galaxy-user August 2009

galaxy-user@lists.galaxyproject.org

19 participants
23 discussions

Problems with links in webpage output...
by Nick Schurch 21 Aug '09

21 Aug '09

Dear Galaxy-gurus, I have a tool I've written myself which runs successfully and generates an HTML file as its output. Included in the webpage are several links for downloading other files produced by the script. I've tried to follow the instructions I found on the wiki -- http://g2.trac.bx.psu.edu/wiki/AddingToolsFAQ -- which gives some (rather vague) instructions about where to put the files and how to reference them in the output webpage, but I'm not having much luck. The script successfully puts the files in the directory where (I think) they are supposed to be: i.e /homes/www-galaxy/galaxy_devel/database/files/000/{myoutputfile}.files_path, and the output links to them very simply with <a href="myfilename.txt">download file</a> - as per the wikipage... But when I view the output webpage from a test run and try and download the links all I get is a page saying: "The resource could not be found. File Not Found (myfilename.txt)." The link itself is pointing to: <my galaxy URL>/datasets/XXX/display/myfilename.txt Is this the right place? Once again, any help would be greatly appreciated! -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

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Re: [galaxy-user] Passing a string with spaces to a tool
by Nick Schurch 21 Aug '09

21 Aug '09

Dear Galaxy-gurus, How can I pass a string with spaces as a parameter from the galaxy interface to a tool that I've written myself in perl? I've tried enclosing the string with quotes (single and double) and various escape characters and all they do is add __dq/sq/X__ to the start of the string and then ignore everything else after the space. my xml looks like: <tool id="blah" name="mytool"> <command interpreter="perl"> /pathto/mycommand.pl -str $str </command> <inputs> <param name="str" type="text" label="Put your string here" /> The kind of commandline i'm looking for this to generate is.... perl mycommand.pl -str "this is my string" but currently it just gives perl mycommand.pl -str this or perl mycommand.pl -str __dq__this or perl mycommand.pl -str X__dq__this Thanks! -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

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Galaxy Template Language
by Dominic Tolle 20 Aug '09

20 Aug '09

Hi, is there any more documentation available for the template language used within the configfile tag in tool config files? Cheers Dominic

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'MySQL server has gone away'
by Pieter Neerincx 19 Aug '09

19 Aug '09

Hi, Every morning when I come back to my lab and login to Galaxy I get the error below. I think it's the 'MySQL server has gone away' part that is the real cruel-pitand simply clicking refresh is enough to 'fix' the problem... This is not specifically a Galaxy problem. It's probably the result of caching connections and I have seen this before when I was using Perl modules to access MySQL databases. I guess this can be solved by fiddling with sqlalchemy settings maybe even in a Galaxy config file, but I'm a Python noob. If anyone has seen this before and knows how to properly fix it, please let me know. Cheers, Pi URL: http://tadpole/galaxy/ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/WebError-0.8a-py2.4.egg/weberror/evalexception/ middleware.py', line 364 in respond File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/debug/prints.py', line 97 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Beaker-0.5-py2.4.egg/beaker/session.py', line 103 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/recursive.py', line 80 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/middleware/remoteuser.py', line 102 in __call__ return self.app( environ, start_response ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/base.py', line 100 in __call__ trans = self.transaction_factory( environ ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 109 in <lambda> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 149 in __init__ self.__ensure_valid_session( session_cookie ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 277 in __ensure_valid_session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 361 in __get_or_create_remote_user user = self .app .model .User .filter( self.app.model.User.table.c.email==remote_user_email ).first() File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 909 in first File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 938 in __iter__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 941 in _execute_and_instances File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/session.py', line 628 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 844 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 895 in execute_clauseelement File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 907 in _execute_compiled File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 916 in __execute_raw File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 960 in _cursor_execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 942 in _handle_dbapi_exception OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.password AS galaxy_user_password, galaxy_user.external AS galaxy_user_external, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged \nFROM galaxy_user \nWHERE galaxy_user.email = %s ORDER BY galaxy_user.id \n LIMIT 0, 1' ['P.B.T.Neerincx(a)uu.nl'] ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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Re: [galaxy-user] Welcome to the "galaxy-user" mailing list (Digest mode)
by Bagdevi 17 Aug '09

17 Aug '09

Thanks a lot Anton. By the way, I did some R&D and found out the direct link to a video tutorial, which otherwise did not come up on the site. Anyone can get it from the following url using wget wget http://screencast.g2.bx.psu.edu/galaxy/WorkFlow_SC7/WorkFlow_SC7-iPhone.m4v Regards, Bagdevi Mishra. Regards, Bagdevi Mishra. On Mon, Aug 17, 2009 at 5:05 PM, <galaxy-user-request(a)bx.psu.edu> wrote: > Welcome to the galaxy-user(a)bx.psu.edu mailing list! > > To post to this list, send your email to: > > galaxy-user(a)bx.psu.edu > > General information about the mailing list is at: > > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > http://mail.bx.psu.edu/cgi-bin/mailman/options/galaxy-user/bagdevi.mishra%4… > > > You can also make such adjustments via email by sending a message to: > > galaxy-user-request(a)bx.psu.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > bag.nin > > Normally, Mailman will remind you of your bx.psu.edu mailing list > passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. >

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hacking galaxy blog - creating an importer
by Ido M. Tamir 17 Aug '09

17 Aug '09

Hi, I started to blog, my first victim is galaxy ;-) http://idotamir.blogspot.com/2009/08/adventures-in-galaxy-pt1.html best wishes, ido

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huge trees in library slow
by Ido M. Tamir 13 Aug '09

13 Aug '09

This is what my importer of our solexa runs currently creates: Structure of the tree: Currently each group (~8 ATM) has a library. Within each library each user has a folder, each sequenced sample of this user has a folder and within the folder of the sequenced sample each analysis (unique combination of image-analysis/basecall/alignment) has its own folder with some of the output files each as a dataset. At the moment I store the paths (not the files) from ~250 solexa samples in galaxy. Some samples are sequenced multiple times, for each run 4-5 files (I will also add some diagnostic files). In total there are now 1200 library datasets in the database (the paths that is). I have also tweaked the permission system a little bit. Each dataset has quite a lot of permissions associated with it. So the tree is not that big, but for galaxy/firefox its big. For one user it takes 20 seconds to bring up the library folder. Then a little bit more than one minute to bring up the tree (sometimes firefox thinks the script is hanging). But its still in development not production and I don't know how much speedup a change from sqlite to postgresql will bring. Of course I guess it will only get worse because its always more data that will come in. I don't know how to profile with python, but check_folder_contents in security/__init__.py could be one of the culprits. best wishes, ido

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Galaxy site address blacklisted
by Chris Cole 13 Aug '09

13 Aug '09

Hi, I have just found out that the main galaxy site address http://main.g2.bx.psu.edu/ has been blacklisted here: http://blacklist.chongqed.org/ I'm not sure how or why, but it meant that additions to our local docuwiki would block additions with that address in them. Cheers, Chris

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multiple outputs
by Davide Cittaro 12 Aug '09

12 Aug '09

Hi all, I would like to integrate some NGS tools in a local instance of galaxy (namely MACS, maq or even some GA pipeline tool). The only problem is that many of these tools generate output in directories and typically they write more than one file. I've installed galaxy some time ago (and I will upgrade it) and I remember some pain in handling multiple outputs. Has this behavior changed? In other words, how can I efficiently manage multiple file output? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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manage_db: MySQL error 1059
by Pieter Neerincx 05 Aug '09

05 Aug '09

Hi, I upgraded today from a Galaxy release from about a month ago and got this error when I ran the manage_db script: 7 -> 8... done 8 -> 9... done 9 -> 10... 0010_hda_display_at_authz_table DEBUG 2009-08-05 13:52:36,228 Creating history_dataset_association_display_at_authorization table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' is too long") u'CREATE INDEX ix_history_dataset_association_display_at_authorization_update_time ON history_dataset_association_display_at_authorization (update_time)' {} 0010_hda_display_at_authz_table DEBUG 2009-08-05 13:52:36,228 Creating history_dataset_association_display_at_authorization table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' is too long") u'CREATE INDEX ix_history_dataset_association_display_at_authorization_update_time ON history_dataset_association_display_at_authorization (update_time)' {} done 10 -> 11... done This is with MySQL 5.0.45-7.el5 (on CentOS 5.3). Manual inspection shows that despite the error the table was created: mysql> describe history_dataset_association_display_at_authorization; +--------------------------------+--------------+------+-----+--------- +----------------+ | Field | Type | Null | Key | Default | Extra | +--------------------------------+--------------+------+-----+--------- +----------------+ | id | int(11) | NO | PRI | NULL | auto_increment | | create_time | datetime | YES | | NULL | | | update_time | datetime | YES | | NULL | | | history_dataset_association_id | int(11) | YES | MUL | NULL | | | user_id | int(11) | YES | MUL | NULL | | | site | varchar(255) | YES | | NULL | | +--------------------------------+--------------+------+-----+--------- +----------------+ 6 rows in set (0.01 sec) and I have the following indices on this table: mysql> show index from history_dataset_association_display_at_authorization; +------------------------------------------------------+------------ +------------------------------------------+-------------- +--------------------------------+-----------+-------------+---------- +--------+------+------------+---------+ | Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | +------------------------------------------------------+------------ +------------------------------------------+-------------- +--------------------------------+-----------+-------------+---------- +--------+------+------------+---------+ | history_dataset_association_display_at_authorization | 0 | PRIMARY | 1 | id | A | 0 | NULL | NULL | | BTREE | | | history_dataset_association_display_at_authorization | 1 | user_id | 1 | user_id | A | NULL | NULL | NULL | YES | BTREE | | | history_dataset_association_display_at_authorization | 1 | ix_hdadaa_history_dataset_association_id | 1 | history_dataset_association_id | A | NULL | NULL | NULL | YES | BTREE | | +------------------------------------------------------+------------ +------------------------------------------+-------------- +--------------------------------+-----------+-------------+---------- +--------+------+------------+---------+ 3 rows in set (0.00 sec) I guess that the ix_hdadaa_history_dataset_association_id is the abbreviated name for ix_history_dataset_association_display_at_authorization_update_time... or not? The question is can I safely ignore the update error or do I have a problem? Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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galaxy-user August 2009