galaxy-dev June 2011

galaxy-dev@lists.galaxyproject.org

77 participants
156 discussions

Regarding saving the file
by shashi shekhar 29 Jun '11

29 Jun '11

Hi All, <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> Can u tell me how it works?.when u click on save button, it will save a file as output file name appended with extension example Galaxy122-[fasta-compute-sequence-length].fasta . i want to remove the first word "Galaxy". how it's possible ? Regards shashi shekhar

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Refreshing/Reloading Files
by Admins de Galaxy 29 Jun '11

29 Jun '11

Hello everyone, we have a problem with one of our selfwritten tools. We have a tool, that compares sequence with a database. The List of the available databases is loaded from a .txt file. One of our other tools, manages that a new database is added to the .txt file. But Galaxy doesn't recognize the change. It would be nice if someone could give us an advice. Best regards Paul K. Deuster @ Technische Hochschule Mittelhessen

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Re: [galaxy-dev] Fail to start galaxy
by Hans-Rudolf Hotz 29 Jun '11

29 Jun '11

On 06/28/2011 07:06 PM, colin molter wrote: > hi hans, > you are right. > it seems that even if i stopped galaxy > (i just stopped the run.sh command) > > i still have a job running: > root 10441 97.0 0.0 77496 1772 pts/6 R 11:59 402:48 python > /opt/galaxy-central/tools/fastq/fastq_groomer.py /fs1/GenomicsData/ERP0005 > > it seems that the transformation of a fastq file is taking a lot of time (it > uses 100%of cpu since 7hours). > does it sound normal? > I am not very familiar with 'fastq_groomer.py' and without knowing the size of your fasta file, it is impossible to tell. Have you tried a subset of your fasta file? May be your data is corrupt resulting in an endless loop? Hans > i think i have better to kill that job and to try another way. > > i stopped the job and it works > thx. > > > 2011/6/28 Hans-Rudolf Hotz<hrh(a)fmi.ch> > >> Hi Colin >> >> >> I launched a big job on my local galaxy server (for which I am admin). The >>> job was to put local dir in the datalist. >>> It took too long and i wanted to stop it .... but how?? i failed to find a >>> solution. >>> >> >> go to the admin view -> 'Manage jobs' and there you can kill individual >> jobs. >> >> >> To stop the job i thought that stopping the galaxy running instance could >>> make it. (AM I RIGHT?) >>> >> >> possible, but sounds like an 'overkill' to me. I would first try the 'soft' >> method described above....and use this only as a last resort. >> >> >> Unfortunately, i failed to restart galaxy. I have the following error: >>> >>> >> are you sure you have killed the galaxy process? Since this part of the >> error message tells me that Galaxy (or another service) is still using the >> port number. >> >> >>> socket.error: (98, 'Address already in use') >> >> >> How did you stop galaxy? >> >> >> >> Regards, Hans >> > > >

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Regarding output file name in save option of history
by shashi shekhar 28 Jun '11

28 Jun '11

Hi All, it's possible to give output file name in tool xml and while downloading same output file name should come. i don't want to change the extension .output file name should not start with "Galaxy" word . Regards shashi shekhar

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postgresql connection error: could not connect to server: No such file or directory...
by W. Augustine Dunn III 28 Jun '11

28 Jun '11

Hello all: Please forgive me if this is a matter of RTFM but I can assure you that I have in fact TRIED that for a day or so now... I am trying to set up a local GALAXY site for my lab so that I can start to offload some of the work that comes my way as the sole biologist in our lab not afraid of the command line. My system is Ubuntu 10.10 64b, i7 quad, 12 GB RAM. Since Multiple people will be using the site I decided to go with the slightly more fancy postgresql db back-end rather than the sqlite default. I had things running fine with the sqlite but can NOT seem to get psql and galaxy to play nice. I have created a galaxy role with rights to make tables on a created "galaxy" database: galaxy@vlad 12:40:20 ~/galaxy-dist: psql psql (8.4.8) Type "help" for help. galaxy=> \l List of databases Name | Owner | Encoding | Collation | Ctype | Access privileges --------------+----------+----------+------------+------------+----------------------- galaxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =Tc/postgres : postgres=CTc/postgres : galaxy=CTc/postgres postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 | template0 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres : postgres=CTc/postgres template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres : postgres=CTc/postgres zabbix_proxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 | (5 rows) I created a PGDATA file at /var/lib/postgresql/8.4/main/PGDATA and export a PGDATA envar upon loading of the galaxy user's .bashrc pointing to this place. I am able to start and stop the server with the postgres user using pg_ctl. Once its running, I change users back to galaxy and try to run run.sh and get the following traceback: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.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/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py", line 80, in connect raise exc.DBAPIError.instance(None, None, e) OperationalError: (OperationalError) could not connect to server: No such file or directory Is the server running locally and accepting connections on Unix domain socket "/tmp/.s.PGSQL.5432"? None None I have reached the point where I am beating my head against a wall and finally decided to ask for help. I am probably not as experienced as a pure compSci person but i have been hacking python/bash/perl for years. However I am not experienced at ALL with SQL flavors. I hope that this give someone enough info to be able to help me! Again I am sorry if this has been addressed already. I searched the archives but came up with nothing. Thanks in advance! Gus Dunn Molecular Biology and Biochemistry Institute for Genomics and Bioinformatics Major Advisor: Anthony James Co-Advisor: Xiaohui Xie University of California, Irvine 2315 McGaugh Hall Irvine, CA 92697-3900 Lab: (949) 824-3210 Fax: (949) 824-8551 Email: dunnw(a)uci.edu Email: wadunn83(a)gmail.com -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*

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updating ToolsMultipleOutput wiki docs new additional datasets file format to include database part
by Leandro Hermida 28 Jun '11

28 Jun '11

Hi, In the last section of https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput, "Number of output datasets cannot be determined until tool run", it should be updated that the new additional datasets file format actually has a sixth part at the end where you can set the database attribute of the output dataset: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, database ) I accidentally discovered this even though I didn't want to set the database attribute because I have some custom datatypes defined and my datatype extension names have underscores in them :) which causes Galaxy to think that the part of my extension names string after the underscore is actually the database name i want to set. I would recommend not to put underscores in your custom datatype extension names :) -Leandro

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Access tool information with mako.
by Michael Cotterell 28 Jun '11

28 Jun '11

Assuming I have the tool object (let's just call this "tool") available and am able to traverse it in mako, I know I can access its name by "tool.name" and id by "tool.id". However, how do I access the input and output parameters? I tried using "tool.inputs" and "tool.outputs" but the results didn't correspond to the actual input and output parameters for the tool. Thanks! -- Sincerely, Michael Cotterell mepcotterell(a)gmail.com mepcott(a)uga.edu P.S. - Check out ScalaTion (http://code.google.com/p/scalation/), a Domain-Specific Language for Modeling & Simulation. #blatantplug

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input security validation
by Russell Bonneville 28 Jun '11

28 Jun '11

Hello all, I am Russell, a student working with Dr. Victor Jin at the Dept. of Biomedical Informatics, OSU Medical Center. I am developing a Galaxy wrapper for our ChIP-seq peak-calling program BELT (PMID: 21138948), and I have a question about input validation. Does Galaxy filter for malicious field entries (such as XSS attacks) or is this our wrapper's responsibility (the MACS wrapper appears to not perform any explicit checks)? Thank you for your time. Sincerely, Russell Bonneville

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Re: [galaxy-dev] [galaxy-user] Configuring Galaxy Server
by Nate Coraor 28 Jun '11

28 Jun '11

Hi Guarav, Since this question is regarding a local install, I've moved the thread to the galaxy-dev list. Please see responses inline below. gaurav thareja wrote: > Hi All, > > Thank you for last reply and links about galaxy structure. The links were > helpful. But still I am uncertain about many files and their uses. To > previous question, I will require further help on following issues: > > 1. Where all users information is stored in file structure so that i can > add custom users for my galaxy server? They are stored in the database, in a table called 'galaxy_user'. By default the database is a SQLite file: galaxy-dist/database/universe.sqlite We recommend using PostgreSQL, however. By default, users can create their own accounts, and anyone can use Galaxy anonymously. This behavior can be modified in galaxy-dist/universe_wsgi.ini with the 'allow_user_creation' and 'require_login' options. You can always register accounts via the 'Register' link under the 'User' tab at the top of the Galaxy interface. You can also create accounts as an administrator from the 'Admin' interface. Once you have created your own account in Galaxy, just set that email address in 'admin_users' in galaxy-dist/universe_wsgi.ini to enable the admin interface for your user. > 2. Is it possible to customize left purple panel? Yes, see the galaxy-dist/tool_conf.xml file. --nate > > My real aim is to customize the galaxy browser instance as per my needs and > use for internal development, which i think is possible?. So, if you guys > have any development documents which can be shared to provide further > insights about file and directory structure will be really helpful. > > Regards > > Gaurav Thareja > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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User creation with upstream authentication
by Steve Thorn 28 Jun '11

28 Jun '11

Hello We would like to force users to register even when they successfully pass through our University's single sign-on service (Apache + cosign). We have: use_remote_user = True allow_user_creation = False in the universe_wsgi.ini, but it appears that use_remote_user takes precedence over allow_user_creation. Ideally, we'd like users who get through the single sign-on to be presented with a message like "to use galaxy please register by emailing someone(a)ed.ac.uk". Is this possible? Many thanks, Steve -- Steve Thorn Research Systems Consultant - ECDF Middleware Team +44 (0)131 650 4941 University of Edinburgh, JCMB, King's Buildings Edinburgh EH9 3JZ, UK The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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galaxy-dev June 2011