galaxy-dev April 2011

galaxy-dev@lists.galaxyproject.org

78 participants
133 discussions

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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improved "view details" button
by Assaf Gordon 12 Apr '11

12 Apr '11

Hi, Kudos on the new "View Details" button implementation, both visually nice and less intrusive tooltips. However, you know me - I can't just give praise without complaining... 1. The "View Details" tooltip (the actual tooltip) is not using JQuery, so the yellow (browser native) tooltip is showing (at least in Firefox 3.5.6 and Chrome on Linux). Other buttons show the black JQuery tooltip. 2. The "modified" date (when viewing the details of a dataset) is a bit misleading: It doesn't give the modification date of the dataset (also: what exactly is "modification" ? all datasets in Galaxy are immutable). It seems that the modification date is affected by any modification to the history. Example: - load any existing old history. - click on "view details" for a dataset: "Created" and "Modified" are in the past, or even identical. - rename the history (and don't modify any other parameter/dataset) - click on "view details" for the same dataset: "Created" stays the same. "Modified" becomes today's date. That is confusing, because the dataset was definitely not modified today. -gordon

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update probelm...
by Liisa Koski 12 Apr '11

12 Apr '11

Hi I just tried to update my local installation of Galaxy but accidentally hit Ctr-C when it asked me a question added 285 changesets with 649 changes to 354 files local changed static/scripts/packed/jquery.jstore.js which remote deleted use (c)hanged version or (d)elete? interrupted! When I tried to do the update again...it says 'no changes found' But...after restarting my instance...I see that the changes did not get implemented. Is there a way to force this? Thanks in advance, Liisa

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another update problem
by Ryan Golhar 11 Apr '11

11 Apr '11

I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Question about cuffcompare tool implementation
by Assaf Gordon 11 Apr '11

11 Apr '11

Hello, I'm trying to write my own wrappers for Cufflinks,Cuffcompare,Cuffdiff, learning mostly by looking at the existing tools. I have a question regarding the multiple input/output implementation in CuffCompare: In CuffCompare, the XML can accept multiple input files (with a <repeat>), and the <output> section contains the following statements (labels removed for brevity): ========= <outputs> <data format="txt" name="transcripts_accuracy" label="" from_work_dir="cc_output" /> <data format="tabular" name="input1_tmap" label="" from_work_dir="input1.tmap" /> <data format="tabular" name="input1_refmap" label="" from_work_dir="input1.refmap"/> <data format="tabular" name="input2_tmap" label="" from_work_dir="input2.tmap"> <filter>len( input_files ) > 0</filter> </data> <data format="tabular" name="input2_refmap" label="" from_work_dir="input2.refmap"> <filter>len( input_files ) > 0</filter> </data> <data format="tabular" name="transcripts_tracking" label=""> <filter>len( input_files ) > 0</filter> </data> <data format="gtf" name="transcripts_combined" label="" from_work_dir="cc_output.combined.gtf"/> </outputs> ====== Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does this mean the wrapper tool retrieves only the first and second input files' TMAP and REFMAP files ? and others are ignored ? Or is there some galaxy black magic python code that iterates multiple inputs and imports them all ? Thanks, -gordon

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galaxy and Stampy
by Vincent Le Texier 11 Apr '11

11 Apr '11

Hello everyone, I would like to integrate Stampy (http://www.well.ox.ac.uk/project-stampy) in Galaxy. I couldn't find any wrapper available on the website. If someone has written a stampy wrapper and would like to share it, please contact me. Thanks in advance for your help; -- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85 letexier(a)lyon.fnclcc.fr

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Recommended Specs for Production System
by Ryan Golhar 11 Apr '11

11 Apr '11

Hi all - So, I been asked to provide specs for a production Galaxy system to support approximately 20-30 users. Most of these users are new to bioinformatics and very new to NGS. I'm targeting a user base that will use a light to moderate amount of NGS data. I've looked at the the Produce Server Wiki page stuff, but I'm curious what everyone else is using or recommends? How big of a compute cluster, how much storage, proxy/web server configurations, etc, etc. If you had to deploy a production system, based on what you know, what would you choose? Ryan -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
by Dave Clements 11 Apr '11

11 Apr '11

Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview *This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration *The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission *Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors *The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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galaxy-dev April 2011