Hi Melissa,
a few remarks to your wrappers, hopefully it will fix a few issues.
* If you put your python files and your java files next to your wrapper
you do not need to install them. I think you can remove the
tool_dependency file and it should work.
* if you stick to this approach you should rename JAVA_JAR_PATH to
XENA_JAR_PATH or something like this
* do you really need the dependencies in the other repositories?
Dependencies are used to access binaries or libaries from other
installations, as far as I could see you are accessing a local port or?
So no dependency
* Question: do you need the server running all the time, or can you that
it during the tool execution (find, import)? We need a proper mechanism
to support such things like servers (on some ports). You will here have
the issue that multiple users can't start a server at once. We need to
get devteam help here. Would you be so kind and create a trello card for it?
Okay, I really need debugging ideas on this one.
I have three repositories I'm developing under the test toolshed. They're
named start_xena, xena_import and xena_find_datasets (they're all under
visualization). start_xena contains a simple tool dependency to a package
named installXena. xena_import and xena_find_datasets contain complex
dependencies to installXena. I've installed these tools on two computers.
On one, everything works great - amazingly well, in fact! Kudos,
Development Team! On the other computer, the env.sh files associated with
the complex dependencies keep referencing the wrong version of
start_xena/installXena.
Here are the gory details.
The start_xena tool is installed in
testtoolshed.g2.bx.psu.edu/repos/melissacline/start_xena/82755b0ee5a5/start_xena.
I'm a bit confused about the revision part of the path, because the latest
revision is different (75c7d80df9c1), and I have uninstalled and
re-installed the tool since its last update. Its package, installXena, is
installed under tool_dependencies at
tool_dependencies/installXena/1.0/melissacline/start_xena/82755b0ee5a5/.
That directory contains all the files I'd expect to be there, and its
env.sh file contains all the environment variables I'd intended to set.
So far, so good.
xena_import is installed on my computer at
testtoolshed.g2.bx.psu.edu/repos/melissacline/xena_import/dc42b6bbc22b/xena_import.
Its tool_dependencies.xml reference installXena under start_xena as:
<?xml version="1.0"?>
<tool_dependency>
<package name="installXena" version="1.0">
<repository toolshed="http://testtoolshed.g2.bx.psu.edu";
name="start_xena" owner="melissacline" changeset_revision="82755b0ee5a5"/>
</package>
</tool_dependency>
(Aside: is it necessary to have the changeset_revision in there? I'm a bit
worried about the maintenance task of updating it for all of my dependent
tools every time I update start_xena, but as I'll explain, it's not clear
that this revision info is getting used).
The tool dependency dir for xena_import is at
tool_dependencies/installXena/1.0/melissacline/xena_import/dc42b6bbc22b/.
Its env.sh reads:
if [ -f
/Users/melissacline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
] ; then .
/Users/melissacline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
; fi
Notice that the wrong revision number is in there. The 06 revision was an
older one. Needless to say, the files and environment variables I need
aren't in the 06 directory.
Where does this incorrect revision number come from? I've deleted all the
06 directories, repeatedly. I've deleted and reinstalled the tools, and
verified that after deletion, the directories in question were in fact
gone. I've tried resetting the metadata for these tools under the Galaxy
Admin menu. Now I need new ideas. As I mentioned, all of this works
beautifully on a second computer. It's as if the first Galaxy
installation, on the first computer, got stuck with some outdated
information, and I haven't figured out how to clear it out.
I don't know but you should remove the toolshed= and the revision= from
your XML files. These fields will be automatically filled by the
toolshed (inserting the latest tip version of your dependencies and the
current toolshed url).
Hope this helps a little bit!
Bjoern
Thanks!
Melissa
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