I was trying to compile latest version of htslib (1.2.1) but an error appeared and broke the compilation. Logs for the "configure" and "make" commands are at the end of the post. It also happened with version 1.2. I'm performing the installation on a CentOS 5.5. I'm compiling with ...
# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, # with symlinks libhts.so (used via -lhts during linking of client programs) # and libhts.so.NN (used by client executables at runtime). install-so: libhts.so installdirs $(INSTALL_LIB) libhts.so...
# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, # with symlinks libhts.so (used via -lhts during linking of client programs) # and libhts.so.NN (used by client executables at runtime).install-so: libhts.so installdirs ...
Installation pip with bundled htslib pip install cyvcf2 pip with system htslib Assuming you have already built and installed htslib version 1.12 or higher. CYVCF2_HTSLIB_MODE=EXTERNAL pip install --no-binary cyvcf2 cyvcf2 windows (experimental, only test on MSYS2) ...
# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, # with symlinks libhts.so (used via -lhts during linking of client programs) # and libhts.so.NN (used by client executables at runtime). install-so: libhts.so installdirs $(INSTALL_LIB) libhts.so...
Dear owner, I've been trying to install pysam from pysam-v0.16.0.1.tar.gz for Python 3.7.6 , and the installation succeed: $ python setup.py install: ... Installed /opt/conda/lib/python3.7/site-packages/pysam-0.16.0.1-py3.7-linux-aarch64.egg Processing...
[plugin installation location [LIBEXECDIR/htslib]])], [case $withval in yes|no) MSG_ERROR([no directory specified for --with-plugin-dir]) ;; esac], [with_plugin_dir='$(libexecdir)/htslib']) AC_SUBST([plugindir], $with_plugin_dir) AC_ARG_WITH([plugin-path], ...
Installation through bioconda is the recommended way to install pysam as it resolves non-python dependencies and uses pre-configured compilation options. Especially for OS X this will potentially save a lot of trouble. The current version of pysam wraps 3rd-party code from htslib-1.21, samtools-1....
# installation. However if you feel that you must bundle htslib source # code with your program, this hook enables Automake-style "make dist" # for this subdirectory. If you do bundle an htslib snapshot, please # add identifying information to $(PACKAGE_VERSION) as appropriate. # (The...
# installation. However if you feel that you must bundle htslib source # code with your program, this hook enables Automake-style "make dist" # for this subdirectory. If you do bundle an htslib snapshot, please # add identifying information to $(PACKAGE_VERSION) as appropriate. # (The...