On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock wrote:
> Hi all,
>
> Using either the legacy upload tool, or the new upload widget, the
> following FTP URL *appears* to load into Galaxy correctly giving
> a green history entry.
>
> However, on closer inspection it is an empty file with this peep text:
Hi Galaxy,
I'm trying to put one of my java tool in galaxy.
I've copied the required files in my tool directory under /tools/jvarkit
(I can see it galaxy)
$ ls
commons-jexl-2.1.1.jar
commons-logging-1.1.1.jar
htsjdk-1.129.jar
snappy-java-1.0.3-rc3.jar
vcffilterjs.jar
On Thu, Feb 26, 2015 at 10:59 AM, Pierre Lindenbaum
wrote:
> Hi Galaxy,
>
> I'm trying to put one of my java tool in galaxy.
>
> I've copied the required files in my tool directory under /tools/jvarkit (I
> can see it galaxy)
>
> $ ls
> commons-jexl-2.1.1.jar
> commons-logging-1.1.1.ja
Hi Peter,
i wrote the tool_dependencies.xml
$INSTALL_DIR
and updated vcffilterjs.xml
jvarkit
On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum
wrote:
> Hi Peter,
>
>
> i wrote the tool_dependencies.xml
>
>
>
>
>
>
>
>
> action="set_to">$INSTALL_DIR
>
>
>
> You'll need to white list the semi-colon which Galaxy has replaced as
a security precaution (user free text can be exploited). See
here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter
Thanks: adding :
Just to make sure - since it hasn't been explicitly stated - is this
tool being installed from the tool shed? The environment variable
setup in tool_dependencies.xml will only be available for tool shed
installs. You will also need a special requirement in your tool to
make it available
(https://gi
On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum
wrote:
>> You'll need to white list the semi-colon which Galaxy has replaced as a
>> security precaution (user free text can be exploited). See here:
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter
>
>
> Thanks: adding :
>
>
Yeah - that is unfortunate - I agree completely that the resulting
datasets should be red. I have created a Trello card here:
https://trello.com/c/A6LrdjUU
-John
On Thu, Feb 26, 2015 at 5:19 AM, Peter Cock wrote:
> On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock wrote:
>> Hi all,
>>
>> Using eithe
On 02/26/2015 02:51 PM, John Chilton wrote:
Just to make sure - since it hasn't been explicitly stated - is this
tool being installed from the tool shed? The environment variable
setup in tool_dependencies.xml will only be available for tool shed
installs.
no, my future plan is to put it in the
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip.
Also not need to escape $_
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton wrote:
>
> Also not need to escape $__tool_directory__ (so use
> $__tool_directory__ instead of \$__tool_directory__).
>
> -John
If this was unclear, $VAR in the XML fragment
is taken to be a Python variable available within the Cheetah
parser. Typi
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote:
> Yeah - that is unfortunate - I agree completely that the resulting
> datasets should be red. I have created a Trello card here:
>
> https://trello.com/c/A6LrdjUU
>
> -John
Thanks John,
Does the new "Download from URL or upload files from dis
Il 26.02.2015 15:57 Peter Cock ha scritto:
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote:
Yeah - that is unfortunate - I agree completely that the resulting
datasets should be red. I have created a Trello card here:
https://trello.com/c/A6LrdjUU [1] -John
Thanks John,
Does the new "Dow
Yes - I believe it does. The top level layer (controller) is a little
different because it is coming through the API - but the next 10 or so
layers related to uploading are the same with the new method :).
-John
On Thu, Feb 26, 2015 at 9:57 AM, Peter Cock wrote:
> On Thu, Feb 26, 2015 at 2:24 PM
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote:
> Yeah - that is unfortunate - I agree completely that the resulting
> datasets should be red. I have created a Trello card here:
>
> https://trello.com/c/A6LrdjUU
>
> -John
I just commented on the Trello issue - as John implied with
the issue
On 02/26/2015 03:43 PM, John Chilton wrote:
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/
Well - this version does feature Sam's complete rewrite of the front
end for tools - so things will be pretty different.
Oddly though your tool loaded for me - can you open up your JavaScript
console and let me know if there are any errors?
-John
On Thu, Feb 26, 2015 at 10:14 AM, Pierre Lindenba
On 02/26/2015 04:20 PM, John Chilton wrote:
Well - this version does feature Sam's complete rewrite of the front
end for tools - so things will be pretty different.
Oddly though your tool loaded for me - can you open up your JavaScript
console and let me know if there are any errors?
my bad, e
Is there any chance I can get you to reproduce this problem on the Galaxy
test server:
https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffcompare%2Fcuffcompare%2F2.2.1.0
and
then share the history with me (jmchil...@gmail.com)?
We have fixed some bugs relate
Helop aI've been testing (using planemo) some tools scheduled for toolshed
publication. My first test works, but Galaxy reports that the second one fails
with:
"Parameter %s requires a value, but has no legal values defined" % self.name
AssertionError: Parameter filter_column requires a value,
Slightly garbled there ... meant to say
Help appreciated once again,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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