Melissa,
The revision recorded in the filesystem path can seem odd at first glance. My inline responses should hopefully clarify that.
--Dave B.
On 09/10/2014 05:49 PM, Melissa Cline wrote:
Hi Folks,
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 http://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 http://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).
It is not necessary to populate the changeset_revision or toolshed attributes. If you omit them, they will be automatically filled in based on the most recent matching repository.
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.
The 0676 revision number is based on the revision that was first installed, and should never change. When you update the repository, the database will record the new revision in a separate field, but the original revision id needs to be recorded in order to find the env.sh file on the filesystem.
Thanks!
Melissa
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