From d6c2053eaaebc0ab0e860153b9b71bed55ca11e8 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Fri, 16 Aug 2019 14:12:58 +0200
Subject: [PATCH] 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).
---
README.md | 21 ++++++++++++++++++++-
setup.py | 6 ++++--
2 files changed, 24 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 1af164b..7621b66 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 fdbd152..dfce3b4 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++"),
]
--
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