#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
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-- 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
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-- 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
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-- 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
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-- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_3240.lst
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