Comments (8)
Current issues: the following dependency formatting doesn't work for some (it worked for joseph, and in a clean virtual environment):
ngslib;platform_system=='Linux'
It either tries to compile it, and fails of course, or it crashes on pip setup.py egg_info
. @jovesus can you paste the error message here?
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Right now, if the user first installs python via Homebrew, there shouldn't be problems. Hopefully.
brew install python
pip install rgt --user
More testing needs to be done.
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Pysam caused MacOS regressions in the last few versions. While waiting for the fix, we've had to block the pysam dependency to version 1.11.1.
For reference: pysam-developers/pysam#475
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Triplexes is not compiled for Mac. @jovesus could you have a look at that (when you are back)?
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SeqAn C++ template is not compatible with LLVM libc++, which used by clang in default settings.
Compile Triplexes with GNU libstdc++ can bypass this problem.
Build Triplexes without OpenMP:
SRC_ROOT=/path/to/triplexes
cmake $SRC_ROOT \
-DCMAKE_CXX_FLAGS="-stdlib=libstdc++" \
-DCMAKE_BUILD_TYPE=Release \
-DSHAREDLIBRARY=TRUE
make
Pre-installed clang on macOS doesn't support OpenMP, so install clang via Homebrew.
Build Triplexes with OpenMP:
brew install llvm # clang with openmp support
export CC=/usr/local/opt/llvm/bin/clang
export CXX=/usr/local/opt/llvm/bin/clang++
cmake $SRC_ROOT \
-DCMAKE_CXX_FLAGS="-I/usr/local/opt/llvm/include -stdlib=libstdc++" \
-DCMAKE_C_FLAGS="-I/usr/local/opt/llvm/include" \
-DCMAKE_SHARED_LINKER_FLAGS="-L/usr/local/opt/llvm/lib" \
-DOpenMP_C_FLAGS="-fopenmp" \
-DOpenMP_CXX_FLAGS="-fopenmp" \
-DCMAKE_BUILD_TYPE=Release \
-DSHAREDLIBRARY=TRUE
make
These cmake
options can let rgt-TDF
run on macOS.
After compile, copy libtriplexator.dylib to rgtdata/lib and modify path_triplexator
in data.config to path_triplexator=$HOME/rgtdata/lib/libtriplexator.dylib
.
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@zjin1126 this is VERY helpful! Thanks. We will give this a try soon.
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@zjin1126 Thank you for your contribution. Last week I tried to install openMP on mac and use llvm to compile, but because of not having sufficient understanding of cmake, I couldn't work it out. Your comment solves our problem exactly. Thank you.
Now if RGT is successfully installed on Mac, it works as nrmal as on Linux.
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I'm fairly sure now RGT works fine on Mac. We'll open specific issues in the future, in case of need.
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Related Issues (20)
- rgt-hint throwing an error (without any other input) post-installation (Linux) HOT 10
- TDF issue HOT 2
- OverflowError: cannot convert float infinity to integer HOT 3
- invalid load key, '\x00'
- RGT installation successful, but rgtdata folder is missing. HOT 5
- Question regarding how Lineplots values are calculated, related to #116 HOT 1
- Issue running on Macbook Pro M1 HOT 18
- Motif enrichment scores HOT 1
- #The version of JASPAR HOT 1
- Number of success in mpbs.bed and fulltest_statistics.txt files did not match
- ResourceWarning: unclosed file (Enable tracemalloc to get the object allocation traceback)
- RGT Hint differential error HOT 5
- Transcription factor scatter plot HOT 2
- aarch64 support
- Result file description
- Fold-change values in THOR differential peaks and post-processed bigwigs
- Extension sizes estimated with THOR HOT 1
- Error in rgt-hint differential for my own data
- Deprecation warnings, non-compatibility with python 3.12, libpng12.so.0
- failed installation on Mac mini with Apple M2 Chip HOT 1
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