local/opt/galaxy-dist/static/june_2007_style/blue/$1 >>> [L] RewriteRule ^/static/scripts/(.*) >>> /panfs/storage.local/opt/galaxy-dist/static/scripts/packed/$1 [L] >>> RewriteRule ^/static/(.*) >>> /panfs/storage.local/opt/galaxy-dist/static/$1 [L] RewriteRule >>> ^/favicon.ico /panfs/storage.local/opt/galaxy-dist/static/favicon.ico >>> [L] >>> >>> RewriteRule ^/robots.txt >>> /panfs/storage.local/opt/galaxy-dist/static/robots.txt [L] >>> RewriteRule >>> ^(.*) http://144.174.51.187:8080$1 [P] >>> >>> >>> What do you think? >>> >>> >>> >>> Iyad Kandalaft >>> Bioinformatics Programmer >>> Microbial Biodiversity Bioinformatics Science & Technology Branch >>> Agriculture & Agri-Food Canada Iyad.Kandalaft(a)agr.gc.ca | (613) >>> 759-1228 ________________________________ >>> From: galaxy-dev-bounces(a)lists.bx.psu.edu >>> [galaxy-dev-bounces(a)lists.bx.psu.edu] on behalf of Eric Rasche >>> [rasche.eric(a)yandex.ru] >>> Sent: August 25, 2014 4:21 PM >>> To: DCShrum(a)admin.fsu.edu >>> Cc: galaxy-dev(a)lists.bx.psu.edu >>> Subject: Re: [galaxy-dev] ssl proxy >>> >>> We use: >>> >>> <VirtualHost *:80> >>> ServerName <our.server.fqdn> >>> DocumentRoot "/var/www/" >>> <Directory "/var/www/"> >>> Options Indexes FollowSymLinks MultiViews >>> AllowOverride None >>> Require all granted >>> </Directory> >>> Redirect permanent / >>> https://<UrlBlockedError.aspx><our.server.fqdn>/ >>> </VirtualHost> >>> >>> Ours is managed with puppet so I've tried to redact the non-relevant blocks, but that should work for you. >>> >>> Cheers, >>> Eric >>> >>> On 08/25/2014 03:03 PM, Shrum, Donald C wrote: >>>> Hi all, >>>> >>>> I have a galaxy install with an apache proxy and ldap authentication. >>>> >>>> <Location /> >>>> RequestHeader set X-URL-SCHEME https >>>> AuthBasicProvider ldap >>>> Other stuff.... >>>> </Location> >>>> >>>> RewriteEngine on >>>> RewriteRule ^/static/style/(.*) >>>> /panfs/storage.local/opt/galaxy-dist/static/june_2007_style/blue/$1 >>>> [L] RewriteRule ^/static/scripts/(.*) >>>> /panfs/storage.local/opt/galaxy-dist/static/scripts/packed/$1 [L] >>>> RewriteRule ^/static/(.*) >>>> /panfs/storage.local/opt/galaxy-dist/static/$1 [L] RewriteRule >>>> ^/favicon.ico >>>> /panfs/storage.local/opt/galaxy-dist/static/favicon.ico >>>> [L] RewriteRule ^/robots.txt >>>> /panfs/storage.local/opt/galaxy-dist/static/robots.txt [L] >>>> RewriteRule >>>> ^(.*) http://144.174.51.187:8080$1 [P] >>>> >>>> What is the best way to manage the redirect from http to https for the authentication? >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this and other >>>> Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>> >>> >>> >>> Eric Rasche >>> Programmer II >>> Center for Phage Technology >>> Texas A&M University >>> College Station, TX 77843 >>> 404-692-2048 <tel:4046922048> >>> esr(a)tamu.edu<mailto:esr@tamu.edu> >>> <mailto:esr@tamu.edu><mailto:esr@tamu.edu> >>> -- >>> Eric Rasche Programmer II Center for Phage Technology Texas A&M >>> University College Station, TX 77843 404-692-2048 >>> esr(a)tamu.edu<mailto:esr@tamu.edu> >>> rasche.eric(a)yandex.ru<mailto:rasche.eric@yandex.ru> >>> >> > -- > Eric Rasche > Programmer II > Center for Phage Technology > Texas A&M University > College Station, TX 77843 > 404-692-2048 > esr(a)tamu.edu > rasche.eric(a)yandex.ru >

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ssl proxy
by Shrum, Donald C 26 Aug '14

26 Aug '14

Hi all, I have a galaxy install with an apache proxy and ldap authentication. <Location /> RequestHeader set X-URL-SCHEME https AuthBasicProvider ldap Other stuff.... </Location> RewriteEngine on RewriteRule ^/static/style/(.*) /panfs/storage.local/opt/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /panfs/storage.local/opt/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /panfs/storage.local/opt/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /panfs/storage.local/opt/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /panfs/storage.local/opt/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://144.174.51.187:8080$1 [P] What is the best way to manage the redirect from http to https for the authentication?

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How to build an application that uses a set of files?
by George Weingart 23 Aug '14

23 Aug '14

Hello, I would like to get advice how to implement the following application into Galaxy: We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9. Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file. How would the xml look? Thanks! George Weingart

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Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
by Peter Cock 22 Aug '14

22 Aug '14

On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > I don¹t know what the stdout and stderr information was. I click on it but > nothing comes up. > > I installed from the main toolshed: > http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler > Yes, I did use the test toolshed for Mira 4. > > Regards, > > Marija If stdout and stderr are empty, this is consistent with MIRA never even starting (as suggested by the next bit of information below). On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > This is the error in history under MIRA log: > > tool error > An error occurred with this dataset:Unable to run job due to a > misconfiguration of the Galaxy job running system. Please contact a site > administrator. > > Regards, > > Marija That suggests your Galaxy job runner is not properly configured, and MIRA itself was never started. Are you the site administrator? Are other Galaxy tools working? Are other Galaxy tools installed from the ToolShed working? On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > One more thing. The data that I am trying to analyse are fastq files of > Ion Torrent reads. I have used them with other assemblers e.g., velvet, > CLC. > > Marija I have not personally used Ion Torrent, but that ought to be fine. Peter P.S. You forgot to CC the mailing list.

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Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
by Marija Atanaskovic 22 Aug '14

22 Aug '14

Mira doesn’t work on Galaxy. This is the log message I receive. Tool: Assemble with MIRA v3.4 Name: MIRA log Created: Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version: 0.0.10 Tool Version: None Tool Standard Output: stdout<http://130.56.251.91/datasets/d5f55b83db1f410a/stdout> Tool Standard Error: stderr<http://130.56.251.91/datasets/d5f55b83db1f410a/stderr> Tool Exit Code: None API ID: d5f55b83db1f410a Full Path: /mnt/galaxy/files/000/dataset_326.dat Input Parameter Value Note for rerun Assembly method De novo Assembly type Genome Assembly quality grade Accurate Backbones/reference chromosomes? false Sanger/Capillary reads? false 454 reads? false Solexa/Illumina reads? false Ion Torrent reads? true Ion Torrent reads file 10: R_2011_10_19_14_30_56_user_SN1-36_Auto_SN1-36_38.fastq Inheritance Chain MIRA log Also I can’t install Mira 4. This is the message I receive. Any suggestions. Thanks. Marija Tauschek -- Dr Marija Tauschek/Atanaskovic Robins-Browne Lab Dept Microbiology & Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia Tel: +61 3 8344 9927 Email: matan(a)unimelb.edu.au Internal Server Error Galaxy was unable to successfully complete your request URL: http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https… Module galaxy.web.framework.middleware.error:149 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> body = method( trans, **kwargs ) Module galaxy.web.framework:369 in decorator >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:983 in prepare_for_install >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> includes_tool_dependencies ) Module tool_shed.util.common_install_util:97 in get_dependencies_for_repository >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) Module tool_shed.util.shed_util_common:1036 in get_repository_for_dependency_relationship >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> ( name, owner, changeset_revision ) ) Module tool_shed.util.shed_util_common:1867 in url_join >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> parts.append( arg.strip( '/' ) ) AttributeError: 'NoneType' object has no attribute 'strip' extra data<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> full traceback<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> text version<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

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Database integrity error when installing new tools from toolshed
by Michael Ta 22 Aug '14

22 Aug '14

Hi, I updated a local Galaxy installation a while back and I followed the steps listed on one of the wiki pages. The update included changes to the database schema and I was careful to backup and restore it according to the directions. However, when I try to install new tools from the tool shed or update a tool to a new revision it does not complete successfully. The following error appears in the log file. File '/home/galaxy/galaxy-dist/lib/tool_shed/util/tool_util.py', line 761 in handle_tool_versions context.flush() File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py', line 114 in do File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1718 in flush File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1789 in _flush File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 331 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 475 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 64 in save_obj File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 558 in _emit_insert_statements File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1449 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.p y', line 331 in do_execute IntegrityError: (IntegrityError) duplicate key value violates unique constraint "tool_version_association_pk ey" DETAIL: Key (id)=(83) already exists. 'INSERT INTO tool_version_association (tool_id, parent_id) VALUES (%(tool_id)s, %(parent_id)s) RETURNING to ol_version_association.id' {'parent_id': 440, 'tool_id': 439} A few of the keys appear to be colliding with values already in the database, did I miss something when I updated and restored the database that is causing this? Thanks, -- Michael Ta

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Galaxy and HTTPS User-authentification
by Matthias Enders 22 Aug '14

22 Aug '14

Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authentification like described here (https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases) Is there any way of using https or an encryption-method for sending user email and password. With kind regards, Matthias Enders

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