[galaxy-dev] Local Toolshed misbehaviours?
Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server? From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on... Thanks, Daniel ___ 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/
[galaxy-dev] Depositing Data in a user's account
Hi all, at InterMine we are looking to improve various aspects of our UI, and also our interaction with Galaxy. To that end, it would be great to find out what ways there are of depositing data in a user's account. The ideal would be to make requests from javascript that either open in another tab, or can be entirely backgrounded. After some reading of the bitbucket repos I note that: a) I can use the current mechanism of a data_source.py tool such as the flymine et al. ones. This would require me to do things like parsing the response headers for the galaxy session though, and I don't see a nice way of depositing data in a user's account without having come originally from galaxy. b) The API provides mechanisms for associating data files with histories, provided that these files have been already uploaded. It is straightforward to operate on a specific account, but I didn't find the API controller that allows individual tools, rather than whole workflows to be run. This would be ok I guess if I could create workflows rather than just run them. So the current situation (please correct me if I am mistaken) is a web-app based workflow that is best originated in galaxy, and an API workflow that lacks certain features to do what I'd like. Again, I'd very much like to be wrong here, and have like just not connected the dots correctly. However, if that is an accurate summation of the situation, I would be happy to contribute to get what I want, rather than expecting others to provide it. If anyone is interested in pull requests and a few questions about internals, I'd be happy to help develop the API so that: a) POST /workflows - creates a new workflow (from one or more tools), rather than running it. b) GET /jobs - lists the status of running or completed jobs. c) POST /jobs - runs a job (from a workflow), returning a job id. d) DELETE /jobs - cancels a job, or removes it from the history if completed. All best, Alex -- Software Developer www.intermine.org University of Cambridge ___ 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/
Re: [galaxy-dev] Stalled upload jobs under Admin, Manage jobs
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor n...@bx.psu.edu wrote: On Feb 10, 2012, at 6:47 AM, Peter Cock wrote: Hello all, I've noticed we have about a dozen stalled upload jobs on our server from several users. e.g. Job ID User Last Update Tool State Command Line Job Runner PID/Cluster ID 2352 21 hours ago upload1 upload None None None ... 2339 19 hours ago upload1 upload None None None The job numbers are consecutive (2339 to 2352) and reflect a problem for a couple of hours yesterday morning. I believe this was due to the underlying file system being unmounted (without restarting Galaxy), and at the time restarting Galaxy fixed uploading files. Test jobs since then have completed normally - but these zombie jobs remain. Using the Stop jobs option does not clear these dead upload jobs. Restarting the Galaxy server does not clear them either. This is our production server and was running galaxy-dist, changeset 5743:720455407d1c - which I have now updated to the current release, 6621:26920e20157f - which makes no difference to these stalled jobs. Does anyone have any insight into what might be wrong, and how to get rid of these zombie tasks? Hi Peter, Are you using the nginx upload module? There's no way to fix these from within Galaxy, unfortunately. You'll have to update them in the database. --nate Hi Nate, Sorry for the delay - I must have missed your reply. No, we're not using nginx here. What should I edit in the database? Presumably rather than deleting these jobs I should set the state to finished with error? (Is there any documentation about the Galaxy database schema, and the values of fields in it - or is that all considered to be an internal detail?) Thanks, Peter ___ 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/
Re: [galaxy-dev] Local Toolshed misbehaviours?
Hi Daniel, What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running. tail -f community_webapp.log Greg Von Kuster On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote: Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server? From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on... Thanks, Daniel ___ 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/ ___ 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/
Re: [galaxy-dev] Local Toolshed misbehaviours?
Hi Greg, The paster log from the toolshed server does not tells me much: 172.22.50.249 - - [16/Mar/2012:12:27:31 +0100] GET /toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy HTTP/1.1 200 - http://myserver/toolshed//repository/browse_valid_repositories?galaxy_url=http://myserver/galaxy/webapp=galaxy; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 172.22.50.249 - - [16/Mar/2012:12:27:44 +0100] GET /toolshed/repository/install_repository_revision?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy HTTP/1.1 302 - http://myserver/toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 But the galaxy paster indicates a failure: 172.22.50.249 - - [16/Mar/2012:12:28:03 +0100] GET /galaxy/admin_toolshed/browse_repositories?status=errormessage=abort%3A+HTTP+Error+404%3A+Not+Found%0A%3Cbr%2F%3E HTTP/1.1 200 - http://myserver/galaxy/admin_toolshed/install_repository?tool_shed_url=http://myserver/toolshed/repo_info_dict=f16fe1e576e5fb5fdc3c94b320b0d6447be8ac7d:7b2267656e657269635f7574696c73223a205b2247656e65726963205574696c73222c2022687474703a2f2f64736f6272616c406d6e656d6f73796e652f7265706f732f64736f6272616c2f67656e657269635f7574696c73222c2022613432633463303334633236225d7dincludes_tools=True; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 Nothing that helps me much. I have has some problems with permissions in the tmp dir, but I reconfigured it and it still does not work. Daniel On 03/16/2012 11:04 AM, Greg Von Kuster wrote: Hi Daniel, What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running. tail -f community_webapp.log Greg Von Kuster On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote: Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server? From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on... Thanks, Daniel ___ 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/ ___ 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/
Re: [galaxy-dev] Error Setting BAM Metadata
On Feb 3, 2012, at 3:14 PM, Liisa Koski wrote: Yes it isand my galaxy is up to date. Hi Liisa, Sorry for not getting back to you. Did you ever figure out what was up with this? Since you're pasting a URL, I'm wondering if the URL fetch is failing. --nate Thanks, Liisa From: Nate Coraor n...@bx.psu.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 01/30/2012 03:07 PM Subject: Re: [galaxy-dev] Error Setting BAM Metadata On Jan 25, 2012, at 2:43 PM, Liisa Koski wrote: Hello, I am trying to upload BAM files (by pasting a URL) to my history(or DataLibrary) and get the following error. These are bam files which I had previously uploaded with no problems. Traceback (most recent call last): File /doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 126, in run_job job_wrapper.finish( stdout, stderr ) File /doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py, line 618, in finish dataset.set_meta( overwrite = False ) File /doolittle/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py, line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File /doolittle/Galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py, line 179, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file) I ran bamtools on the unix command line to see if there was anything wrong with the file(s) but nothing. I tried uploading different bam files from other projects and get the same error. I did do an update to the latest release yesterday...if that helps? Hi Liisa, Is this a regular upload via a browser? --nate Thanks in advance, Liisa ___ 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/ ___ 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/
Re: [galaxy-dev] Importing data from password protected UCSC Genome Browser
On Feb 7, 2012, at 5:52 AM, Federico De Masi wrote: Dear colleagues, I have been struggling with this issue for quite a while now, and I don't seem to find a solution (neither in situ nor in webo). here it is: Because of the confidentiality of our data, I have setup both a Galaxy server and a UCSC Genome Browser locally on my server. Both are run through Apache, using the same .htpasswd authentication method and file (ie: same usernmae/password combo for each). Everything works great except that I do not seem to be able to send/receive data from Galaxy to UCSC and vice versa. When I try to get data from UCSC main (my local instance), I get the followin error: Tool execution generated the following error message: The remote data source application may be off line, please try again later. Error: EOF when reading a line The tool produced the following additional output: Enter username for SG at 127.0.0.1: where SG is the AuthName in vhost.conf and 127.0.0.1 is UCSC's IP. Whenever I try to to send data to UCSC (Display at UCSC main in the history boxes), I get this guy: Expected 200 http://127.0.0.3/display_application/48916fac0de9a85d/ucsc_bigwig/main/b9ba5eb40e0fec32/param/track: 401 Authorization Required Where 127.0.0.3 is galaxy's IP. I have: - hardcoded username:passowrd on UCSC's send to galaxy routine but to no avail - hardcode username:passowrd on Galaxy's definiton of UCSC's main URL, but to no avail - I have removed UCSC authentication, and everything works fine - I have kept UCSC authentication and let Galaxy open, doesn't work - I remove authentication to both servers, and it all works cool. Somehow, Galaxy doesn't like to talk to a protected UCSC browser. I'll be happy to post my vhost.conf files if needed. Can anyone help, please? Hi Fred, Sorry for not replying sooner. I have just committed a fix that should make this a bit easier. Previously, you had to modify a bit of the Galaxy source to allow your UCSC server to access data in Galaxy. I've made this in to an option in the config file, and the details are in the wiki documentation at: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy This change will be available in our next stable release. For the reverse direction (fetching data from UCSC), if you're proxying your UCSC server via Apache, I'd suggest using the Satisfy Any method shown in our documentation to allow the Galaxy server to bypass authentication to access the UCSC server. Assuming your UCSC server has its own VirtualHost, you'd do something like: AuthType your_authtype ... other site-specific authentication directives ... Satisfy Any Order deny,allow Deny from all Allow from galaxy.example.org Note that you need both - The Galaxy server needs an Allow to talk to the UCSC server (in the UCSC vhost) and the UCSC server needs an Allow to talk to the Galaxy server (in the Galaxy vhost). --nate Thanks a lot, Fred -- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk ___ 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/ ___ 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/
[galaxy-dev] Compare two datasets fails due to encoding error
Hi; I have developed a Perl tool that generates a tabular file with 3 columns. I need to compare it with another tabular file (Gene Ontology Annotation file) and I use Join, substract, group, Compare two datasets. When I try to do so, I get the error pasted bellow. I assume my perl code is generating the file with the wrong encoding, but I have tried to generate the file in UTF8 to no avail. Any clues? Thanks Traceback (most recent call last): File /home/megana/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 125, in run_job job_wrapper.finish( stdout, stderr ) File /home/megana/galaxy-dist/lib/galaxy/jobs/__init__.py, line 658, in finish self.sa_session.flush() File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py, line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py, line 1356, in flush self._flush(objects) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py, line 1434, in _flush flush_context.execute() File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 261, in execute UOWExecutor().execute(self, tasks) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 753, in execute self.execute_save_steps(trans, task) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 773, in execute_save_steps self.execute_cyclical_dependencies(trans, task, False) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 789, in execute_cyclical_dependencies self.execute(trans, [t], isdelete) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 753, in execute self.execute_save_steps(trans, task) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 768, in execute_save_steps self.save_objects(trans, task) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py, line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 824, in execute return Connection.executors[c](self, object, multiparams, params) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 874, in _execute_clauseelement return self.__execute_context(context) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File /home/megana/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE history_dataset_association SET update_time=?, info=?, blurb=?, peek=?, tool_version=?, metadata=? WHERE history_dataset_association.id = ?' ['2012-03-16 15:20:29.158287', 'join (GNU coreutils) 7.4\nCopyright \xc2\xa9 2009 Free Software Foundation, Inc.\nLicencia GPLv3+: GNU GPL versi\xc3\xb3n 3 o superior http://gnu.org/licenses/gpl.html.\nEsto es software libre: es libre de cambiarlo y redistribuirlo.\nNO HAY NINGUNA GARANT\xc3\x8dA, en la me', '5,547 lines', u'UniProtKB\tB5B2P3\tNFATC2\t\tGO:0001816\tGO_REF:019\tIEA\tEnsembl:ENSMUSP0074198\tP\tNuclear factor of activated T-cells c2 isoform IB-IIL-deltaXa\tB5B2P3_HUMAN|NFATC2|hCG_2018585|IPI00297845\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tE7DVW4\tFABP4\t\tGO:0001816\tGO_REF:019\tIEA\tEnsembl:ENSMUSP0029041\tP\tFatty acid binding protein 4,
Re: [galaxy-dev] problem after last upgrade
Hi Greg,
Database downgrade and then upgrade succeeded! galaxy instance is
working now!
many thanks!
michal
On 03/15/2012 08:57 PM, Greg Von Kuster wrote:
Hi Michel,
No idea why, but for some reason your database migration script number 92
failed. You should try the following from your Galaxy installation directory:
%sh manage_db.sh downgrade 91
and then:
%sh manage_db.sh upgrade
If this succeeds, try starting Galaxy. If Galaxy starts, great - all is good!
If you see the same problem you reported below, try running this sql statement
in your psotgres database:
INSERT INTO migrate_tools VALUES ('GalaxyTools',
'lib/galaxy/tool_shed/migrate', 1);
Now start your Galaxy server.
Let me know how this turns out.
Greg Von Kuster
On Mar 15, 2012, at 3:40 PM, Michal Stuglik wrote:
Hi Greg,
migrate_tools table is empty. Any idea?
best,
michal
W dniu 2012-03-14 18:14, Greg Von Kuster pisze:
Hi Michal,
Looks like you're running with a postgres database - can you get into your
database and execute the following sql command and send me the result?
select * from migrate_tools;
Thanks!
Greg Von Kuster
On Mar 14, 2012, at 12:04 PM, Michal Stuglik wrote:
Dear galaxy,
I have upgraded my galaxy-dist with last official version ( upgrade: % hg pull
-u -r 40f1816d6857 ). I also upgraded database (sh manage_db.sh upgrade).
now I have problem with running galaxy instance and this is what I get:
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is:
/home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/wcharty!
pe-0.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/home/galaxy/galaxy-dist/lib, /usr/lib/python2.6,
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload,
/usr/local/lib/python2.6/dist-packages, /usr/lib/python2.6/dist-packages/PIL,
/usr/lib/pymodules/python2.6/gtk-2.0,
/usr/lib/python2.6/dist-packages/gst-0.10,
/usr/lib/python2.6/dist-packages/gtk-2.0,
/usr/lib/pymodules/python2.6/ubuntuone-storage-protocol,
/usr/lib/pymodules/python2.6/ubuntuone-client, /usr/lib/python2.6/dist-!
packages, /usr/lib/pymodules/python2.6
galaxy.model.migrate.check DEBUG 2012-03-14 16:29:23,928 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-03-14 16:29:24,000 At database version 93
galaxy.tool_shed.migrate.check DEBUG 2012-03-14 16:29:24,007 psycopg2 egg
successfully loaded for postgres dialect
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 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File /home/galaxy/galaxy-dist/lib/galaxy/tool_shed/migrate/check.py, line
42, in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File
/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File
/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range
best,
michal
___
Please keep all
[galaxy-dev] CAGE data - trimming SAM files (functionality suggestion)
Hello, I work sometimes with galaxy analysing of short reads but actually I very much lack the function of keeping only first nucleotide of the read in SAM file. This is not so straightforward to do, I need to modifiy sequence, quality scores and CIGAR. It would be very useful for looking e.g on CAGE (cap analysis of gene expression) data where only 5' most of the read indicates end of mRNA molecule and rest of the read is needed only to map it to its location, then is unnecessary. Hope it can be easily implemented Best, Lukasz -- Lukasz J. Kielpinski PhD student Department of Biology, University of Copenhagen RNA Biology Group Ole Maaløes Vej 5, room 3.1.17 2200 Copenhagen N DENMARK ___ 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/
Re: [galaxy-dev] sharplabtool in Galaxy Tool Shed
Hello Xuebing, Your updates that will be available for an installed repository are restricted to the version that is installed where the version is defined by the change set revision number. This enables different versions of tools in the repository to always be accessible and installable. The following explanation is taken from the tool shed wiki. http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance A very important point to convey here is that updates retrieved from the relevant Galaxy tool shed will be restricted to the latest change set that includes those versions of tools that are currently in your installed tool shed repository. Remember that the tool shed repository revision values are a number followed by a : and an alpha-numeric string (e.g., 6:98d05121d41e). Let's assume that at some point you installed revision 0:sdj45ger5fr4 of a tool shed repository into your local Galaxy instance. Then at some later point the related repository in the Galaxy tool shed was updated with revision 1:si88rhjk8hfh. Then even later the same repository in the Galaxy tool shed was updated to a new revision number, say 2:srjls89ojf8e. Let's assume that this latest version resulted in a Revision select list for the repository in the Galaxy tool shed because the version of one or more tools within the repository changed. If you updated your locally installed tool shed repository after these changes to the repository within the Galaxy tool shed were made, your local repository would be updated to revision 1:si88rhjk8hfh, but would not be updated to include the change in revision 2:srjls89ojf8e. Since revision 2:srjls89ojf8e of the repository within the Galaxy tool shed includes tools that have different versions, you have to install that revision into your local Galaxy instance as a separate tool shed repository installation if you want to use the new versions of the tools. On Mar 16, 2012, at 3:52 PM, Xuebing Wu wrote: Hi Dave, I'm not sure if this is the right way to ask questions about tool shed: I'm having trouble updating my tools installed in a local instance. I deleted old xml files and uploaded a new one. I can see revision number changes in toolshed website, but when I tried to manually update tools by clicking Get Updates item in Repository Actions, I got message saying that there is no updates available. best, Xuebing On Tue, Mar 13, 2012 at 7:01 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Xuebing, if you are planning to make these available in small pieces, then I won't Tweet sharplabtool (unless you tell me to!). However, I will Tweet the smaller repositories, if and when they show up. Thanks for sharing this with the community, Dave C On Tue, Mar 13, 2012 at 3:34 PM, Xuebing Wu wu...@mit.edu wrote: I see. It's a set of tools we have on our local galaxy server. So it's pretty heterogeneous, including interval manipulation, meta-gene analysis, sequence and motif analysis, and some others. I don't have a good description for them. I'm planning to separately them anyway. best, Xuebing On Tue, Mar 13, 2012 at 6:26 PM, Greg Von Kuster g...@bx.psu.edu wrote: Xuebing, it's fine to have many tools in the same repository, so please don't feel you have to separate them into multiple repositories unless it is something you were planning anyway. Dave is just wondering if you have a good description for the set of tools you have made available. Thanks! On Mar 13, 2012, at 5:58 PM, Xuebing Wu wrote: Sorry about this. I'm just testing. May be I should try the test website first. I'll remove them and then create separate repositories. best, Xuebing On Tue, Mar 13, 2012 at 5:22 PM, Dave Clements cleme...@galaxyproject.org wrote: Dear Xuebing, Several days ago you created the new sharplabtool in the Galaxy Tool Shed. Normally, I tweet newly deposited tools, but I am not sure how to summarize this repository. It is enormous and includes many tools that would be generally useful at many Galaxy installations. Is there a more informative summary than sharplabtool that I could use in the Tweet? I can also make something up. Thanks, Dave C -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
