Merge pull request #258 from CostaLab/develop

Develop

README.md

@@ -18,16 +18,21 @@ ChIP-Seq differential peak caller
 
 See https://reg-gen.readthedocs.io for documentation and tutorials.
 
-# Installation
+# Installation with conda
 
-The quickest and easiest way to get RGT is to to use pip. First some dependencies:
+We recommend using conda to manange the python environmont to avoid issues.
+
+You can install conda from [here](https://docs.conda.io/en/latest/miniconda.html)
+
+Once you successfully installed conda, first create a specific environment:
 
 ```shell
-pip install cython numpy scipy
+conda create -n rgt python=3.9
 ```
 
-Then install the full RGT suite with all other dependencies:
+Then activate your environment and install the full RGT suite with all other dependencies:
 ```shell
+conda activate rgt
 pip install RGT
 ```
 

docs/rgt/installation.md

@@ -7,8 +7,8 @@ These instructions are only to be attempted if you know what you are doing and t
 The recommended way of installing RGT is via [pip](https://pip.pypa.io/en/stable/), the main python package manager. After installing pip, type in this order:
 
 ```shell
-pip install --user cython numpy scipy
-pip install --user RGT --no-binary RGT
+pip install cython numpy scipy
+pip install RGT
 ```
 
 This will install the full RGT suite with all python dependencies. A few more libraries will be needed, but should be installed via your own distribution’s package manager.
@@ -44,6 +44,13 @@ pip install cython numpy scipy
 pip install RGT --no-binary RGT
 ```
 
+<!-- ### Installation with Apple silicon 
+When you are using Mac with Apple Silicon chip (M1/2), the installation can be complicated, since they are based on arm64.
+
+We have 
+
+there are two scenarios,  -->
+
 ## Windows
 Sorry. We don’t support windows environment this moment.
 

rgt/__version__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

setup.py

@@ -77,21 +77,28 @@ def find_version(*file_paths):
                "pysam>=0.12.0",
                "pyBigWig"]
 
-def is_apple_m1():
-    chip = subprocess.check_output(['sysctl','-n','machdep.cpu.brand_string']).decode('utf-8')
-    if chip in ['Apple M1\n', 'Apple M1 Pro\n']:
+def is_arm64():
+    import platform
+
+    if platform.uname()[4] == 'arm64':
         return True
     else:
         return False
+
+    # chip = subprocess.check_output(['sysctl','-n','machdep.cpu.brand_string']).decode('utf-8')
+    # if chip in ['Apple M1\n', 'Apple M1 Pro\n']:
+    #     return True
+    # else:
+    #     return False
 
 if platform.startswith("darwin"):
     bin_dir = "mac"
-    # check if being installed on Apple M1 chip
-    if is_apple_m1():
-        #libRGT = "librgt_mac_m1.so"
-        libRGT = "librgt_mac.so"
+    # check if being installed on arm64 or x86_64
+    if is_arm64():
+        libRGT = "librgt_mac_arm64.so"
     else:
         libRGT = "librgt_mac.so"
+
     triplexes_file = "lib/libtriplexator.dylib"
 else:
     bin_dir = "linux"