Shantanu Pavgi wrote:
>
> I need some help in configuring galaxy with SGE scheduler using unified
> method. The galaxy is running on a system distinct from SGE scheduler
> install. The cluster nodes can access galaxy install, galaxy-tools and
> dataset files using NFS. I am not sure how drmaa w
Vipin TS wrote:
> Hello Nate,
>
> Can you make sure that your dump was created with '-E UTF-8' flag?
> >
>
> I didn't use any customized encoding for my dump, took the default one, I
> believe which is the database encoding.
>
>
> > Also, in your old database server, use psql's '\l' command to
I need some help in configuring galaxy with SGE scheduler using unified method.
The galaxy is running on a system distinct from SGE scheduler install. The
cluster nodes can access galaxy install, galaxy-tools and dataset files using
NFS. I am not sure how drmaa works and how galaxy submits jobs
This is probably not a galaxy problem at all, however it is manifesting
itself in the history pane of galaxy. The history widgets don't expand
-- everything else works fine.
The relevant javascript error looks to be:
Uncaught TypeError: Cannot call method 'init' of undefined
init_history_items
On Thu, May 12, 2011 at 6:03 PM, Leandro Hermida wrote:
> Hi, how do you make float parameter types fully optional? optional="true"
> doesn't work.
>
> -Leandro
Sadly this is a known bug I reported some time ago:
https://bitbucket.org/galaxy/galaxy-central/issue/403
Peter
Thanks for letting me know. I'm also forwarding this galaxy-dev, so the thread
in complete.
Thanks,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On May 12, 2011, at 2:30 PM, Katie Hyma wrote:
> Hi Anton,
>
> You're right, sorry for the false alarm. After a more car
Frederick,
The API is distributed along with galaxy. To enable it, set the following in
your universe_wsgi.ini:
enable_api = True
Once that's enabled, each user can create an API key using the "API Keys"
option in the user menu of the main masthead. For additional information, see
/scripts/
Hello Nate,
Can you make sure that your dump was created with '-E UTF-8' flag?
>
I didn't use any customized encoding for my dump, took the default one, I
believe which is the database encoding.
> Also, in your old database server, use psql's '\l' command to show the
> encoding of your database
Anyone know where i can get the galaxy API?
Regards
Fred
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On Thu, Apr 7, 2011 at 7:00 PM, Peter Cock wrote:
> On Thu, Apr 7, 2011 at 4:28 PM, Peter Cock wrote:
>> Hi all,
>>
>> I have just found a problem using the "Filter data on any column using
>> simple expressions" tool, i.e. files tools/stats/filters.xml and
>> tools/stats/filters.py
>>
>> I have
Hi, how do you make float parameter types fully optional? optional="true"
doesn't work.
-Leandro
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Vipin TS wrote:
> Hello Nate,
>
> Was your original dump from a database using an encoding other than
> > UTF-8?
> >
> > --nate
> >
> >
> My database was in postgres 8.3 and I took the database dump using postgres
> 8.4.
> I did not understand your question at right way.
Can you make sure that yo
Katie:
"Filter pileup" outputs 0-based coordinates if you use the "Convert
coordinates to intervals" option. So the issue may be related to aaChanges
tools. Can you give us a specific example, so we can track things down.
Thanks!
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
h
Hello Nate,
Was your original dump from a database using an encoding other than
> UTF-8?
>
> --nate
>
>
My database was in postgres 8.3 and I took the database dump using postgres
8.4.
I did not understand your question at right way.
Vipin
_
Hi all,
I ran into this problem, and thought others might run in to it as well:
When using bowtie and samtools, positions are formatted with a 1-base
offset, whereas interval format requires 0-base offset.
Recently, I used the 'Filter pileup on coverage and SNPs' tool with the
'convert coordinates
Vipin TS wrote:
> Sorry for the relayed response from my side.
>
> As you suggested I tried with --disable-triggers option for restoring the
> database from the dump file,
> Apparently this returns some notice message associated with circular
> foreign-key constraints for few
> tables. Here are s
Hello Nate,
>
> When restoring, I generally use the --disable-triggers, which instructs
> Postgres to ignore foreign key constraints.
>
> --nate
>
>
Sorry for the relayed response from my side.
As you suggested I tried with --disable-triggers option for restoring the
database from the dump file,
Hello,
There's a small bug when entering a double-quote character in a dataset name:
The double-quote confuses some later-on processing (templates and
Display-Application XML), resulting in some problems.
Example:
This history has one BAM dataset with a name of:
Hello "world"
http://main.g2.b
Hello,
When adding a new tool, we used a cheetah'ed shell script defined in the
tags of the tool's xml file. To get the absolute path of
an external script located in the tools directory, I used the following
code in the script:
${ os.getcwd() }/${ $__app__.config.tool_path }/toolsubdir/sc
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