Merge branch 'v2.7.1' of github.com:GenomiqueENS/toulligQC into v2.7.1

README.md

@@ -53,26 +53,39 @@ $ cd toulligqc && python3 setup.py build install
 ToulligQC is written with Python 3.
 To run ToulligQC without Docker, you need to install the following Python modules:
 
-* matplotlib
-* plotly
-* h5py
+ * matplotlib
+ * plotly
+ * h5py
 * pandas
 * numpy
 * scipy
 * scikit-learn
 * pysam
+* tqdm
+* pod5
 
+<a name="Conda-environemnt"></a>
+### 1.2 Conda environemnt**
+
+You can use a conda environment to install the required packages:
+
+```
+git clone https://github.com/GenomicParisCentre/toulligQC.git
+cd toulligqc && python3 setup.py build install
+conda env create -f environment.yml
+conda activate toulliqc
+```
 
 <a name="pypi-installation"></a>
-### 1.2 Using a PyPi package
+### 1.3 Using a PyPi package
 
 ToulligQC can be more easlily installed with a pip package availlable on the PyPi repository. The following command line  will install the latest version of ToulligQC:
 ```bash
 $ pip3 install toulligqc
 ```
 
 <a name="docker"></a>
-### 1.3 Using Docker
+### 1.4 Using Docker
 ToulligQC and its dependencies are available through a Docker image. To install docker on your system, go to the Docker website (<https://docs.docker.com/engine/installation/>).
 Even if Docker can run on Windows or macOS virtual machines, we recommend to run ToulligQC on a Linux host.
 <a name="docker-image-recovery"></a>

environment.yml

@@ -2,27 +2,27 @@ name: toulligqc
 channels:
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - bzip2=1.0.8=h5eee18b_6
-  - ca-certificates=2024.7.2=h06a4308_0
-  - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.4=h6a678d5_1
-  - libgcc-ng=11.2.0=h1234567_1
-  - libgomp=11.2.0=h1234567_1
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - libuuid=1.41.5=h5eee18b_0
-  - ncurses=6.4=h6a678d5_0
-  - openssl=3.0.14=h5eee18b_0
-  - pip=24.0=py311h06a4308_0
-  - python=3.11.9=h955ad1f_0
-  - readline=8.2=h5eee18b_0
-  - setuptools=69.5.1=py311h06a4308_0
-  - sqlite=3.45.3=h5eee18b_0
-  - tk=8.6.14=h39e8969_0
-  - wheel=0.43.0=py311h06a4308_0
-  - xz=5.4.6=h5eee18b_1
-  - zlib=1.2.13=h5eee18b_1
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=5.1
+  - bzip2=1.0.8
+  - ca-certificates=2024.7.2
+  - ld_impl_linux-64=2.38
+  - libffi=3.4.4
+  - libgcc-ng=11.2.0
+  - libgomp=11.2.0
+  - libstdcxx-ng=11.2.0
+  - libuuid=1.41.5
+  - ncurses=6.4
+  - openssl=3.0.14
+  - pip=24.0
+  - python=3.11.9
+  - readline=8.2
+  - setuptools=69.5.1
+  - sqlite=3.45.3
+  - tk=8.6.14
+  - wheel=0.43.0
+  - xz=5.4.6
+  - zlib=1.2.13
   - pip:
       - contourpy==1.2.1
       - cycler==0.12.1
@@ -54,4 +54,3 @@ dependencies:
       - tqdm==4.66.4
       - tzdata==2024.1
       - vbz-h5py-plugin==1.0.1
-prefix: /users/depbio/hamraoui/miniconda3/envs/toulligqc2.7