testtoolshed.g2.bx.psu.edu not compatible with galaxy-central stable
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
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/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/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 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-mtdM9orSY/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/libphast.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 <rico@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
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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/ 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/ 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
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-mtdM9orSY/ 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/libphast.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 <rico@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/
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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-v... Greg Von Kuster On Sep 20, 2013, at 1:00 PM, Richard Burhans <rico@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/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/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
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-mtdM9orSY/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/libphast.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 <rico@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
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Hi Greg and Rico,
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
Hopefully fixed in newest release. I just will try so long until all OS-X installations work :)
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
fortran needs to be installed. I think we agreed that we can assume that? We really need to write that down somewhere ...
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-mtdM9orSY/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/libphast.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 ubuntu its installing fine for me. Have a nice weekend! Bjoern
'/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
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___________________________________________________________ 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/
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participants (3)
-
Björn Grüning -
Greg Von Kuster -
Richard Burhans