Install Cmake Centos
2021年1月6日Download: http://gg.gg/nr274
The kallisto GitHub repository is here. Source code can also be downloaded from the download page. Currently, kallisto can be built on Linux, Mac, and Rock64. If you are compiling kallisto on the Rock64 (or equivalent ARM64 processor architecture) follow these steps. If building on Mac, we suggest using a package manager such as Homebrew to download dependencies. Homebrew is easily installed by copying and pasting the command below at a terminal prompt:
Sudo yum install git-core boost-devel gcc-c sudo yum install postgresql-server postgresql-devel flex. Since cmake3 is provided by the cmake package, that package will be installed by yum install, since no package with the exact cmake3 name exists: # yum provides cmake3 cmake-3.11.4-7.el8.x8664: Cross-platform make system Repo: AppStream Matched from: Provide: cmake3 = 3.11.4-7.el8. Download cmake-filesystem-3.11.4-3.el8.x8664.rpm for CentOS 8 from OKey repository.
ruby -e ’$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)’
Other dependencies are included, or can be installed using package managers on the system. Instructions for building kallisto from source without a package manager are here.Requirements:
*A 64-bit operating system
*g++ version >= 4.8
*CMake version >= 2.8.12
*Mac: brew install cmake
*Ubuntu: sudo apt-get install cmake
*CentOS: sudo yum install cmake
*zlib (should be installed on OSX >= 10.9)
*Mac: Should be installed by default
*Ubuntu: sudo apt-get install zlib1g-dev
*CentOS: sudo yum install zlib-devel
*autoconf
*Mac: brew install autoconf
*Ubuntu: sudo apt-get install autoconf
*CentOS: sudo yum install autoconf
*HDF5 C library version >= 1.8.12
*Mac: brew install hdf5
*Ubuntu: sudo apt-get install libhdf5-dev
*CentOS: sudo yum install hdf5-develDownload
kallisto is hosted on GitHub. The source code can be obtained by cloning the repository as follows:
git clone https://github.com/pachterlab/kallisto.gitHow To Install Cmake CentosCompile
Begin by moving to the source directory:
cd kallistoMake htslib
Run autoconf on ext/htslib: (note, this only needs to be done once, not when you recompile)
cd ext/htslib
autoheader
autoconf
cd ../..
For old Linux systems, if you get an error reportingthread_pool.c:658:38: error: ‘PTHREAD_MUTEX_RECURSIVE’ undeclared (first use in this function)
you might need to make htslib using this command in the htslib folder
make -j CFLAGS=-D_GNU_SOURCE lib-staticBuild kallisto
Make a build directory and move there:
mkdir build
cd build
Run cmake:
cmake ..
Build the code:
make
The kallisto executable is now located in build/src. To install kallisto into the cmake install prefix path type:
make installTest
The kallisto source code package comes with a small test transcriptome and read files that can be used to test that the package was compiled and installed correctly. The Getting started page provides a complete description of how to run kallisto on these files.Using the conda package¶
A package for xeus-cling is available on the conda package manager.From source with cmake¶
You can also install xeus-cling from source with cmake. This requires that you have all the dependencies installed in the same prefix.
On Windows platforms, from the source directory:
When installing xeus-cling in a given installation prefix, the corresponding Jupyter kernelspecs are installed in the same environment and are automatically picked up by Jupyter if it is installed in the same prefix.
However, if Jupyter is installed in a different location, it will not pick up the new kernels. The xeus-cling kernels (for C++11, C++14 and C++17 respectively) can be registered with the following commands:Install Cmake Centos 6
For more information on the jupyterkernelspec command, please consult the jupyter_client documentation.
Download: http://gg.gg/nr274 https://diarynote-jp.indered.space
The kallisto GitHub repository is here. Source code can also be downloaded from the download page. Currently, kallisto can be built on Linux, Mac, and Rock64. If you are compiling kallisto on the Rock64 (or equivalent ARM64 processor architecture) follow these steps. If building on Mac, we suggest using a package manager such as Homebrew to download dependencies. Homebrew is easily installed by copying and pasting the command below at a terminal prompt:
Sudo yum install git-core boost-devel gcc-c sudo yum install postgresql-server postgresql-devel flex. Since cmake3 is provided by the cmake package, that package will be installed by yum install, since no package with the exact cmake3 name exists: # yum provides cmake3 cmake-3.11.4-7.el8.x8664: Cross-platform make system Repo: AppStream Matched from: Provide: cmake3 = 3.11.4-7.el8. Download cmake-filesystem-3.11.4-3.el8.x8664.rpm for CentOS 8 from OKey repository.
ruby -e ’$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)’
Other dependencies are included, or can be installed using package managers on the system. Instructions for building kallisto from source without a package manager are here.Requirements:
*A 64-bit operating system
*g++ version >= 4.8
*CMake version >= 2.8.12
*Mac: brew install cmake
*Ubuntu: sudo apt-get install cmake
*CentOS: sudo yum install cmake
*zlib (should be installed on OSX >= 10.9)
*Mac: Should be installed by default
*Ubuntu: sudo apt-get install zlib1g-dev
*CentOS: sudo yum install zlib-devel
*autoconf
*Mac: brew install autoconf
*Ubuntu: sudo apt-get install autoconf
*CentOS: sudo yum install autoconf
*HDF5 C library version >= 1.8.12
*Mac: brew install hdf5
*Ubuntu: sudo apt-get install libhdf5-dev
*CentOS: sudo yum install hdf5-develDownload
kallisto is hosted on GitHub. The source code can be obtained by cloning the repository as follows:
git clone https://github.com/pachterlab/kallisto.gitHow To Install Cmake CentosCompile
Begin by moving to the source directory:
cd kallistoMake htslib
Run autoconf on ext/htslib: (note, this only needs to be done once, not when you recompile)
cd ext/htslib
autoheader
autoconf
cd ../..
For old Linux systems, if you get an error reportingthread_pool.c:658:38: error: ‘PTHREAD_MUTEX_RECURSIVE’ undeclared (first use in this function)
you might need to make htslib using this command in the htslib folder
make -j CFLAGS=-D_GNU_SOURCE lib-staticBuild kallisto
Make a build directory and move there:
mkdir build
cd build
Run cmake:
cmake ..
Build the code:
make
The kallisto executable is now located in build/src. To install kallisto into the cmake install prefix path type:
make installTest
The kallisto source code package comes with a small test transcriptome and read files that can be used to test that the package was compiled and installed correctly. The Getting started page provides a complete description of how to run kallisto on these files.Using the conda package¶
A package for xeus-cling is available on the conda package manager.From source with cmake¶
You can also install xeus-cling from source with cmake. This requires that you have all the dependencies installed in the same prefix.
On Windows platforms, from the source directory:
When installing xeus-cling in a given installation prefix, the corresponding Jupyter kernelspecs are installed in the same environment and are automatically picked up by Jupyter if it is installed in the same prefix.
However, if Jupyter is installed in a different location, it will not pick up the new kernels. The xeus-cling kernels (for C++11, C++14 and C++17 respectively) can be registered with the following commands:Install Cmake Centos 6
For more information on the jupyterkernelspec command, please consult the jupyter_client documentation.
Download: http://gg.gg/nr274 https://diarynote-jp.indered.space
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