The "default branch" ( i.e., the galaxy-central repository on bitbucket) is 
backward compatible to the December 20, 2012 Galaxy release with regard to 
communication between a Galaxy instance and a Tool Shed instance.  It is not 
guaranteed that this communication will be forward compatible as new features 
are continually introduced.  Since the test Tool Shed is generally running the 
galaxy-central tip, it is most likely necessary to run that in your local 
Galaxy instance if you want to use the new features running on the test Tool 
Shed that have been introduced after the December 20, 2012 Galaxy release.

With regard to forward-compatiblity between Galaxy and the Tool Shed, there is 
a Trello card here:

https://trello.com/c/cd3hBnnH/30-tool-shed-decoupling-galaxy-and-tool-shed-versions

Greg Von Kuster


On Sep 20, 2013, at 1:00 PM, Richard Burhans <r...@bx.psu.edu> wrote:

> Greg,
> 
> I still get the same traceback.  The issue is with installing a repository 
> from testtoolshed, which is running code on the default branch, to a galaxy 
> instance running on the stable branch.  My understanding was that the default 
> branch is supposed to be backward-compatible to the stable branch.  Please 
> let me know if this is not the case (which would mean that this is not a bug).
> 
> The atlas and lapack errors are begin caused by 
> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7.  I'm cc'ing 
> galaxy-iuc so they can look into it further.
> 
> Thanks for the report on phast.  I'll probably need to use the 
> architecture-dependent compilation stuff you're working on to fix this.
> 
> -rico
> 
> On Sep 20, 2013, at 11:21 AM, Greg Von Kuster wrote:
> 
>> Hi Rico,
>> 
>> The test tool shed is now running my latest commit - 10629:ab20415126a7. I 
>> was successful with installing the genome diversity repository and all of 
>> it's dependencies using that changeset in my local Galaxy environment 
>> (although 3 tool dependencies encountered the following errors while 
>> attempting to compile).
>> 
>> Can you try again and let me know if you encounter additonal problems?
>> 
>> atlas        3.10.1  package Error   cat: ..//CONFIG/src/Makefile: No such 
>> file or directory cp: ..//CONFIG/src/atlcomp.txt: No such file or directory 
>> make: *** No rule to make target `xconfig'. Stop. /bin/sh: line 1: 
>> ./xconfig: No such file or directory
>> 
>> lapack       3.4.2   package Error   CMake Error: your Fortran compiler: 
>> "CMAKE_Fortran_COMPILER-NOTFOUND" was not found. Please set 
>> CMAKE_Fortran_COMPILER to a valid compiler path or name. CMake Error at 
>> /opt/local/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27 
>> (get_filename_component): get_filename_component called with incorrect 
>> number of arguments Call Stack (most recent call first): CMakeLists.txt:2 
>> (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage 
>> CMake Error: Internal CMake error, TryCompile configure of cmake failed 
>> CMake Error at 
>> /opt/local/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27 
>> (get_filename_component): get_filename_component called with incorrect 
>> number of arguments Call Stack (most recent call first): CMakeLists.txt:2 
>> (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage 
>> CMake Error: Internal CMake error, TryCompile configure of cmake failed 
>> CMake Error at /opt/local/share/cmake-2.8/Modules/CMak!
 eFortranInformation.cmake:27 (get_filename_component): get_filename_component 
called with incorrect number of arguments Call Stack (most recent call first): 
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after 
EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake 
failed CMake Error at 
/opt/local/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27 
(get_filename_component): get_filename_component called with incorrect number 
of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) 
CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: 
Internal CMake error, TryCompile configure of cmake failed CMake Error at 
/opt/local/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27 
(get_filename_component): get_filename_component called with incorrect number 
of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) 
CMake Error: CMAKE_Fortran_COMPILER not set, after E!
 nableLanguage CMake Error: Internal CMake error, TryCompile co!
 nfigure 
of cmake failed
>> 
>> 
>> phast        1.3     package Error   make[1]: *** No rule to make target 
>> `/Users/gvk/workspace/tool_dependencies/clapack/3.2.1/rico/package_clapack_3_2_1/56a949e5f998/lapack.a',
>>  needed by 
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/lib/../../lib/liblapack.a'.
>>  Stop. make[1]: *** No rule to make target 
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/dless/../../lib/libphast.a',
>>  needed by 
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/dless/../../bin/dless'.
>>  Stop. make[1]: *** No rule to make target 
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/exoniphy/../../lib/libphast.a',
>>  needed by  
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/exoniphy/../../bin/exoniphy'.
>>  Stop. make[1]: *** No rule to make target 
>> `/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src!
 /phastCons/../../lib/libphast.a', needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastCons/../../bin/phastCons'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastOdds/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastOdds/../../bin/phastOdds'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastMotif/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastMotif/../../bin/phastMotif'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloFit/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9o!
 rSY/phast-1.3/src/phyloFit/../../bin/phyloFit'. Stop. make[1]:!
  *** No 
rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloBoot/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloBoot/../../bin/phyloBoot'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloP/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloP/../../bin/phyloP'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/prequel/../../lib/libphast.a',
 needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/prequel/../../bin/pbsDecode'.
 Stop. make[1]: *** No rule to make target 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/util/../../lib/libphas!
 t.a', needed by 
`/Users/gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/util/../../bin/all_dists'.
 Stop. make: *** [all] Error 2
>> 
>> 
>> 
>> On Sep 19, 2013, at 6:28 PM, Richard Burhans <r...@bx.psu.edu> wrote:
>> 
>>> my galaxy instance:
>>>     parent: 10587:1f34ec186fcf
>>>      Pack script.
>>>     branch: stable
>>>     commit: 3 modified, 91 unknown
>>>     update: (current)
>>> 
>>> testtoolshed.g2.bx.psu.edu:
>>>     parent: 10592:ea0c57f1cdf0 tip
>>>      Fix for unicode values in rst_to_html.
>>>     branch: default
>>>     commit: 34 unknown (clean)
>>>     update: (current)
>>> 
>>> Try to install this repository:
>>>     http://testtoolshed.g2.bx.psu.edu/view/rico/genome_diversity
>>> 
>>> URL: 
>>> https://oocyte.bx.psu.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=d43c67507430e220&changeset_revisions=b63d27fdf040
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
>>>  line 364 in respond
>>> app_iter = self.application(environ, detect_start_response)
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>>>  line 84 in __call__
>>> return self.application(environ, start_response)
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/framework/middleware/remoteuser.py',
>>>  line 91 in __call__
>>> return self.app( environ, start_response )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>>>  line 633 in __call__
>>> return self.application(environ, start_response)
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/framework/base.py',
>>>  line 132 in __call__
>>> return self.handle_request( environ, start_response )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/framework/base.py',
>>>  line 190 in handle_request
>>> body = method( trans, **kwargs )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/framework/__init__.py',
>>>  line 221 in decorator
>>> return func( self, trans, *args, **kwargs )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>>>  line 911 in prepare_for_install
>>> includes_tool_dependencies )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/common_install_util.py',
>>>  line 85 in get_dependencies_for_repository
>>> installed_rd, missing_rd = 
>>> get_installed_and_missing_repository_dependencies_for_new_install( trans, 
>>> repo_info_tuple )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/common_install_util.py',
>>>  line 214 in 
>>> get_installed_and_missing_repository_dependencies_for_new_install
>>> tool_shed, name, owner, changeset_revision, prior_installation_required = 
>>> suc.parse_repository_dependency_tuple( rd_tup )
>>> File 
>>> '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/shed_util_common.py',
>>>  line 1197 in parse_repository_dependency_tuple
>>> prior_installation_required = str( prior_installation_required )
>>> UnboundLocalError: local variable 'prior_installation_required' referenced 
>>> before assignment
>>> 
>>> contains_error = False
>>> repository_dependency_tuple =  ['http://testtoolshed.g2.bx.psu.edu/', 
>>> 'package_clapack_3_2_1', 'rico', '56a949e5f998', 'True', 'False']
>>> 
>>> -rico
>>> 
>>> ___________________________________________________________
>>> 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:
>>> http://lists.bx.psu.edu/
>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>> 
> 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to