OpenMS caused Error downloading from URL
Hello I tried to install OpenMS ( toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms), but I have got the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package initial_download=True ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download raise Exception( err_msg ) Error downloading from URL http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10.0/OpenMS... : HTTP Error 404: Not Found Thank you in advance. Mic
Hello Mic, You should try to change the link in the tool_dependencies.xml of openMS with this link : <http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz/> http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10... and then repair the package regards, Olivier. De : galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] De la part de Mic Envoyé : jeudi 5 novembre 2015 15:21 À : galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : [galaxy-dev] OpenMS caused Error downloading from URL Hello I tried to install OpenMS (toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms <http://toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms> ), but I have got the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package initial_download=True ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download raise Exception( err_msg ) Error downloading from URL http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10.0/OpenMS...: HTTP Error 404: Not Found Thank you in advance. Mic
Hi Mic and Olivier, if there is broader interest in OpenMS please let me know. We have new wrappers and new installation instructions here: https://github.com/bgruening/galaxytools/tree/master/tools/openms + pre-compiled binaries as this takes ages to compile. Cheers, Bjoern Am 05.11.2015 um 15:24 schrieb Olivier CLAUDE:
Hello Mic,
You should try to change the link in the tool_dependencies.xml of openMS with this link :
<http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz/> http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10...
and then repair the package
regards,
Olivier.
De : galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] De la part de Mic Envoyé : jeudi 5 novembre 2015 15:21 À : galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : [galaxy-dev] OpenMS caused Error downloading from URL
Hello
I tried to install OpenMS (toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms <http://toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms> ), but I have got the following error:
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict )
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package
initial_download=True )
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
initial_download=initial_download )
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums )
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download
raise Exception( err_msg )
Error downloading from URL
http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10.0/OpenMS...:
HTTP Error 404: Not Found
Thank you in advance.
Mic
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Hello Bjoern and Oliver. Thank you for the emails. I changed to testtoolshed, but recieved the following error with openms 1.2 (testtoolshed.g2.bx.psu.edu/repos/bgruening/openms/ec62782f6c68/openms): *CMake Error at libraries.cmake/boost.cmake:122 (message): Performing configuration checks - gcc visibility : yes - long double support : yes - has_icu builds : yes Component configuration: - chrono : not building - context : not building - date_time : building - exception : not building - filesystem : not building - graph : not building - graph_parallel : not building - iostreams : building - locale : not building - math : building - mpi : not building - program_options : not building - python : not building - random : not building - regex : building - serialization : not building - signals : not building - system : not building - test : not building - thread : not building - timer : not building - wave : not building ...patience... ...patience... ...found 23291 targets... ...updating 11320 targets... common.mkdir bin.v2/libs/date_time common.mkdir bin.v2/libs/iostreams common.mkdir bin.v2/libs/math/build common.mkdir bin.v2/libs/math/config/gcc-4.8/release common.mkdir bin.v2/libs/regex/build/gcc-4.8/release common.mkdir bin.v2/libs/math/config/gcc-4.8/debug/link-static common.mkdir bin.v2/libs/regex/build/gcc-4.8/debug/link-static common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/nondet_random.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/current_function.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/bimap.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/memory_order.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/intrusive_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/any.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/range.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/format.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/regex.h common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/type.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/cstdlib.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/bind.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/signals2.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/ref.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/scoped_array.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/visit_each.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/assign.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/smart_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/shared_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/asio.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/blank_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/shared_array.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/weak_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/wave.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/checked_delete.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/cast.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/function.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/signal.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/throw_exception.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/progress.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/none.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/make_shared.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/math_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/random.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/non_type.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/config.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/geometry.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/date_time.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/ratio.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/utility.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/parameter.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/multi_array.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/circular_buffer_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/local_function.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/concept_check.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/next_prior.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/crc.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/tokenizer.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/compressed_pair.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/variant.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/function_output_iterator.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/call_traits.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/dynamic_bitset.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/python.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/cerrno.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/preprocessor.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/multi_index_container.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/scope_exit.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/concept_archetype.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/foreach.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/type_traits.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/rational.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/signals.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/io_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/unordered_map.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/regex_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/none_t.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/noncopyable.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/blank.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/pointee.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/mpi.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/flyweight.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/exception_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/integer_traits.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/aligned_storage.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/cstdint.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/functional.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/multi_index_container_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/dynamic_bitset_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/get_pointer.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/is_placeholder.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/array.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/pointer_to_other.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/scoped_ptr.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/spirit.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/shared_container_iterator.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/static_assert.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/filesystem.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/swap.hpp ...on 100th target... common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/foreach_fwd.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/pointer_cast.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/version.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/cregex.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/integer.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/implicit_cast.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/iterator_adaptors.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/mem_fn.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/assert.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/regex.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/last_value.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/function_equal.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/iterator.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/locale.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/operators.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/enable_shared_from_this.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/chrono.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/phoenix.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/optional.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/unordered_set.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/program_options.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/circular_buffer.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/generator_iterator.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/thread.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/token_functions.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/strong_typedef.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/limits.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/indirect_reference.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/exception.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/timer.hpp common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/token_iterator.hpp common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/intrusive common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/parameter common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/geometry common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/format common.mkdir /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/include/boost/pool common.mkdir /home/lorencm/galaxy/files_tmp/t..bs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/erff.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/fpclassifyf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/hypotf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/llroundf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/lgammaf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/cbrtf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/log1pf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/lroundf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/roundf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/nextafterf.o gcc.compile.c++ bin.v2/libs/math/build/gcc-4.8/release/link-static/runtime-link-static/threading-multi/nexttowardf.o gcc.compile.c++ 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/home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/lib/libboost_date_time.a gcc.archive bin.v2/libs/date_time/build/gcc-4.8/release/link-static/threading-multi/libboost_date_time-mt.a common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/lib/libboost_date_time-mt.a gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.8/debug/link-static/gregorian/greg_month.o ...on 11300th target... gcc.archive bin.v2/libs/date_time/build/gcc-4.8/debug/link-static/libboost_date_time-d.a common.copy /home/lorencm/galaxy/files_tmp/tmp-toolshed-mtd3RB5ND/OpenMS/contrib/lib/libboost_date_time-d.a ...failed updating 126 targets... ...skipped 18 targets... ...updated 11176 targets...Call Stack (most recent call first): CMakeLists.txt:461 (OPENMS_CONTRIB_BUILD_BOOST)* What did I do wrong? Thank you in advance. Mic On Fri, Nov 6, 2015 at 1:13 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Mic and Olivier,
if there is broader interest in OpenMS please let me know. We have new wrappers and new installation instructions here:
https://github.com/bgruening/galaxytools/tree/master/tools/openms
+ pre-compiled binaries as this takes ages to compile. Cheers, Bjoern
Am 05.11.2015 um 15:24 schrieb Olivier CLAUDE:
Hello Mic,
You should try to change the link in the tool_dependencies.xml of openMS with this link :
< http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz/>
http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10...
and then repair the package
regards,
Olivier.
De : galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] De
Envoyé : jeudi 5 novembre 2015 15:21 À : galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : [galaxy-dev] OpenMS caused Error downloading from URL
Hello
I tried to install OpenMS ( toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms < http://toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms> ), but I have got the following error:
File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py",
la part de Mic line 128, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package(
install_environment, tool_dependency, actions_dict )
File
"/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package
initial_download=True )
File
"/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
initial_download=initial_download )
File
"/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url,
extract=True, checksums=checksums )
File
"/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download
raise Exception( err_msg )
Error downloading from URL
http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10.0/OpenMS... :
HTTP Error 404: Not Found
Thank you in advance.
Mic
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participants (3)
-
Björn Grüning -
Mic -
Olivier CLAUDE