- galaxy-dev - lists.galaxyproject.org

pre-set fields
by nsfox＠uwaterloo.ca 15 Mar '10

15 Mar '10

Hi, Is it possible to have textFields pre-set within a form or somewhere so that when someone goes and creates the sequence request certain fields are already set? Thanks, Natalie

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Re: [galaxy-dev] Database migration problem
by Jeremy Goecks 13 Mar '10

13 Mar '10

Hi Freerk, Can you be more specific about the problems that you're seeing? Also, please continue to cc galaxy-dev as you're more likely to get help with your issues since it's going to a larger audience. Thanks, J. On Mar 11, 2010, at 10:42 AM, Dijk, F van wrote: > Hi Jeremy, > > Thanks for the fast replay. The first issue is solved, a new one occured during the second point. When I migrate the sqlite database to SQL and try to import it into the MySQL database some errors occur. > MySQL is complaining about the syntax used in the SQLdump. > We are using the following MySQL version: > mysql Ver 14.12 Distrib 5.0.75, for debian-linux-gnu (x86_64) using readline 5.2 > I also read the info on the link you provided in your answer, but this won't solve this problem I think. So, do you have a solution? > > Sincerely, > > > Freerk van Dijk > > > Van: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] > Verzonden: donderdag 11 maart 2010 15:25 > Aan: Dijk, F van > CC: galaxy-dev(a)bx.psu.edu > Onderwerp: Re: [galaxy-dev] Database migration problem > > Hi Freerk, > >> When we change the databaseconnection to "mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock" in the universe_wsgi.ini file and run Galaxy we receive an error like: >> >> "Access denied for user 'root'@'localhost' (using password: NO)") None None >> >> So is there an option somewhere which we also have to change to make the connection work? >> > You need to specify a username and password to access your database. Try this URL: > > mysql://user:password@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock > (exchanging 'user' and 'password' according to your settings) > >> And question two: >> Do we need to migrate the content from the sqlite database to the MySQL database by hand or does this happen automatically? >> > > You need to do the migration manually. Kanwei provided a nice solution to this problem a while back: > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-February/001996.html > > -- > What I would suggest is to dump the sqlite database to standard sql, > and then creating a new instance of galaxy that has mysql as the > configured database. When you run the setup and run script, you'll > have a freshly instantiated galaxy with empty mysql tables. Then you > can just import the standard sql file into the mysql database. > -- > > Good luck and let us know if you have any more problems. > > J. > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. >

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run.sh error
by Lin Jiang 11 Mar '10

11 Mar '10

Hi, I am trying to install galaxy in my macbook with python version 2.5.2. But I got error messages when I sh run.sh. Could you please help me with this? Best regards, Lin Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 218, in run result = self.command() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 313, in loadapp **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 413, in get_context section) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/Users/linjiang/galaxy_dist/lib/pkg_resources.py", line 1912, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/linjiang/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/Users/linjiang/galaxy_dist/lib/galaxy/web/framework/ __init__.py", line 29, in <module> from babel.support import Translations File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se

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run.sh error
by Lin Jiang 11 Mar '10

11 Mar '10

Hi, I am trying to install galaxy in my macbook with python version 2.5.2. But I got error messages when I sh run.sh. Could you please help me with this? Best regards, Lin Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 218, in run result = self.command() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 313, in loadapp **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 413, in get_context section) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/Users/linjiang/galaxy_dist/lib/pkg_resources.py", line 1912, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/linjiang/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/Users/linjiang/galaxy_dist/lib/galaxy/web/framework/ __init__.py", line 29, in <module> from babel.support import Translations File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se

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Galaxy not finding DRMAA_python
by Chris Cole 11 Mar '10

11 Mar '10

Hi, We have two parallel installs of Galaxy one which runs with python2.4 and the other with 2.6. The 2.6 is working fine (other than the issues I've posted) however, the 2.4 won't start as it can't find DRMAA_python. I have scrambled the egg and it does exist: www-galaxy@ge-002: galaxy_live> ls -l /homes/www-galaxy/galaxy_live/eggs/DRMAA_python-0.2-py2.4-linux-x86_64-ucs4.egg -rw-r--r-- 1 www-galaxy barton 62374 Mar 5 14:22 /homes/www-galaxy/galaxy_live/eggs/DRMAA_python-0.2-py2.4-linux-x86_64-ucs4.egg What am I missing? Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

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Why goes galaxy think rpy's hist wants a matrix?
by Ry4an Brase 11 Mar '10

11 Mar '10

Hi, let me lead in with how impressed I am at the professional packaging of galaxy -- dropped right in. Amazing! Now on to the problem, I'm sure we're just missing something here on our end, but we're seeing an error when running the histogram tool which says hist wants a vector not a matrix. An error occurred running this job: Error in hist.default(list(68, 71, 62, 75, 58, 60, 67, 68, 71, 69), xlab = "V1", : 'x' must be numeric Looking at http://bitbucket.org/galaxy/galaxy-central/src/tip/tools/plotting/histogram… and the history thereof it's clear that's always been the case back to revision 0, but when we try from the console we get rpy complaining that a matrix isn't a vactor, and it works when we try a vector. By hand with a matrix: $ python Python 2.6.4 (r264:75706, Mar 9 2010, 10:00:44) [GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> from rpy import * >>> matrix = [] >>> vals = ["23","14","32","25","12","9","35","18","24"] >>> for i in vals: ... row = [];row.append(float(i));matrix.append(row) ... >>> matrix [[23.0], [14.0], [32.0], [25.0], [12.0], [9.0], [35.0], [18.0], [24.0]] >>> a = array(matrix) >>> r.pdf("histtest.pdf", 8, 8) >>> title = "Histogram Test";xlab="Count";breaks="Sturges" >>> r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks ) Traceback (most recent call last): File "<stdin>", line 1, in <module> rpy.RPy_RException: Error in hist.default(list(23, 14, 32, 25, 12, 9, 35, 18, 24), xlab = "Count", : 'x' must be numeric >>> a array([[ 23.], [ 14.], [ 32.], [ 25.], [ 12.], [ 9.], [ 35.], [ 18.], [ 24.]]) However, when we build a vector instead of rows R/rpy is happy: >>> v = [] >>> for i in vals: ... v.append(float(i)) ... >>> v [23.0, 14.0, 32.0, 25.0, 12.0, 9.0, 35.0, 18.0, 24.0] >>> r.hist(v, probability=True, main=title, xlab=xlab, breaks=breaks ) {'density': [0.022222217777778667, 0.044444444444444446, 0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 'equidist': True, 'breaks': [5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0], 'intensities': [0.022222217777778667, 0.044444444444444446, 0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 'counts': [1, 2, 1, 3, 0, 2], 'xname': 'c(23, 14, 32, 25, 12, 9, 35, 18, 24)', 'mids': [7.5, 12.5, 17.5, 22.5, 27.5, 32.5]} >>> >>> a = array(v) >>> r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks ) {'density': [0.022222217777778667, 0.044444444444444446, 0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 'equidist': True, 'breaks': [5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0], 'intensities': [0.022222217777778667, 0.044444444444444446, 0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 'counts': [1, 2, 1, 3, 0, 2], 'xname': 'c(23, 14, 32, 25, 12, 9, 35, 18, 24)', 'mids': [7.5, 12.5, 17.5, 22.5, 27.5, 32.5]} The relevant versions are: Galaxy: 297d8c9c5eb0 (galaxy-dist from a few weeks ago) R: 2.10.1 rpy: 1.0.3 (slightly tweaked for two-digit R minor-version strings, sigh) So after all that, how does your histogram work passing a matrix to something that wants a vector and can ours work that way too please? :) Thanks, -- Ry4an Brase 612-626-6575 University of Minnesota Supercomputing Institute for Advanced Computational Research http://www.msi.umn.edu

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Fwd: Adding custom genome
by Nathaniel Street 11 Mar '10

11 Mar '10

Hi I just noticed (after a history refresh) that when I try to use a GFF3 file to extract genomic DNA a job is created that converts the GFF to BED. Using the GFF file directly gives the error I detailed earlier (see below) but using the BED file works fine and I get the genomic sequence I want. If I first convert the GFF to a BED file everything is also fine (as expected from the above). So, it looks as though the problem is actually associated with the process of GFF-->BED-->extract genomic and not the actual extraction of sequences. Has anyone else seen this behaviour? Thanks Nathaniel -------- Original Message -------- Subject: Adding custom genome Date: Thu, 11 Mar 2010 14:24:13 +0100 From: Nathaniel Street <nathaniel.street(a)plantphys.umu.se> To: galaxy-dev(a)lists.bx.psu.edu Hi I'm trying to add a custom genome to a local galaxy install. So far I have done this: 1)Create a fasta file per scaffold (it's an unfinished genome) 2)Create a nib file per one of those scaffold fasta files 3)Add an entry to build.txt nis Test genome (nis) 4)Add a line to alignseq.loc seq nis /data/nib/nis 5)Add a line to faseq.loc nis /data/sequences/nis Is there more that I need to do to be able to extract sequences using the Extract Genomic DNA tool? I tried to use the tool by uploading a GFF3 file, extracting a small part of that for testing and then using that small part to extract genomic DNA. When I try this I get an error message returned AttributeError: 'tuple' object has no attribute 'iteritems' And the text version of the Traceback gives this URL: http://XXX:XXX:XX:XX:8080/tool_runner/index File '/home/nat/work/software/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 807 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 1079 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 140 in execute inp_data = self.collect_input_datasets( tool, incoming, trans ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 101 in collect_input_datasets tool.visit_inputs( param_values, visitor ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 754 in visit_inputs callback( "", input, value[input.name] ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 85 in visitor input_datasets[ prefix + input.name ] = process_dataset( value ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 47 in process_dataset new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] File '/home/nat/work/software/galaxy-dist/lib/galaxy/datatypes/data.py', line 264 in convert_dataset for name, value in converted_dataset.iteritems(): AttributeError: 'tuple' object has no attribute 'iteritems' Can anyone tell me what I'm doing wrong? Do I need more than only the nib files? Many thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

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running galaxy tools on cluster with a specified amount of memory.
by Vipin TS 11 Mar '10

11 Mar '10

Dear Galaxy Team, I need to run a galaxy tool in cluster which would like to consume a more amount of memory than the default. Any Idea how can I manage this ? I am using 'sge'. Many thanks, Vipin

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Database migration problem
by Dijk, F van 11 Mar '10

11 Mar '10

Hi, I send this mail again, because the last time I didn't receive a reply. We have a local installation of Galaxy running on our system. We are trying to migrate the contents from the sqlite database to our own MySQL database. When we change the databaseconnection to "mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock" in the universe_wsgi.ini file and run Galaxy we receive an error like: "Access denied for user 'root'@'localhost' (using password: NO)") None None So is there an option somewhere which we also have to change to make the connection work? And question two: Do we need to migrate the content from the sqlite database to the MySQL database by hand or does this happen automatically? I hope to receive an answer soon. Sincerely, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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[hg] galaxy 3511: Remove deprecated rgenetics Lmap datatype from...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/44e9b5ca9cf0 changeset: 3511:44e9b5ca9cf0 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 21:01:20 2010 -0500 description: Remove deprecated rgenetics Lmap datatype from datatypes_conf.xml.sample Was causing buildbot problems.. diffstat: datatypes_conf.xml.sample | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 2af472aa0844 -r 44e9b5ca9cf0 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Wed Mar 10 17:10:43 2010 -0500 +++ b/datatypes_conf.xml.sample Wed Mar 10 21:01:20 2010 -0500 @@ -194,7 +194,6 @@  <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>  - <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/> <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>  <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">

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