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
Here are the gory details.
The start_xena tool is installed in
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
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
Its tool_dependencies.xml reference installXena under start_xena as:
<package name="installXena" version="1.0">
name="start_xena" owner="melissacline" changeset_revision="82755b0ee5a5"/>
(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
Its env.sh reads:
if [ -f
] ; then .
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installation, on the first computer, got stuck with some outdated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.
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