Hi Greg,
Indeed, I mean the tool config wrapper, named razers3_wrapper.xml, when
I mention 'tool config'.
This xml is the alpha version, and is loaded correctly in my
development Galaxy. So I pushed it to the repository
=================================
Changeset 997118f8f033
added:
razers3_wrapper.xml
razers3_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/razers3_wrapper.xml Thu Sep 27 14:39:54 2012 +0200
@@ -0,0 +1,372 @@
+<tool id="rasers3" name="Map reads with rasers3" version="1.0.0">
+ <!-- Additional info: wrapper compatible with versions ..... -->
+ <description>
+ a read mapping program for all kinds of reads with adjustable
sensitivity.
+ </description>
+
+ <version_command>
+ razers3 --version
+ </version_command>
+
(etc.)
=============================
But it still displayed the wrong name in the interface. I just found
out the reason: the original file "wrapper_template.xml" was not
removed from the repo (although not anymore present in my local repo).
After removal, the tool is displayed correctly!
One more question though about mercurial: how come that when I changed
the name of the "wrapper_template.xml" to razers3_wrapper.xml, and that
after pushing the commits "wrapper_template.xml" was still on the
toolshed? Is this default behaviour of Mercurial?
Many thanks for the assistance,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On Thu 27 Sep 2012 03:08:27 PM CEST, Greg Von Kuster wrote:
Hello Joachim,
On Sep 27, 2012, at 8:05 AM, Joachim Jacob wrote:
Hi all,
As a test, I have uploaded some template files to a newly created repository on
our test toolshed.
This is great! It's good to hear when the Galaxy community is using local tool
sheds within their environments.
I pulled that repository on my development machine using mercurial: from this
folder I start now developing the tool wrapper.
This is a great approach because the tool shed is not a source code repository
for developing tools, so development generally takes place within an
environment running a development Galaxy instance. When the tool development
is stabilized and the tool's functionality is proven to be correct within the
Galaxy development instance, the tool and all of it's associated files can be
uploaded to the tool shed for sharing with others. Treating the tool shed as a
source code repository for tools while they are in development will undoubtedly
result in undesired behavior by the tool shed.
I have noticed that once the tool name has been set in the tool config (<tool
name="xxxxx" >) during the initial upload, pushing a subsequent change to this
name, this does not change the name on the repository anymore (and the other settings, for this
matter). Is this correct?
I'm not quite clear on your question here. If by "tool config" you mean the
Galaxy tool config wrapper (e.g., my_tool.xml), the tool shed never makes any changes to
them when they are uploaded to a repository in the shed. The repository in the tool shed
is just an enabler for sharing what is there. Changes to the content must be made in
your development environment and pushed to the repository in the tool shed.
The name of the tool shed repository itself can be changed only until the first
clone occurs. Once a clone occurs, the cloned repository path includes the
name of the repository, so if it was subsequently changed in the tool shed,
those that cloned it previously could not get updates to their local clones.
Greg Von Kuster
Thanks,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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