Hi All,

I have withdrawn the pull request after useful comments from [X] Nicola Soranzo 
and John Chilton and upon finding a bug that results in a worse error in testing

I have had another go at adding this feature.
This time as a new resolver to be plugged in.

Adding at John Chilton suggestion ranking in cases where more that one possible 
revision of the same dependency can be found.

I have the code in a fork:

If I want to submit a pull request is this best done against master or dev?
Also should I submit a Jira(ish) ticket for this as well? If so where?

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, July 01, 2015 1:17 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Problem finding depency for none toolshed tools

I have been testing tools not yet ready for a tool-shed but had trouble finding 
the dependencies as there was no database entries to load these.

The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the 
env.sh or bin directory will be in dependency_dir/package/version when in fact 
it is often in dependency_dir/

I have created a pull request with some code to find the dependency in the sub 


As I am relatively new to galaxy I have probably broken lots of 
rules/agreements on how I did the pull request. If so please let me know where 
I went wrong so I can redo it properly.


This is my proposed change to 
    def _find_dep_versioned( self, name, version, type='package', **kwds ):
        #First try the way without owner/name/revision
        path = join( self.base_path, name, version )
        package = self._galaxy_package_dep(path, version)
        if package != INDETERMINATE_DEPENDENCY:
            return package
        #now try with an owner/name/revision
        for owner in listdir(path):
            owner_path = path + "/" + owner
            for package_name in listdir(owner_path):
                if package_name.startswith("package_"+name):
                    package_path = owner_path + "/" + package_name
                    for revision in listdir(package_path):
                        revision_path = package_path + "/" + revision
                        package = self._galaxy_package_dep(revision_path, 
                        if package != INDETERMINATE_DEPENDENCY:
                            return package

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:

Reply via email to