Pysam installation error

[KJ Lim]

Dear Pysam developers & community,

Good day.

I got error messages when installing pysam (pip install pysam) on Ubuntu 12.04 64-bit machine.

The error messages are:

$ sudo pip install pysam

Downloading/unpacking pysam
  Downloading pysam-0.8.0.tar.gz (1.2MB): 1.2MB downloaded
  Running setup.py (path:/tmp/pip_build_root/pysam/setup.py) egg_info for package pysam
   
    warning: no files found matching 'tests/pysam_data'
    warning: no files found matching 'tests/tabix_data'
Downloading/unpacking cython>=0.20.1 (from pysam)
  Downloading Cython-0.20.2.tar.gz (1.4MB): 1.4MB downloaded
  Running setup.py (path:/tmp/pip_build_root/cython/setup.py) egg_info for package cython
.
.
.
.
.

​.

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.7/pysam/csamtools.o -Wno-error=declaration-after-statement

pysam/csamtools.c:16:20: fatal error: Python.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1
----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/pysam/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-g6QS8p-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/pysam

Could someone please sharing with me your experience how to solve the problem like this?

Thank you.

Best regards,
KJ Lim

[Saket Choudhary]

Hi Kean,

This should fix it:

sudo apt-get install python-dev

Saket

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[KJ Lim]

Dear Saket,

Thanks for the solution. Indeed, it fixed.

Thanks a lot.

Best regards,

KJ Lim