Hi again,
I've realised that my current Blast2GO install script would be a perfect
example of where this tweak to fabric_util.py would help - when I wrote
the tool_dependencies.xml I didn't appreciate that the download_by_url
action was only allowed as the first action - currently it is ignored
On Mon, May 13, 2013 at 8:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, May 13, 2013 at 11:42 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
...
This would explain the behaviour I am seeing with effectivet3 and
other tools on the Tool Shed - despite the tool_dependencies.xml
Hi Peter,
I'm going to be enhancing this new feature further today, creating a new list
Latest revision: installation errors, so this category will be extracted from
the current failing tests category. At the same time I'll be adding the new
feature allowing the owner of a repository to set
On Fri, May 10, 2013 at 8:11 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Dave,
that was fast.
Thanks a lot!
Björn
Thanks Dave,
I see this also should fix handling of JAR files in download_by_url :)
On Mon, May 13, 2013 at 10:34 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, May 10, 2013 at 8:11 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Dave,
that was fast.
Thanks a lot!
Björn
Thanks Dave,
I see this also should fix handling of JAR files in
On Thu, May 9, 2013 at 4:39 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to
Hi Peter,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to work, but not all. For instance, this one
appears not to be downloading
Björn, Peter,
I've created a trello card (https://trello.com/c/QY0Z7L7p) for this
requirement, and will be working on enhancing that feature as my next
priority.
--Dave B.
On 5/10/13 09:59:37.000, Björn Grüning wrote:
Hi Peter,
For defining the 'install script' for some of my tool
On Fri, May 10, 2013 at 2:59 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
I believe that either I have a simple error in both install descriptions,
leading to the install to 'work' but not put things where I expect them
(which is my problem), or the install is
Peter,
Yes, jar files are just a directory of .class (and other) files packaged
with the zip algorithm, which has its benefits and drawbacks, as you've
discovered. In the new action type I'm working on, I do intend to
include the option to extract a downloaded file, or leave it as-is,
which
Peter,
As of 9696:b4733e42a2c9, Galaxy now supports an additional tool
dependency installation action called download_file, which downloads a
file from the specified URL and saves it to the current working
directory, without extracting it. The format is:
action
Hi all,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to work, but not all. For instance, this one
appears not to be downloading or moving
Hi Peter,
Hi all,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to work, but not all. For instance, this one
appears not to be
On Thu, May 9, 2013 at 4:57 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
Afaik download_by_url is only supported as first action. To work
around that limitation, until its fixed, I used wget to fetch any
additional file.
Ciao,
Björn
Interesting tip - I
Currently I feel that a tool dependency definition should allow for only a
singe download of some item, and if that item requires other items. they should
be defined as separate dependencies that are installed using the
prior_installation_required=True attribute.
Is there a case where this is
Hi Greg and Peter,
two examples from my side.
One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick
for example, makes sense to include as separate repo. But I feel that
the other are too special.
- openbabel (is an extra repo)
- GraphicsMagick
- potrace
- gocr
- tclap
-
On Thu, May 9, 2013 at 6:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Currently I feel that a tool dependency definition should allow for only a
singe
download of some item, and if that item requires other items. they should be
defined as separate dependencies that are installed using the
On Thu, May 9, 2013 at 6:21 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Greg and Peter,
two examples from my side.
One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick
for example, makes sense to include as separate repo. But I feel that
the
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