galaxy-dev August 2014

galaxy-dev@lists.galaxyproject.org

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102 discussions

September 2014 Galaxy News
by Dave Clements 29 Aug '14

29 Aug '14

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Grouping of tools inside of toolbox does not work
by Björn Grüning 28 Aug '14

28 Aug '14

Hi, I have multiple version of the ncbi-blast+ wrapper installed. But they appear twice or a few of them even tripled in the toolbox. Expected behavior is only one tool in the toolbox and a select box inside of the tool. I have prepared a docker galaxy-blast container as test case. https://registry.hub.docker.com/u/bgruening/galaxy-blast/ https://github.com/bgruening/docker-recipes/tree/master/galaxy-blast Reproducible bugs with Docker! Cheers, Bjoern

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refresh_on_change : is this a valid attribute? Any other ideas/options??
by Lukasse, Pieter 27 Aug '14

27 Aug '14

Hi, I'm trying to get a wrapper from someone else working and I found this "refresh_on_change" attribute in his select boxes which are filled using the dynamic_options feature: <param name="col_type" type="select" label="Select column type" refresh_on_change="true" display="radio" dynamic_options='get_column_type(library_file)' help="" /> <param name="polarity" type="select" label="Select polarity" refresh_on_change="true" display="radio" dynamic_options='filter_column(library_file,col_type)' help="" /> ... When searching the documentation/wiki I do not find a reference to this, but it would be a nice option to have ;) Question: is there any way I can force a refresh when the user selects another option from such a select box. As you can see in the example above, this is needed because the next select box has its dynamic options built up by a function that takes the value from the previous select (col_type - highlighted above) as an input parameter. Currently this tool only works by showing each select in its own <page> , which is a deprecated option and prevents the tool from being used in a workflow... :( Thanks for your help! Best regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Multiple output datasets
by Martin Christiansen 27 Aug '14

27 Aug '14

Hi all, I'm implementing a tool for our local galaxy instance which has multiple output datasets. The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files. As I understand, the $__new_file_path__ option is changed in the universe_wsgi.ini file. Regardless, the extra files created from the tool does not show in the galaxy history. Any ideas? Best, Martin Christiansen

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Re: [galaxy-dev] Cluster jobs running as real user
by Linda Cham 27 Aug '14

27 Aug '14

Follow the Galaxy wiki https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_… setup permission instructions. Follow these 2 steps to get Galaxy to run as real users with IBM Platform LSF: Step 1) Download the latest LSF DRMAA 1.1.1 from github. https://github.com/PlatformLSF/lsf-drmaa Level commit e4d5c1ab10fcba572eaede68fc2fc05332198bec or above This fixes the LSF job id not found issue. Step 2) LSF needs to disable message being printed out via the LSF environment variable "BSUB_QUIET". This can be done either in in Galaxy drmaa_external_runner.py file or in the galaxy admin environment profile Edit the drmaa_external_runner.py file to add in the LSF environment variable "BSUB_QUIET" to disable message print out. Line in blue below. scripts/drmaa_external_runner.py: def main(): userid, json_filename, assign_all_groups = validate_paramters() set_user(userid, assign_all_groups) json_file_exists(json_filename) os.environ['BSUB_QUIET'] = 'Y' s = drmaa.Session() s.initialize() jt = s.createJobTemplate() load_job_template_from_file(jt, json_filename) OR Disable LSF message in the galaxy admin profile e.g. export BSUB_QUIET=Y in .bash_profile Regards, Linda

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proxy / ssl
by Shrum, Donald C 26 Aug '14

26 Aug '14

Thanks for the help today Eric... I'm not sure if this is worth adding to the docs but I thought I'd post it in case someone would like to. I have an apache proxy setup for galaxy with ldap authentication. I wanted the user sign on to be over https as users are using their HPC accounts to sign in. I modified /etc/httpd/conf/httpd.conf to redirect requests from http to https: RewriteEngine On RewriteCond %{HTTPS} !=on RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L] I then added the proxy configuration to /etc/httpd/conf.d/ssl.conf to the virtual host section: <VirtualHost _default_:443> 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]

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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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galaxy-dev August 2014