- galaxy-dev - lists.galaxyproject.org

Galaxy's recent problems
by Dave Clements 13 Apr '11

13 Apr '11

Hello all, Galaxy has been ill recently due to disk space on the server filling up. In the short term we are working on freeing up space. In the longer term we are working on adding a quota system to limit how much space any one user can take, and we've also ordered a lot more disk. In the mean time, *please take a look at your saved histories and datasets and delete anything you no longer need*. This will greatly help us get through the current rough patch. In the longer term, you can also consider setting up your own local Galaxy instance, or running Galaxy on the cloud. See: http://getgalaxy.org/ https://bitbucket.org/galaxy/galaxy-central/wiki/cloud Thanks for your patience while we work this out, Dave C and the Galaxy Team -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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direct http links from galaxy
by Sarah Diehl 13 Apr '11

13 Apr '11

Hello, currently we are using Galaxy as our main data storage to try and keep as few duplicates of the data as possible. However, some of our biologists prefer to view their data for example in IGV. Due to the many files it is bothersome for them to download all the data to their own computer to display it (they are running out of disc space). IGV has the possibility to access data through an http link, but the download links in Galaxy don't work, because they do not have a file ending. So my question is: is there a way to get an http link from Galaxy that directly points to the file? Best regards, Sarah Diehl

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MySQL to PostgreSQL migration scripts available here
by Louise-Amélie Schmitt 13 Apr '11

13 Apr '11

Hello everyone I finally managed to finish my two scripts. It's kind of dirty coded (I'm not a Perl fan + I was in a hurry), but at least they worked for me. I could successfully transfer the data from an old MySQL Galaxy to my new PSQL Galaxy. Before running the scripts, you should already have run your new Galaxy instance so that the tables are properly created. Please note that the scripts will erase everything the target database might contain. It's aimed to make a 'clone' of the old database, not to merge both. Here is how to do the transfer: Requirements: DBD::mysql and DBD:Pg Perl modules 1: run galaxy-My2Pg.pl with the appropriate arguments (see the comments in the script's first lines) 2: start your Galaxy instance If the galaxy instance starts without throwing a fit, you can probably stop here. (I didn't have that chance though) Otherwise you most certainly have the wrong database version: 3: run sh manage_db.sh upgrade (to get the version right) 4: run galaxy-My2Pg_fix-seq.pl with the appropriate arguments blah, it will set the sequences at the right number since manage_db.sh seems to mess them up. Please note that even if it might work for some other databases, it was only tested on Galaxy, and I decline any responsibility if it doesn't work, throws data trhough the windows or blows your whole office up. You should back your data up beforehand in any case. Cheers, LA

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Re: [galaxy-dev] Apache configuration problem?
by Yu Wang 12 Apr '11

12 Apr '11

hi, sarah, sorry for the confusion. I did change those lines with my own directories. And the files are readable for others. Regards, Yu Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.wang(a)wzw.tum.de D-85354 Freising Germany

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Apache configuration problem?
by Yu Wang 12 Apr '11

12 Apr '11

Hello, I installed Galaxy on Fedora 13. Everything works fine at http://127.0.0.1:8080 Then I followed instruction from https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. I add the following lines to httpd.conf: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/nate/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/nate/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/nate/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/nate/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] and changed universe_wsgi.ini with [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I restarted Apache and Galaxy. At http://127.0.0.1:8080 everything works fine but at http://xx.xx.xx.xx/galaxy I got a scrambled page. Apache error log said "[Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/base.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/tool_menu.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/jquery.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/galaxy.base.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu " Can anyone point out what was configured wrong? Many thanks in advance. Best regards, Yu Wang Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.wang(a)wzw.tum.de D-85354 Freising Germany

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"fetch failed" error during first execution of run.sh
by Paul Cantalupo 12 Apr '11

12 Apr '11

Hello, I downloaded galaxy-central with the command "hg clone https://bitbucket.org/galaxy/galaxy-central". Then I changed directory to "cd galaxy-central/" and typed "sh run.sh". I got the following output: ..... Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in res olve egg.resolve() File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, in res olve return self.version_conflict( e.args[0], e.args[1] ) File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, in ver sion_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/usr/local/galaxy-central/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.3.0 Fetch failed. (2812) sirius-pipas:/usr/local/galaxy-central $ What do I try now? I'm working in a Cygwin environment and my python version is 2.6.5. Thank you, Paul U. of Pitt

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Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th!
by Brad Chapman 12 Apr '11

12 Apr '11

Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (Lawrence Hunter and Matt Wood) and session topics that include parallel and cloud-based approaches to bioinformatics, genome content management, and tools for next-generation sequencing. We'd love to hear about your Open Source bioinformatics project! The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) July 15-16, 2011, in Vienna, Austria http://www.open-bio.org/wiki/BOSC_2011 Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. All students whose abstracts are accepted for talks will be considered for this award. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor

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postgresql to galaxy
by hari krishna 12 Apr '11

12 Apr '11

Hi, I am planning to change database from sqlite to postgresql . for this i installed postgresql 8.1.2 and created user and database at my home location. from my home i can able to login to that database psql -d galaxy -U galaxy -h 192.168.65.8 where database and user name as galaxy and hostname I modified universal.wsgi.ini file as database_connection =postgres:///galaxy<?user=galaxy&password=galaxy123!@#[?host=/var/run/postgresql] database_engine_option_strategy = threadlocal database_engine_option_server_side_cursors = True database_engine_option_pool_size = 5 database_engine_option_max_overflow = 10 after these modification when i ran the server am getting error like this: ***************************** Traceback (most recent call last): File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/app.py", line 30, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py", line 80, in connect raise exc.DBAPIError.instance(None, None, e) OperationalError: (OperationalError) FATAL: no pg_hba.conf entry for host "[local]", user "galaxy", database "galaxy<", SSL off ********************************************* Can any one help me for integrating postgresql to galaxy.... waiting for ur kind reply -- Thanks & Regards, Hari Krishna .M

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Re: [galaxy-dev] Fwd: configuration of reports at galaxy
by Hans-Rudolf Hotz 12 Apr '11

12 Apr '11

On 04/12/2011 09:20 AM, hari krishna wrote: > Hi, > Thanks for your immediate reply, > ya same thing i tried but i cant able to open that page.. giving > error as "" cant able to locate http://<your host>:<different port number>/ > address " is coming . > my be i did wrong at configuration , can you give proper link for > that. > always do a 'reply all' so everybody can benefit from any comments/questions.... do you mean the link to the wiki? https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010… Hans > On Tue, Apr 12, 2011 at 12:35 PM, Hans-Rudolf Hotz<hrh(a)fmi.ch> wrote: > >> Hi >> >> are you looking at the right page? The "reports" are not part of the admin >> view. You have to go to a different URL which probably looks like: >> >> >> http://<your host>:<different port number>/ >> >> see the "June 8, 2010 New Development News Brief" for a quick explanation >> >> >> >> Regards, Hans >> >> >> >> >> On 04/12/2011 08:32 AM, hari krishna wrote: >> >> >>> Hi, >>> hi can any one explain how can i get reports per tool option in >>> galaxy, >>> I tried by configurating reports_wsgi.ini by changing the different >>> port number. >>> and started #sh ru_reports.sh >>> >>> As an galaxy administrator i didnt find the "Jobs per tool" option. >>> >>> can any one explain the configuration procedure for getting "job per >>> tool" option. >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> 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/ >>> >> > >

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configuration of reports at galaxy
by hari krishna 12 Apr '11

12 Apr '11

Hi, hi can any one explain how can i get reports per tool option in galaxy, I tried by configurating reports_wsgi.ini by changing the different port number. and started #sh ru_reports.sh As an galaxy administrator i didnt find the "Jobs per tool" option. can any one explain the configuration procedure for getting "job per tool" option. -- Thanks & Regards, Hari Krishna .M

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