Update of cufflinks
by Sarah Diehl
Hello everybody,
I just found out that there was a major update to cufflinks on 5/5/2011.
At least for us it now makes no sense anymore to use the old version,
besides the fact that the cufflinks team highly recommends upgrading.
Does anybody already have new wrappers for all the cuff... tools ready?
Do you know if/when the Galaxy codebase will be updated to the new
cufflinks version?
Best regards,
Sarah
11 years, 8 months
Blast2GO in Galaxy
by Peter Cock
Hi all,
As I mentioned on Twitter, at the end of last week I wrapped Blast2GO
for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See
http://blast2go.org/
Currently current code is on bitbucket under my tools branch,
https://bitbucket.org/peterjc/galaxy-central/src/tools/
Specifically files tools/ncbi_blast_plus/blast2go.* viewable here:
https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_p...
I've using a Galaxy location file, tool-data/blast2go.loc, to offer
one or more Blast2GO configurations (properties files), mapping this
to the -prop argument. This way you could have for example the Spanish
Blast2GO server with its current database (May 2010), and a local
Blast2GO database. I want to setup a local database and try this
before submitting the wrapper to the Tool Shed.
The input to the tool is a BLAST XML file, specifically blasting
against a protein database like NR (so blastp or blastx, not blastn
etc). I want to try some very large BLAST XML files to confirm
b2g4pipe copes with the current BLAST+ output files - I gather there
were some problems in this area in the past, so having the wrapper
script fragment the XML might be a workaround. Currently the only real
function of the wrapper script is to rename the output file - b2g4pipe
insists on using the *.annot extension.
Right now the only output is a tabular three column *.annot file,
which can be loaded into the Blast2GO GUI. For analysis within Galaxy,
I'm wondering about an option to split the first column (which holds
the original FASTA query's identifier and any description) in two.
i.e. Split at the first white space to give the FASTA identifier, and
any optional description as a separate column. That would make
linking/joining/filtering on the ID much easier.
If anyone has any comments or feedback now, that would be welcome.
Yesterday Alex Bossers indicated on Twitter that Gerrit had also been
looking at this (CC'd).
Regards,
Peter
11 years, 8 months
SMTP auth in galaxy?
by Holger Klein
Dear all,
for our galaxy setup I have to use an SMTP server which requires
authentication. Since I didn't find any documentation about galaxy's
capabilities in that regard, I'd like to ask you either for pointers or
a hint, if and how this can be handled.
For the smtp_server variable in universe_wsgi.ini I saw that people used
either a hostname or the path to a sendmail binary. Is something like
user:pass@smtpserver.organisation.org possible as well?
Cheers,
Holger
--
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de/
Tel: +49(6131) 39 21511
11 years, 8 months
history export tool loading panic
by Louise-Amélie Schmitt
Hi
I just blew everything up, I have no idea why. Galaxy doesn't start
anymore. When I run the run.sh script, it stops after loading the
converters and just crashes. Here's the traceback:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82,
in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__
load_history_imp_exp_tools( self.toolbox )
File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py",
line 34, in load_history_imp_exp_tools
history_exp_tool = toolbox.load_tool( tmp_name.name )
File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line
131, in load_tool
tree = util.parse_xml( config_file )
File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104,
in parse_xml
tree = ElementTree.parse(fname)
File
"/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 859, in parse
tree.parse(source, parser)
File
"/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 584, in parse
self._root = parser.close()
File
"/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 1251, in close
self._parser.Parse("", 1) # end of data
ExpatError: no element found: line 1, column 0
Exception IOError: (28, 'No space left on device') in <bound method
_TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at
0x8539a50>> ignored
Since the message is not really self-explanatory, I have no idea as to
what's gone wrong. The only thing I know is that the file referred by
tmp_name.name is empty. Do you have an idea where I should be looking?
I really can't relate that to anything I did recently, I just modified
some parameter labels in two tools, which should be really harmless, and
the display name of a reference genome, which shouldn't make any
difference either.
Thanks,
L-A
11 years, 8 months
Error when adding datasets
by Louise-Amélie Schmitt
Hello everyone
I have an issue when trying to import new datasets or when putting a
dataset into a history. I saw Edward Kirton had the same problem but he
got no answer:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html
Here is the error message I get when clicking the "Add datasets" button
in a library, in the admin's "Manage data libraries" panel:
UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped
URL:
http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db...
File
'/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line
539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/g/funcgen/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py',
line 109 in __call__
return self.app( environ, start_response )
File
'/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/g/funcgen/galaxy/lib/galaxy/web/framework/base.py', line 145 in
__call__
body = method( trans, **kwargs )
File '/g/funcgen/galaxy/lib/galaxy/web/controllers/library_common.py',
line 907 in upload_library_dataset
trans.sa_session.refresh( history )
File
'/g/funcgen/galaxy/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
'/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py', line 925 in refresh
raise exc.UnmappedInstanceError(instance)
UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped
Now when does it occur:
I have two databases. One test database I created a month ago which
works fine, even now. The other one I created recently which is supposed
to be the final database. But the latter keeps triggering the above
message, even when I drop it and create it all over again. I even tried
to create a third one, all clean and new but the problem remains. I
tried to trash all the eggs so Galaxy gets fresh new eggs, with no
effect at all. The error's still there.
If you have any clue, I'll be forever grateful.
Cheers,
L-A
11 years, 8 months
Updates to Galaxy Community Conference website
by Peter Cock
Hi all,
I have a couple of minor suggestions for improving the website
http://galaxy.psu.edu/gcc2011/Home.html
First, please fill in a meaningful HTML titles since that will be used
as the default caption in a bookmark, tab or window title.
Second, please add a link to the presentation slides and videos,
e.g. from the programme page and main page?
http://wiki.g2.bx.psu.edu/GCC2011
I realise this isn't complete yet, but it is already a useful resource.
Also once you have all the slides, could the links in the wiki table
be made to point straight to the file?
Thanks,
Peter
11 years, 8 months
Conventions for tool names and descriptions
by Peter Cock
Hi all,
Are there any guidelines on tool names and lengths? There is a tendency
due to the way the tool name and description are run together in the left
hand pane listing to write the description as an extension of the name:
e.g.
Name: Select
Description: lines that match an expression
Many of the default tool's descriptions do not make sense without the
name. I brought this up in in this thread at the end of last year, about
how the tool shed showed these fields:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html
Again based on observation, the tool names are generally up to four
words, short enough to fit on one line in the left hand pane. Description
lengths vary from nothing (e.g. the "Indel Analysis" tool) to over four
lines (e.g. the "Cuffcompare" tool). Note the line count depends on font
settings and if the user has altered the left hand pane column width.
Clearly there is a balance - shorter means more tools fit on screen at
once making navigation easier, longer makes it less likely the user will
have to click on each tool to read its more details description to find
what they are looking for.
This is also an issue for browsing the tool shed - I had an email
exchange with Alex about this tool of mine:
Name: Filter sequences by ID
Description: from a tabular file
I wrote it like this so that once installed the entry in Galaxy's left hand
pane reads "Filter sequences by ID from a tabular file", where I mean
the ID comes from a tabular file (not the sequences). This is however
ambiguous, Alex interpreted it as meaning the sequences come from
a tabular file. Including the words FASTA, FASTQ, or SFF in the text
would help, but also makes the tool entry in the left hand pane bigger.
Are there any guidelines for desirable name/description lengths?
Having a tool mock-up in the Tool Shed would help when browsing
potential tools of interest (enhancement issue 565), but that isn't
likely to happen in the short term:
https://bitbucket.org/galaxy/galaxy-central/issue/565
Thanks,
Peter
11 years, 8 months
Separate histories between localhost and 127.0.0.1
by Lewis, Brian Andrew
For some odd reason, when I try to import data using the URL http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will even show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy the jobs run fine. Here's a snip from my httpd.conf file:
RewriteEngine on
RewriteRule ^/static/style/(.*) /usr/local/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /usr/local/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /usr/local/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /usr/local/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /usr/local/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8081$1 [P]
The host lines are commented out in my universe_wsgi.ini files, so I'm guessing they should be set to the default "localhost."
~ Brian
11 years, 8 months
how can i get all the output file names in local.py file
by shashi shekhar
Hi All,
I am using standalone system for galaxy and am doing some modification
in galaxy .i need the all output file names in local.py .How can i get all
the output file names in local.py file.
Regards
shashi shekhar
11 years, 8 months
