On Sun, May 17, 2015 at 5:44 PM, Brian Haas wrote:
> Greetings.
>
> Does anyone per chance have a simple working example of using composite data
> types? I've gotten as far as I can with the galaxy documentation, and I
> can't seem to get the additional files bundled into an extra files
> direct
Thanks, Peter! I've verified that I can get your code to work - bundling
the composite files. I'll keep plugging away at my little example and see
if I can figure out what's going awry.
more later. Thx again!
~brian
___
Please keep all r
On Mon, May 18, 2015 at 1:55 PM, Brian Haas wrote:
> Thanks, Peter! I've verified that I can get your code to work - bundling
> the composite files. I'll keep plugging away at my little example and see
> if I can figure out what's going awry.
>
> more later. Thx again!
Good luck - compound da
In the next couple of hours, if I'm not able to resolve this, I'll post my
ultra-simple example on github and I'll be grateful for others to take a
look.
cheers,
~brian
On Mon, May 18, 2015 at 9:23 AM, Peter Cock
wrote:
> On Mon, May 18, 2015 at 1:55 PM, Brian Haas
> wrote:
> > Thanks, Peter!
Hi,
I have configured apache as reverse proxy for galaxy and I also configured
apache to access my openldap for authentication. It's working fine but I
was getting some trouble to logout the users as explained in the
documentation here
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth#L
Hi Brian,
Your original email with attachments has made it to the list now,
http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html
Title: "difficulty creating composite data type"
Peter
On Mon, May 18, 2015 at 2:25 PM, Brian Haas wrote:
> In the next couple of
Fantastic!
I've actually made a few changes. I'm putting my latest code up on github
now and will share it in just a moment. It'll be much easier this way -
as you suggested.
best,
~brian
On Mon, May 18, 2015 at 9:58 AM, Peter Cock
wrote:
> Hi Brian,
>
> Your original email with attachme
I've uploaded my simple example here:
https://github.com/brianjohnhaas/galaxy_composite_datatype_test
I can't seem to get it to bundle the output files no matter what I've
tried. Help is much appreciated. :)
best,
~brian
___
Please keep a
I'm trying to create a tool that user's can use that will interact with
Galaxy 's API, however the tool needs to be able to determine the user's
API key.Is this possible? Can a tool determine what the user's API key
is when the user actually runs the tool?
_
Hey Ryan,
I would review the following threads - they have hacks for doing this
and required warnings:
http://dev.list.galaxyproject.org/find-UUID-of-current-history-in-tool-XML-wrapper-td4667113.html
http://dev.list.galaxyproject.org/Possible-to-pass-hostName-to-a-tool-td4667108.html
-John
On
Hi Peter,
I'm actually more confused now that I was when I started... I was able to
get your code working, focusing on the 'makeblastdb' with a nucleotide
fasta file. I figured that experimenting with this example would lead to
some key insights, particularly by dropping certain files that are s
I always recommend installing a virtualenv for Galaxy - and it should
be pretty easy to install ldap into that with pip. But you are
certainly right - longer term it probably makes sense to create a
dynamic egg for this (for consistency if no other reason). I have
created a Trello issue for that he
I will admit I don't understand how the mapper problem is related or
why it would occur in monitor_step or custom builds, but I do know
there is an important bug fix in release 15.05 from Dannon
(https://github.com/galaxyproject/galaxy/pull/198) that multiple
people have reported fixing the problem
Hi Brian,
In your example tool, you need to pass “${ test_cdt.files_path }" to your perl
script, which is a not-yet-existing directory for the files you want to be part
of the dataset’s extra files path.
Then you create that directory and place the files you want within that
directory.
Than
THANK YOU!!! :)
The fundamental piece that I was missing at:
https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
was the
someTool.sh $input1 ${os.path.join( input1.extra_files_path,
'results.txt' )} ${os.path.join( input1.extra_files_path,
'results.dat' )} $output1
It would be
It is a wiki, if you miss something - please add it.
Thanks
Martin
On Mon, May 18, 2015 at 3:08 PM Brian Haas wrote:
> THANK YOU!!! :)
>
> The fundamental piece that I was missing at:
> https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
>
> was the
>
> someTool.sh $input1 ${o
Ah! will do. :)
On Mon, May 18, 2015 at 3:09 PM, Martin Čech wrote:
> It is a wiki, if you miss something - please add it.
>
> Thanks
>
> Martin
>
>
> On Mon, May 18, 2015 at 3:08 PM Brian Haas
> wrote:
>
>> THANK YOU!!! :)
>>
>> The fundamental piece that I was missing at:
>> https://wiki.gal
I've updated my code, which now generates the .extra_files directory:
https://github.com/brianjohnhaas/galaxy_composite_datatype_test
I'm now trying to get the
composite_type = 'auto_primary_file*' *to work, but all I'm getting is an
empty file. My module code simply includes:
class Composite
I think this may be a limitation with the workflow forms... there is
much less dynamism in the workflow run dialog then in the tool run
dialog. I think Aysam is working on workflow modifications that will
bring these various forms closer together - I don't know if that will
be enough to implement t
19 matches
Mail list logo
