Problem installing celescope, cannot build wheel for pysam

[elquinessyang]

 ranlib libhts.a
  Compiling pysam/libchtslib.pyx because it changed.
  [1/1] Cythonizing pysam/libchtslib.pyx
  building 'pysam.libchtslib' extension
  creating build/temp.linux-x86_64-cpython-39
  creating build/temp.linux-x86_64-cpython-39/pysam
  gcc -pthread -B /home/svu/xxxx/.conda/envs/celescope/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/svu/xxxx/.conda/envs/celescope/include -fPIC -O2 -isystem /home/svu/xxxx/.conda/envs/celescope/include -fPIC -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/pysam -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/htslib -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/samtools -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/samtools/lz4 -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/bcftools -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d -I/home/svu/xxxx/.conda/envs/celescope/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-39/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
  gcc -pthread -B /home/svu/xxxx/.conda/envs/celescope/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/svu/xxxx/.conda/envs/celescope/include -fPIC -O2 -isystem /home/svu/xxxx/.conda/envs/celescope/include -fPIC -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/pysam -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/htslib -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/samtools -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/samtools/lz4 -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d/bcftools -I/tmp/pip-install-si48z4un/pysam_b89b3406ea9549cf8b79b11bc185998d -I/home/svu/xxxx/.conda/envs/celescope/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-39/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
  In file included from pysam/libchtslib.c:133:
  /home/svu/xxxx/.conda/envs/celescope/include/python3.9/Python.h:44:10: fatal error: crypt.h: No such file or directory
     44 | #include <crypt.h>
        |          ^~~~~~~~~
  compilation terminated.
  error: command '/home/svu/xxxx/.conda/envs/celescope/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pysam
Failed to build pysam
ERROR: Could not build wheels for pysam, which is required to install pyproject.toml-based projects

Could anyone help? thanks~

[zhouyiqi91]

stanford-futuredata/ColBERT#309 (comment)
Similar issue here. This might help.

[zhouyiqi91]

#27 (reply in thread)
You can also try to install pysam with conda(mamba).