Hi,
I've a setup a local instance of galaxy in our server using
PostgreSQL/nginx.
I've followed the instructions from the production server configuration as
stated from here:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server.
Galaxy is running and tried the "Galaxy 101" tuto
on_string seems to be defined for datatool parameters only.
There's a common idiom for looking up fields from the relevant .loc
files for things like all_fasta - it's not pretty but it does work -
eg from the bowtie wrapper:
--ref="${ filter( lambda x: str( x[0] ) == str(
$refGenomeSource.index
While ${on_string} works well for items in the history, I found that for
a dataset in a data table, for example in the 'all_fasta' table, the
content of ${on_string} is the null string.
Is that expected? Is there a better to get the name or some sort of
identifier of the dataset?
Thank you,
F
I use the latest stable version of Galaxy, which seems to have the fix.
However, I still experience some issues with optional parameters:
https://bitbucket.org/galaxy/galaxy-central/issue/661/optional-arguments-problems#comment-655611
Florent
On 04/07/11 23:27, Sarah Diehl wrote:
Hi Peter,
th
Alex,
I've created the following ticket for this issue as it looks to be a bug with
Galaxy / mysql. You can follow the ticket to be aware of progress.
https://bitbucket.org/galaxy/galaxy-central/issue/660/galaxy-installation-with-mysql-database
Thanks for reporting this,
Greg Von Kuster
On
2011/9/15 Mikel Egaña Aranguren :
> Hi;
>
> I'm sure this has been mentioned before but perhaps it has been fixed.
>
Not yet, but you can follow this issue:
https://bitbucket.org/galaxy/galaxy-central/issue/325/
> I'm writting a wrapper of a Java tool for Galaxy. The tool throws info to
> stderr
Hi;
I'm sure this has been mentioned before but perhaps it has been fixed.
I'm writting a wrapper of a Java tool for Galaxy. The tool throws info
to stderr even when working properly, and Galaxy interprets it as a bug.
Is there any way of redirecting stderr (It seems that normal UNIX
redirect
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Jennifer Jackson
http://use
Hello Joe,
Functional test-data is located here in the source:
http://bitbucket.org/galaxy/galaxy-central/src/07c5fbd618f3/test-data/
The name/comments of each is the best way to understand the link between
a test and a tool (could be many-to-many).
Next time, a question like this about a loc
On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu <2hug...@gmail.com> wrote:
> On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock wrote:
>
>> On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
>> >
>> > I think I need some kind of "data source" implementation that allow user
>> to
>> > obta
On Thu, Sep 15, 2011 at 10:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
> On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock
> wrote:
>>
>> Perhaps I have misunderstood you, but I'd just use the provided
>> "Upload Data" tool, and paste in the FTP URL for the file, e.g.
>> an NCBI FTP URL.
>
> I wasn't a
On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock wrote:
> On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
> >
> > I think I need some kind of "data source" implementation that allow user
> to
> > obtain the data themselves. However with the current tool XML definition,
> I
> > do
On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
>
> I think I need some kind of "data source" implementation that allow user to
> obtain the data themselves. However with the current tool XML definition, I
> don't know how to have a FTP download tool to download EST data from
If you need every output as an item in your history, does the example
in http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html
help? Naming might be a wart.
Otherwise the html datatype is really handy for throwing variegated
output into a single history item page. It can look lik
On Wed, Sep 14, 2011 at 5:21 PM, Hans-Rudolf Hotz wrote:
>
>
> On 09/14/2011 10:39 AM, Timothy Wu wrote:
>
> //
>
>
>> Alternatively, I can just ask user to download from NCBI ftp themselves,
>> decompress them, and upload it to galaxy.
>>
>> What's the best approach here?
>>
>
> How about: you d
Hi,
I too would be interested in knowing how to handle tools that might
generate multiple output files for the Grinder wrapper I am developing.
Any news on this? Has a ticket been recorded?
How about when the tool generate an number of files that cannot be
determined from the values the user
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