From 6666fe7b98ac7538d2c524257892c3930eb34f52 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 27 Jan 2020 10:56:44 +0100
Subject: [PATCH] Back to custom pybedtools.
---
install.sh | 2 ++
requirements.txt | 4 ++--
setup.py | 4 ++--
3 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/install.sh b/install.sh
index f24e57c..532590a 100755
--- a/install.sh
+++ b/install.sh
@@ -1,5 +1,7 @@
#!/bin/sh
/usr/bin/env python3 setup.py build_ext
# .egg-link does not work with PYTHONPATH ?
+# Install custom pybedtools first
+/usr/bin/env python3 -m pip install -r requirements.txt
/usr/bin/env python3 -m pip install -e .
/usr/bin/env python3 -m pip install --no-deps --ignore-installed .
diff --git a/requirements.txt b/requirements.txt
index 4f038f0..641ceef 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,7 @@ networkx
numpy
pandas
pyBigWig
-# pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
-pybedtools
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+# pybedtools
scipy
seaborn
diff --git a/setup.py b/setup.py
index caea281..512701d 100644
--- a/setup.py
+++ b/setup.py
@@ -28,8 +28,8 @@ setup(
"numpy",
"pandas",
"pyBigWig",
- # "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
- "pybedtools",
+ "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
+ # "pybedtools",
"scipy",
"seaborn"],
# specific versions and index would rather belong to requirements.txt
--
GitLab