update env-yml

README.md

@@ -55,7 +55,11 @@ deepsignal-plant is built on [Python3](https://www.python.org/) and [PyTorch](ht
 Install deepsignal-plant, its dependencies, and [tombo](https://github.com/nanoporetech/tombo) in one step using [conda](https://conda.io/docs/) and [environment.yml](environment.yml):
 
 ```shell
-conda env create --name deepsignalpenv -f environment.yml
+# download deepsignal-plant
+git clone https://github.com/PengNi/deepsignal-plant.git
+
+# install tools in environment.yml
+conda env create --name deepsignalpenv -f /path/to/deepsignal-plant/environment.yml
 
 # then the environment can be activated to use
 conda activate deepsignalpenv
@@ -95,20 +99,20 @@ python setup.py install
 [PyTorch](https://pytorch.org/) can be automatically installed during the installation of deepsignal-plant. However, if the version of [PyTorch](https://pytorch.org/) installed is not appropriate for your OS, an appropriate version should be re-installed in the same environment as the [instructions](https://pytorch.org/get-started/locally/):
 ```bash
 # install using conda
-conda install pytorch==1.11.0 cudatoolkit=10.2 -c pytorch
+conda install pytorch==1.10.0 cudatoolkit=10.2 -c pytorch
 
 # or install using pip
-pip install torch==1.11.0
+pip install torch==1.10.0
 ```
 
 ##### (4) Install tombo
-[tombo (version 1.5.1)](https://github.com/nanoporetech/tombo) is required to be installed in the same environment:
+[tombo (version 1.5.1)](https://github.com/nanoporetech/tombo) is required to be installed:
 ```bash
-# install using conda
-conda install -c bioconda ont-tombo
-
-# or install using pip
+# install using pip
 pip install ont-tombo
+
+# or install using conda
+conda install -c bioconda ont-tombo
 ```
 
 **Note:**

environment.yml

@@ -1,20 +1,21 @@
-name: deepsignalpenv
-channels:
- - bioconda
- - pytorch
- - conda-forge
-dependencies:
- - python>=3.8
- - pip
- - cudatoolkit=10.2 # 10.2 is ok for 1.7.0-1.11.0
- - numpy>=1.19.2
- - h5py>=2.8.0
- - statsmodels>=0.13.2
- - scikit-learn>=1.0.2
- - pytorch::pytorch=1.10.0 # add channel prefix (pytorch::) to make sure the cuda version being installed?
- - scipy
- - pandas
- - samtools>=1.12 # will install dependence->htslib, which includes tabix and bgzip
- - minimap2>=2.23
- - deepsignal-plant=0.1.6
- - ont-tombo>=1.5.1
+name: deepsignalpenv
+channels:
+ - bioconda
+ - pytorch
+ - conda-forge
+dependencies:
+ - python>=3.8
+ - pip
+ - cudatoolkit=10.2 # 10.2 is ok for 1.7.0-1.11.0
+ - numpy>=1.19.2,<1.20 # <1.20 is for tombo
+ - h5py>=2.8.0,<3 # <3 is for tombo
+ - statsmodels>=0.13.2
+ - scikit-learn>=1.0.2
+ - pytorch::pytorch=1.10.0 # add channel prefix (pytorch::) to make sure the cuda version being installed?
+ - scipy
+ - pandas
+ - samtools>=1.12 # will install dependence->htslib, which includes tabix and bgzip
+ - minimap2>=2.23
+ - deepsignal-plant=0.1.6
+ - pip:
+ - ont-tombo==1.5.1 # using conda to install tombo causes conflicts?