Commit d6c2053e authored by Blaise Li's avatar Blaise Li

Half-workaround pybedtools issue.

For the moment, bam25prime needs bedtools sources to be installed, in a
specific location, and in a specific version (2.27.0).
parent 55b750c4
......@@ -9,9 +9,28 @@ It might also work directly:
python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/bam25prime.git
### Troubleshooting
Compilation may fail if the version of `gcc` is too old.
On a cluster with environment modules, a workaround might be something like running `module load gcc/7.2.0`.
You may encounter the following error:
ImportError: liblzma.so.5: cannot open shared object file: No such file or directory
You need to locate this `liblzma.so.5` file. If you find it, then set the
`LD_LIBRARY_PATH` environment variable so that it points to the directory
containing it. For instance:
export LD_LIBRARY_PATH="/local/gensoft2/exe/xz/5.2.2/lib"
## Usage
This package provides a `bam25prime`.
This package provides a `bam25prime` script.
Its help can be obtained using option `-h` or `--help`.
```
......
from os import environ
from setuptools import setup, find_packages
from glob import glob
# If you have .pyx things to cythonize
from distutils.extension import Extension
from Cython.Build import cythonize
from pybedtools.helpers import get_includes as pybedtools_get_includes
# https://github.com/daler/pybedtools/issues/253
# from pybedtools.helpers import get_includes as pybedtools_get_includes
from pysam import get_include as pysam_get_include
name = "bam25prime"
......@@ -16,7 +18,7 @@ extensions = [
include_dirs=pysam_get_include()),
Extension(
"bam25prime.libcollapsebed", ["bam25prime/libcollapsebed.pyx"],
include_dirs=glob("/home/bli/src/bedtools2-2.27.1/src/utils/*"),
include_dirs=glob("%s/src/bedtools2-2.27.1/src/utils/*" % environ["HOME"]),
#include_dirs=pybedtools_get_includes(),
language="c++"),
]
......
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