Peter, Pieter and Dave, thank you for the pointers to your tools - they've
been extremely helpful!  Now I can see how the process is supposed to work.
 I'm not really sure where mine is going wrong, but maybe someone here will
have ideas.

So folks, I've had partial success with a repository that includes a
tool_dependencies.xml, which sets two environment variables and moves a JAR
file from REPOSITORY_INSTALL_DIR to INSTALL_DIR.  But the following things
suggest to me that it's only a partial success, and I'm very interested in
any insights to clear them up.


1. I have my repository checked into an internal tool shed.  Somewhere in
the course of development, I specified a buggy dependency, and now I can't
seem to clear it up.  When I go to (re)install my tool from the tool shed,
here's what I see in the way of dependencies:

 Tool dependencies* - these dependencies may not be required by tools in
this repository*
NameVersionTypeOrphanJAR_PAHTset_environmentyes
and as you might imagine, I've checked the obvious things, and there is no
more reference to "JAR_PAHT" (typos and all) anywhere in or around my tool,
or in my galaxy-dist directory.  It seems like there's some old metadata
cruft that hasn't been cleared out.  How can I clear it out?


2. When I install my tool, I see the following messages in paster.log:

---

tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
DEBUG 2014-09-02 17:13:59,279 Building repository dependency
relationships...

172.30.0.22 - - [02/Sep/2014:17:13:59 -0700] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 200 - "
http://tcga1:1235/admin_toolshed/prepare_for_install?tool_shed_url=http://medbook.ucsc.edu:9009/&repository_ids=decab5ee1e95b10b&changeset_revisions=ff9b02e50bcf";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/36.0.1985.143 Safari/537.36"

172.30.0.22 - - [02/Sep/2014:17:14:02 -0700] "POST
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "
http://tcga1:1235/admin_toolshed/prepare_for_install"; "Mozilla/5.0
(Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/36.0.1985.143 Safari/537.36"

tool_shed.util.shed_util_common DEBUG 2014-09-02 17:14:03,477 Error
attempting to get tool shed status for installed repository start_xena:
HTTP Error 404: Not Found

Attempting older 'check_for_updates' method.

---

Should I be concerned about these last messages?  I don't remember seeing
them with Peter, Pieter and Dave's tools.


3. After my tool has installed, there is no INSTALLATION.log in my
INSTALL_DIR.  Does this mean that the installation process somehow
terminated early?  There is an env.sh file, with the correct values of the
environment variables I'm setting in my tool_dependencies.xml, and my jar
file is copied to INSTALL_DIR.  In my Galaxy window, my tool is indicated
as "Installed", in green.  Here are the last messages I see in paster.log:

tool_shed.galaxy_install.install_manager DEBUG 2014-09-02 17:14:04,630
Changing status for tool dependency installXena from Installing to
Installed.

tool_shed.galaxy_install.install_manager DEBUG 2014-09-02 17:14:04,669 Tool
dependency installXena version 1.0 has been installed in
/inside/home/cline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/3e4683c94d8d.

172.30.0.22 - - [02/Sep/2014:17:13:59 -0700] "POST
/admin_toolshed/manage_repositories HTTP/1.1" 302 - "
http://tcga1:1235/admin_toolshed/prepare_for_install"; "Mozilla/5.0
(Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/36.0.1985.143 Safari/537.36"

172.30.0.22 - - [02/Sep/2014:17:14:04 -0700] "GET
/admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=3f5830403180d620
HTTP/1.1" 200 - "http://tcga1:1235/admin_toolshed/prepare_for_install";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/36.0.1985.143 Safari/537.36"

172.30.0.22 - - [02/Sep/2014:17:14:05 -0700] "POST
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "
http://tcga1:1235/admin_toolshed/prepare_for_install"; "Mozilla/5.0
(Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/36.0.1985.143 Safari/537.36"


Thanks for the insights, folks!  It actually seems like my tool is running
post-install, but I just want to make sure that everything is in place
before I go on to the next step.


Melissa





On Sat, Aug 30, 2014 at 5:50 AM, Dave Bouvier <d...@bx.psu.edu> wrote:

> Melissa,
>
> You can find additional examples in the following repository:
>
> https://toolshed.g2.bx.psu.edu/view/devteam/package_picard_1_56_0
>
> Which is then sourced by the following two repositories:
>
> https://toolshed.g2.bx.psu.edu/view/devteam/picard
> https://toolshed.g2.bx.psu.edu/view/devteam/sam_merge
>
>
>  --Dave B.
>
>
> On 2014-08-30 08:13, Lukasse, Pieter wrote:
>
>> Hi Melissa,
>>
>> See also
>>
>> https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb
>> or
>> https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_proteomics
>>
>> Regards,
>>
>> Pieter.
>>
>>
>> -----Original Message-----
>> From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-bounces@
>> lists.bx.psu.edu] On Behalf Of Peter Cock
>> Sent: zaterdag 30 augustus 2014 4:32
>> To: Melissa Cline
>> Cc: Galaxy Dev
>> Subject: Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that
>> install and run JAR files properly?
>>
>> On Sat, Aug 30, 2014 at 11:17 AM, Melissa Cline <cl...@soe.ucsc.edu>
>> wrote:
>>
>>> Hi folks,
>>>
>>> I'm attempting something that should be straightforward, but it's not.
>>> I have a tool that runs a JAR file, which I have bundled with the
>>> tool.  I simply want to run the JAR file.  And to paraphrase Thomas
>>> Edison, I've tried several thousand things that do not work (at least
>>> for me), from setting the JAVA_JAR_PATH environment variable in the
>>> tool_dependencies.xml file to trying to copy the JAR file into the
>>> tool-data/shared/jars subdirectories (which is the closest thing I've
>>> got to working).  So, at long last I'm doing the sensible thing and
>>> looking for one simple working example that I can use as a template.
>>> Who can suggest a good toolshed tool (either main or test) that
>>> involves running its own JAR file, and that works?
>>>
>>> Thanks!
>>>
>>> Melissa
>>>
>>
>> Here are a couple of my wrappers for Java tools, but I would suggest you
>> invoke the Java script with an absolute path to the JAR file:
>>
>> $ java -jar ...
>>
>> Here is two examples done via a Python wrapper script (mainly used for
>> pre or post processing the data files):
>>
>> https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
>> https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
>>
>> For EffectiveT3 which is open source and can therefore be easily
>> redistributed, I set an environment variable EFFECTIVET3 for the location
>> of the Jar file, which is used to invoke it via Java:
>>
>> $ java -jar ...
>>
>> For the Blast2GO wrapper, I require the person installing it setup an
>> environment variable B2G4PIPE pointing at the folder with the JAR file.
>> Older versions of this tool you be launched with the same -jar approach,
>> but the current release requires setting a class path instead:
>>
>> $ java -cp ...
>>
>> I hope that helps, if not there are bound to be other Java examples in
>> the ToolShed.
>>
>> Peter
>> ___________________________________________________________
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>>
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