Thanks, folks!  Everything you've said has clarified many things, and I'm
working on putting them into practice.  But in the meantime, I've got a new
error condition, with the same repositories (and complex repository
dependencies), and could use some guidance.

I started to see this error condition when I removed the toolshed and
changeset_revision tags in the tool_dependencies.xml for the dependent
repository xena_install.  It now reads:

<?xml version="1.0"?>


  <package name="installXena" version="1.0">

    <repository name="start_xena" owner="melissacline"/>



Short and simple.  But lately, when I try to install this repository from
the test toolshed, I get a pop-up window from Chrome (my web browser) that
says "The page at says:", "Initializing repository
installation failed", with an OK button.  There is no error message visible
in paster.log.  Here is what I do see: - - [12/Sep/2014:11:45:57 -0700] "GET


ad0de2d&changeset_revisions=fe95cf1ae864 HTTP/1.1" 200 - "-" "Mozilla/5.0

ntosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)

0.2062.94 Safari/537.36"


DEBUG 2014-09-12 11:46:05,937 Creating repository dependency objects...

tool_shed.util.shed_util_common DEBUG 2014-09-12 11:46:07,214 Updating an

ing row for repository 'xena_import' in the tool_shed_repository table,
status \

set to 'New'.


DEBUG 2014-09-12 11:46:07,241 Skipping installation of revision
75c7d80df9c1 of\

 repository 'start_xena' because it was installed with the (possibly
updated) r\

evision 75c7d80df9c1 and its current installation status is 'Installed'.


DEBUG 2014-09-12 11:46:07,241 Building repository dependency
relationships... - - [12/Sep/2014:11:46:05 -0700] "POST

stall HTTP/1.1" 200 - "\


e2d&changeset_revisions=fe95cf1ae864" "Mozilla/5.0 (Macintosh; Intel Mac OS
X 1\

0_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94


warning: certificate with fingerprint

:e6:f8:5c:1c:b8:3e:8d:89:f0:0e:88:9a:ac:2b:61 not verified (check

nts or web.cacerts config setting) - - [12/Sep/2014:11:46:07 -0700] "POST

ories HTTP/1.1" 500 - "\

" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36
(KHTML, li\

ke Gecko) Chrome/37.0.2062.94 Safari/537.36"

Debug at:

Then when I click OK, the status of the tool changes to "Cloning", and
stays in that state indefinitely while paster.log keeps logging a repeat of
this message: - - [12/Sep/2014:11:55:28 -0700] "POST

tallation_status_updates HTTP/1.1" 200 - "\

prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4)

t/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94 Safari/537.36"

Just in case this is from some cruft from a previous installation, I tried
starting over with a brand new galaxy-dist directory.  It doesn't look like
that changed anything.

Any ideas?  Many thanks in advance!


On Fri, Sep 12, 2014 at 10:30 AM, Dave Bouvier <> wrote:

> 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 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
>> 82755b0ee5a5/start_xena
>> <
>> 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
>> file contains all the environment variables I'd intended to set.
>>    So far, so good.
>> xena_import is installed on my computer at
>> import/dc42b6bbc22b/xena_import
>> <
>> 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="";
>> 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
>> reads:
>> if [ -f
>> /Users/melissacline/src/galaxy-dist/tool_dependencies/
>> installXena/1.0/melissacline/start_xena/0676a227dbc6/
>> ] ; then .
>> /Users/melissacline/src/galaxy-dist/tool_dependencies/
>> installXena/1.0/melissacline/start_xena/0676a227dbc6/
>> ; 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 file on the
> filesystem.
>> Thanks!
>> Melissa
>> ___________________________________________________________
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