OK, so toolshed running on galaxy-central is not an option. Then I need to remove the white ghosts by hand everytime they appear.

Cheers,
Joachim


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 10/01/2013 09:39 AM, Bjoern Gruening wrote:
Hi Joachim,

I don't think that is possible at the moment (its not a general problem,
but in this cycle it seems to be). Currently I can not install from the
test toolshed in my stable test branch. Because the tool shed is not
forward compatible (yet). I can be wrong, but if you get an error, that
is probably the reason. There is a trello card about forward
compatibility, somewhere.

Ciao,
Bjoern

Thanks, then I will run toolshed from a separate galaxy-central clone if
that's advisable - different from the Galaxy service. I prefer to keep
galaxy-dist on the stable branch.

In this process, I will move the tools from the old toolshed to my new
toolshed running from galaxy-central. When I have time, I will upload
everything to the test-toolshed.

Cheers,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 05:11 PM, Bjoern Gruening wrote:
Hi Joachim,

I had such problems if my XML file is invalid. Than I get immediately
the 'installed:' text and can click install again, without any change.
Also I would really recommend to reset your toolshed. These "white
ghosts" can have unpredictable effects.

If you can upload your tools to the test tool shed I can try to install it 
debug it.

Please make sure that you run the latest Galaxy central version. Greg and
Dave invested a lot of time to get rid of "white ghosts". But these changes are
only in central.

Cheers,
Bjoern



Still having a hard time and some strange situations. It is almost too
much to report via email.

Basically, the tool_dependencies.xml get recognised sometimes. Please,
watch this video to see what I mean (1'30''), and pause as you like:
https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv

I am afraid I cannot invest this amount of time to make my repo's
public-proof. There are weird things happening which make no sense to
me. And debugging of tool_dependencies.xml is very hard, since I find
almost no logs of this process.


Joachim.

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,

For sourceforge URLs, you can safely omit the question mark and
everything after it, since that's part of the browser download load
balancing process. When downloading with wget, curl, or python's
urllib, downloads.sourceforge.net does its own behind-the-scenes load
balancing. As for hyphens, I don't believe they need to be escaped,
since they're not XML entities like the ampersand is. The following
download_by_url action should work:

<action
type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip</action>


     --Dave B.

On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,


Not fixed yet. Somehow the download does not work: I have escaped the
ampersands and the hyphens. The download seems to have to proceed, since
I receive no error from the download step. The next step in the
dependencies file gives an error: mv: cannot stat transpose.zip': No
such file or directory



Cheers,
J


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as &amp; and then it should
work.

Peter

On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
<joachim.ja...@vib.be> wrote:
Hi all,


The download URL seems not to be accepted in tool_dependencies.xml.
It is an
URL from sourceforge, the direct link to a package.

The error upon uploading the tool to my toolshed:
**************
Metadata may have been defined for some items in revision
'5665a799775d'.
Correct the following problems if necessary and reset metadata.
tool_dependencies.xml - Exception attempting to parse
/mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not
well-formed
(invalid token): line 6, column 149
**************

The tool_dependencies.xml file:
**************
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="transpose" version="2.0.0">
4        <install version="1.0">
5             <actions>
6     <action
type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet</action>


7                <action type="shell_command">mkdir bin</action>
8              <action type="shell_command">unzip
transpose-2.0.zip</action>
                   <action type="shell_command">cd
transpose-2.0/src</action>
                   <action type="shell_command">gcc transpose.c -o
transpose</action>
                   <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source>
<destination>$INSTALL_DIR/bin</destination>
                   </action>
                   <action type="shell_command">chmod +x
$INSTALL_DIR/bin/transpose</action>
                   <action type="set_environment">
                       <environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                   </action>
               </actions>
           </install>
           <readme>
           Compiling transpose and putting in the path.
           </readme>
</package>
</tool_dependency>
**************


Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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