diff --git a/README.md b/README.md index 1af164bd799596db32ec313a620b9f6d45eead93..7621b66fa05df0c0c79db419bf24fc3d442e6b64 100644 --- a/README.md +++ b/README.md @@ -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`. ``` diff --git a/setup.py b/setup.py index fdbd1527949e5fff627172c4f2f0b812bbfc032f..dfce3b4d0f1e7daee882b1a5792ab6263a221849 100644 --- a/setup.py +++ b/setup.py @@ -1,9 +1,11 @@ +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++"), ]