problem with getting the tables up in Profile Annotations
by CHAN Chee Seng
Hi,
I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the "Tables to Use" to be displayed on the web interface.
I have looked at the following files.
1. annotation_profiler_options.xml
2. annotation_profiler_valid_builds.txt
I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line,
hg18
which is fine since I am starting with human.
Where do I specify the location of my hg18?
Please let me know if you need more information.
Thanks for your help.
Best regards,
Chee Seng, Chan
Genome Institute of Singapore
60 Biopolis Street, Genome
#02-01 Singapore 138672
DID 64788065
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10 years, 9 months
Issue with deleting multiple histories
by Tam, Oliver
Hi,
I recently discovered an issue that prevents me from easily deleting
multiple histories at once.
This is the method I use:
Click ³Options² on the right side menu -> Go to ³Saved Histories² -> Click
on the check box of the history to be deleted -> Click ³Delete² button at
the bottom (next to ³For selected histories:²).
When I do this, nothing happens, and the history remains.
However, if I click on the the downward triangle and click on ³Delete² from
the pull down menu, the history is correctly deleted.
Deleting using the check-boxes and the Delete button works in changeset
3446:143c920af25c
But fails in changeset 3447:f5d383525d68.
Please let me know if you cannot reproduce the problem.
Cheers,
Oliver
10 years, 9 months
run.sh paste error
by Nathaniel Street
Hi
I have a problem that I've not been able to track down. I've tried
searching the mailing list archive and googling.
When I enable paste in universe_wsgi.ini and then run run.sh I get this
error. The same occurs for both the stable and development branches.
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in <module>
command.run()
File
"/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 274, in command
relative_to=base, global_conf=vars)
File
"/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 308, in loadserver
relative_to=relative_to, **kw)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 210, in loadserver
return loadobj(SERVER, uri, name=name, **kw)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 409, in get_context
section)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 431, in _context_from_use
object_type, name=use, global_conf=global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 361, in get_context
global_conf=global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 285, in _loadegg
return loader.get_context(object_type, name, global_conf)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 561, in get_context
object_type, name=name)
File
"/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 600, in find_egg_entry_point
for prot in protocol_options] or '(no entry points)'))))
LookupError: Entry point 'gzip' not found in egg 'Paste' (dir:
/home/nat/work/software/galaxy-central/eggs/Paste-1.6-py2.6.egg;
protocols: paste.server_factory, paste.server_runner; entry_points: )
The strange thing is on another machine I don't get the error but I
can't find out what the missing dependency is on the machine the
generates the error despite comparing installed packages etc.
I'm running Ubunutu 9.1 64bit on both machines.
Can anyone tell me what I'm missing that leads to the above error?
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
10 years, 9 months
Re: [galaxy-dev] Weird problem with importing datasets
by Chris Cole
On 09/03/10 15:42, Chris Cole wrote:
> On 09/03/10 14:53, Nate Coraor wrote:
>> Chris Cole wrote:
>>> Anyone got any ideas on this?
>>>
>>> It's still not working (following the most recent updates) and we've
>>> got some NGS data to import into Galaxy.
>>
>> Hi Chris,
>>
>> To use this feature, the contents of library_import_dir should
>> themselves be directories (or symlinks to the same). Selecting that
>> directory from the dropdown in the library upload form will then import
>> the contents of those directories.
>
> Ah, right. That's not clear in the docs.
>
> How come it works with locally symlinked files, then?
Just checked it again (sorry I shouldn't have sent the previous email)
with a directory and it still isn't working.
www-galaxy@ge-002: tmp> cd ~/data_import/
www-galaxy@ge-002: data_import> ls
README
www-galaxy@ge-002: data_import> ln -s /homes/pschofield/data/TOH
www-galaxy@ge-002: data_import> ls TOH/
0min_1.txt 30m_1.txt 60min_1.txt Cd_inuc_1.txt Cmono_1.txt
Dd_inuc_1.txt Dmono_1.txt processed
0min_2.txt 30m_2.txt 60min_2.txt Cd_inuc_2.txt Cmono_2.txt
Dd_inuc_2.txt Dmono_2.txt
www-galaxy@ge-002: data_import> ls -l
total 96
-rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README
lrwxrwxrwx 1 www-galaxy barton 26 Mar 9 15:59 TOH ->
/homes/pschofield/data/TOH
I got the TOH option in the 'Upload directory of files', which I
selected, but the upload failed. Again, this is the error I get when
selecting one of the filenames in the dataset:
Traceback (most recent call last): File
"/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326,
in __main__() File
"/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318,
in __main__ add_file( dataset,
error
Thanks for help.
Chris
10 years, 9 months
Wiki Addition: Site Map and Site Index
by Kelly Vincent
Everyone,
Bitbucket (our code and wiki host) does not offer any way to search
the wiki, so there are now two new pages to fill the void: SiteMap and
SiteIndex. These are both generated automatically. The idea is that
the pages should be generated by a script that is scheduled to run
each night, but I'm still getting that going--in the meantime, I'll be
running the script manually.
SiteMap is a simple listing of all the pages found under the base wiki
directory. You can get a pretty good idea what the page is about just
by the name of it, which is all that's included in this list. You can
see SiteMap at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap.
SiteIndex is more complicated. It is a traditional index, which means
that (almost) every word that appears in the wiki is included with a
list of the pages on which it appears following it. A stoplist was
used to remove useless or meaningless words, but there is still some
junk that has made it past this filter. The index involves multiple
pages, divided up alphabetically. It's available at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteIndex
.
Regards,
Kelly
10 years, 9 months
change_format and conditonal vars
by Edward Kirton
hi, how do i reference conditional variables from within the
change_format tag? i couldn't find any examples that did this. an
example tool config xml file follows.
thanks!
ed kirton
us doe jgi
<tool id="fasta_get_seqs" name="Get Sequences">
<description>Create a Fasta/Qual file of selected sequences</description>
<command interpreter="perl">fasta_get_seqs.pl $intype.infile
$input_table $id_column $ignorecase $cosorted $output
#for $i in $filters
"${i.condition} ${i.column} ${i.value}"
#end for
</command>
<inputs>
<conditional name='intype'>
<param name='sel' type='select' label='Input file type'>
<option value='Fasta'>Fasta</option>
<option value='Qual454'>Qual454</option>
</param>
<when value='Fasta'>
<param name="infile" type="data" format="fasta" label="Fasta file"/>
</when>
<when value='Qual454'>
<param name="infile" type="data" format="qual454"
label="Qual454 file"/>
</when>
</conditional>
<param name="input_table" type="data" format="tabular" label="File
containing target IDs"/>
<param name='id_column' type='data_column' data_ref='input_table'
label='Column containing sequence IDs'/>
<param name='ignorecase' type='boolean' truevalue='1'
falsevalue='0' label='Ignore case?' />
<param name="cosorted" type="boolean" checked="true" truevalue='1'
falsevalue='0' label='Sequences appear in same order in both files'/>
<repeat name='filters' title='Filter'>
<param name='condition' type='select' label='Condition'>
<option value='s_eq'>text equals</option>
<option value='s_ne'>text not equals</option>
<option value='s_contains'>text contains</option>
<option value='s_startswith'>text starts with</option>
<option value='s_endswith'>text ends with</option>
<option value='n_eq'>number ==</option>
<option value='n_ne'>number !=</option>
<option value='n_gt'>number ></option>
<option value='n_lt'>number <</option>
</param>
<param name='column' type='data_column' data_ref='input_table'
label='On column'/>
<param name='value' type='text' label='Value'/>
</repeat>
</inputs>
<outputs>
<data name="output" format="fasta">
<change_format>
<when input="intype.sel" value="Qual454" format="qual454" />
</change_format>
</data>
</outputs>
<help>
**What it does**
Produces a Fasta/Qual file of selected sequences.
If the files are cosorted, a much faster algorithm is used. If it
fails, it assumes the files were not cosorted and automatically tries
again
using the slower algorithm which does not require cosorted files.
One or more filters may be included to evaluate text (equal, not
equal, contains, starts with) or numeric data (==, !=, >, <).
</help>
</tool>
10 years, 9 months
'Never ending' jobs in history
by Chris Cole
Hi,
Occasionally, we see jobs that are constantly in the 'job running' state
in the history. This is despite the fact that the job completed
correctly. I can also see in the paster.log file that Galaxy has picked
up on the fact that the job ended, but it just hasn't updated the UI.
Clicking the eye for the 'running' history items does show the results
of the run.
This does not happen all the time. Is this a known issue and/or how can
I resolve it?
Thanks,
Chris
10 years, 10 months
Re: [galaxy-dev] Python crashing after latest changeset update (OSX) (Fixed)
by Roy Weckiewicz
Solved this problem by creating a new instance of galaxy via hg clone and
creating a new MySQL database followed by the setup.sh, modifying
universe_wsgi.ini to point to my MySQL database and finally run.sh which
migrated the database and started the server without a Python crash.
On Thu, Mar 25, 2010 at 4:35 PM, Roy Weckiewicz <roystefan(a)gmail.com> wrote:
> Hello,
>
>
> After doing a hg pull and update a few minutes ago, my Python (2.5.1) is
> crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem
> to contain any information about the error and seems to start the galaxy
> server just fine (localhost). I've attached osx error report details. Any
> ideas?
>
>
>
>
> Thank you,
>
>
> Roy Weckiewicz
>
> --
> Roy Weckiewicz
> Texas A&M University
>
--
Roy Weckiewicz
Texas A&M University
10 years, 10 months
Python crashing after latest changeset update (OSX)
by Roy Weckiewicz
Hello,
After doing a hg pull and update a few minutes ago, my Python (2.5.1) is
crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem
to contain any information about the error and seems to start the galaxy
server just fine (localhost). I've attached osx error report details. Any
ideas?
Thank you,
Roy Weckiewicz
--
Roy Weckiewicz
Texas A&M University
10 years, 10 months
