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  • Install and set up i-adhore for synteny and wgd analysis ! -- step by step --

Install and set up i-adhore for synteny and wgd analysis ! -- step by step --

Jit
  • Public
By Jit 1195 days ago
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow these steps (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ tar -zxvf i-adhore-3.0.01.tar.gz (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ cd i-adhore-3.0.01 (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ mkdir -p build && cd build (wgd) ➜ build git:(master) ✗ which wgd /home/urbe/anaconda3/envs/wgd/bin/wgd (wgd) ➜ build git:(master) ✗ cmake .. -DCMAKE_INSTALL_PREFIX=/home/urbe/anaconda3/envs/wgd/ CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.34") -- Configuring done -- Generating done -- Build files have been written to: /home/urbe/Tools/i-adhore-3.0.01/build (wgd) ➜ build git:(master) ✗ ls CMakeCache.txt CMakeFiles cmake_install.cmake Makefile src unittest (wgd) ➜ build git:(master) ✗ make -j 4 Scanning dependencies of target bmp Scanning dependencies of target alignment [ 3%] Building CXX object src/bmp/CMakeFiles/bmp.dir/bmp.cpp.o [ 3%] Building CXX object src/bmp/CMakeFiles/bmp.dir/grafix.cpp.o [ 4%] Building CXX object src/bmp/CMakeFiles/bmp.dir/color.cpp.o [ 6%] Building CXX object src/alignment/CMakeFiles/alignment.dir/GGAligner.cpp.o [ 8%] Building CXX object src/bmp/CMakeFiles/bmp.dir/pnghandling.cpp.o [ 9%] Building CXX object src/alignment/CMakeFiles/alignment.dir/GGAligner2.cpp.o [ 13%] Building CXX object src/alignment/CMakeFiles/alignment.dir/NWAligner.cpp.o [ 13%] Linking CXX static library libbmp.a [ 13%] Built target bmp [ 14%] Building CXX object src/alignment/CMakeFiles/alignment.dir/Node.cpp.o [ 16%] Linking CXX static library libalignment.a [ 16%] Built target alignment Scanning dependencies of target i-adhore Scanning dependencies of target i-visualize [ 18%] Building CXX object src/CMakeFiles/i-visualize.dir/PostProcessor.cpp.o [ 21%] Building CXX object src/CMakeFiles/i-visualize.dir/AlignmentVisualizer.cpp.o [ 21%] Building CXX object src/CMakeFiles/i-visualize.dir/threadPool.cpp.o [ 22%] Building CXX object src/CMakeFiles/i-adhore.dir/threadPool.cpp.o [ 24%] Building CXX object src/CMakeFiles/i-visualize.dir/higherLevel.cpp.o [ 26%] Building CXX object src/CMakeFiles/i-adhore.dir/higherLevel.cpp.o [ 27%] Building CXX object src/CMakeFiles/i-visualize.dir/levelTwo.cpp.o [ 29%] Building CXX object src/CMakeFiles/i-visualize.dir/alignComp.cpp.o [ 31%] Building CXX object src/CMakeFiles/i-visualize.dir/SvgWriter.cpp.o [ 32%] Building CXX object src/CMakeFiles/i-adhore.dir/levelTwo.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp: In member function ‘std::__cxx11::string SvgWriter::convertColor(const Color&)’: /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wformat-overflow=] string SvgWriter::convertColor(const Color& color) ^~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6361, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.h:4, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 8 __bos (__s), __fmt, __va_arg_pack ()); ^ [ 34%] Building CXX object src/CMakeFiles/i-visualize.dir/AlignmentDrawer.cpp.o [ 36%] Building CXX object src/CMakeFiles/i-visualize.dir/parallel.cpp.o [ 37%] Building CXX object src/CMakeFiles/i-adhore.dir/alignComp.cpp.o [ 39%] Building CXX object src/CMakeFiles/i-visualize.dir/SynthenicCloud.cpp.o [ 40%] Building CXX object src/CMakeFiles/i-adhore.dir/SvgWriter.cpp.o [ 42%] Building CXX object src/CMakeFiles/i-adhore.dir/AlignmentDrawer.cpp.o [ 44%] Building CXX object src/CMakeFiles/i-adhore.dir/parallel.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp: In member function ‘std::__cxx11::string SvgWriter::convertColor(const Color&)’: /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wformat-overflow=] string SvgWriter::convertColor(const Color& color) ^~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6361, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.h:4, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 8 __bos (__s), __fmt, __va_arg_pack ()); ^ [ 45%] Building CXX object src/CMakeFiles/i-visualize.dir/BaseCluster.cpp.o [ 47%] Building CXX object src/CMakeFiles/i-adhore.dir/SynthenicCloud.cpp.o [ 49%] Building CXX object src/CMakeFiles/i-adhore.dir/BaseCluster.cpp.o [ 50%] Building CXX object src/CMakeFiles/i-adhore.dir/Cluster.cpp.o [ 52%] Building CXX object src/CMakeFiles/i-adhore.dir/DataSet.cpp.o [ 54%] Building CXX object src/CMakeFiles/i-visualize.dir/Cluster.cpp.o [ 55%] Building CXX object src/CMakeFiles/i-adhore.dir/GHM.cpp.o [ 57%] Building CXX object src/CMakeFiles/i-visualize.dir/DataSet.cpp.o [ 59%] Building CXX object src/CMakeFiles/i-adhore.dir/GHMProfile.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp: In member function ‘void DataSet::prepareOutput()’: /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp:306:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command.append(outputPath).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp: In member function ‘void DataSet::prepareOutput()’: /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp:306:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command.append(outputPath).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/i-visualize.dir/GHM.cpp.o [ 62%] Building CXX object src/CMakeFiles/i-adhore.dir/Gene.cpp.o [ 63%] Building CXX object src/CMakeFiles/i-visualize.dir/GHMProfile.cpp.o [ 65%] Building CXX object src/CMakeFiles/i-adhore.dir/GeneFamily.cpp.o [ 67%] Building CXX object src/CMakeFiles/i-adhore.dir/GeneList.cpp.o [ 68%] Building CXX object src/CMakeFiles/i-visualize.dir/Gene.cpp.o [ 70%] Building CXX object src/CMakeFiles/i-adhore.dir/GenePairs.cpp.o [ 72%] Building CXX object src/CMakeFiles/i-adhore.dir/ListElement.cpp.o [ 73%] Building CXX object src/CMakeFiles/i-visualize.dir/GeneFamily.cpp.o [ 75%] Building CXX object src/CMakeFiles/i-visualize.dir/GeneList.cpp.o [ 77%] Building CXX object src/CMakeFiles/i-adhore.dir/Multiplicon.cpp.o [ 78%] Building CXX object src/CMakeFiles/i-adhore.dir/Profile.cpp.o [ 80%] Building CXX object src/CMakeFiles/i-visualize.dir/GenePairs.cpp.o [ 81%] Building CXX object src/CMakeFiles/i-adhore.dir/Settings.cpp.o [ 83%] Building CXX object src/CMakeFiles/i-adhore.dir/iADHoRe.cpp.o [ 85%] Building CXX object src/CMakeFiles/i-visualize.dir/ListElement.cpp.o [ 86%] Building CXX object src/CMakeFiles/i-adhore.dir/hpmath.cpp.o [ 88%] Building CXX object src/CMakeFiles/i-adhore.dir/util.cpp.o [ 90%] Building CXX object src/CMakeFiles/i-visualize.dir/Multiplicon.cpp.o [ 91%] Building CXX object src/CMakeFiles/i-visualize.dir/Profile.cpp.o [ 93%] Building CXX object src/CMakeFiles/i-visualize.dir/Settings.cpp.o [ 95%] Linking CXX executable i-adhore [ 95%] Built target i-adhore [ 96%] Building CXX object src/CMakeFiles/i-visualize.dir/hpmath.cpp.o [ 98%] Building CXX object src/CMakeFiles/i-visualize.dir/util.cpp.o [100%] Linking CXX executable i-visualize [100%] Built target i-visualize (wgd) ➜ build git:(master) ✗ make install [ 8%] Built target bmp [ 16%] Built target alignment [ 59%] Built target i-visualize [100%] Built target i-adhore Install the project... -- Install configuration: "Release" -- Installing: /home/urbe/anaconda3/envs/wgd/./API -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/central.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/record_structure.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/list_element.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/settings.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/nw_path.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/profile.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/basecluster.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/anchorpoint.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/gene.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/multiplicon.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/agent.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/cluster.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/genelist.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/ghm.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/listfile.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/genepairs.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/alignment_plot.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/generate_overview.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/multiplicon_plot.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/plot_ghms.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/collinearityViz.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/multiplicated_portions.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/profile_plot.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/colinear_portions.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/dupliStacks.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./post_processing/dupliviz.pl -- Installing: /home/urbe/anaconda3/envs/wgd/./testset -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/alignment.csv -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201 -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_2830.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_929.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_379.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_312.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_254.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_1696.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_344.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_451.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_2653.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_442.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_41.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/LG_XI.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_159.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_499.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_273.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_309.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_179.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_799.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_692.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_487.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_626.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_1058.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_173.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_797.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_764.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_1377.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_305.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/LG_XV.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_438.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_3102.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_2563.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_372.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_1363.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_123.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_635.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_409.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_645.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_215.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/LG_XVIII.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/LG_X.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/LG_XIX.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_255.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_683.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_77.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_1548.lst -- 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