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:
<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 127.0.0.1:8080 says:", "Initializing repository
installation failed", with an OK button. There is no error message visible
in paster.log. Here is what I do see:
127.0.0.1 - - [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)
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,
set to 'New'.
DEBUG 2014-09-12 11:46:07,241 Skipping installation of revision
repository 'start_xena' because it was installed with the (possibly
evision 75c7d80df9c1 and its current installation status is 'Installed'.
DEBUG 2014-09-12 11:46:07,241 Building repository dependency
127.0.0.1 - - [12/Sep/2014:11:46:05 -0700] "POST
stall HTTP/1.1" 200 - "
e2d&changeset_revisions=fe95cf1ae864" "Mozilla/5.0 (Macintosh; Intel Mac OS
0_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94
warning: testtoolshed.g2.bx.psu.edu 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)
127.0.0.1 - - [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
ke Gecko) Chrome/37.0.2062.94 Safari/537.36"
Debug at: http://127.0.0.1:8080/_debug/view/1410547505
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
127.0.0.1 - - [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 <d...@bx.psu.edu> wrote:
> 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
>> 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:
>> <?xml version="1.0"?>
>> <package name="installXena" version="1.0">
>> <repository toolshed="http://testtoolshed.g2.bx.psu.edu"
>> name="start_xena" owner="melissacline" changeset_revision="
>> (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
>> env.sh reads:
>> if [ -f
>> ] ; then .
>> ; 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
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: