Merge pull request #5 from data-fun/fix-env

Fix production environment and create dev env

README.md

@@ -53,7 +53,7 @@ mamba env create -f binder/environment.yml
 Load conda environment:
 
 ```bash
-conda activate 3d-genome-builder
+conda activate 3DGB
 ```
 
 ### Download  HiC-Pro Singularity image

binder/environment-dev.yml

@@ -0,0 +1,34 @@
+name: 3DGB-dev
+# channels priority
+# see https://bioconda.github.io/
+# conda-forge has highest priority
+channels:
+  - defaults
+  - bioconda
+  - conda-forge
+dependencies:
+  - python=3.10
+  # Data analysis
+  - pandas
+  - scipy
+  - matplotlib
+  - jupyterlab
+  # Snakemake
+  - snakemake-minimal
+  # Build DAG with Snakemake
+  - graphviz
+  # Code formating
+  - black
+  - flake8
+  - pydocstyle
+  # FASTQ file manipulation
+  # https://anaconda.org/bioconda/seqkit
+  # https://bioinf.shenwei.me/seqkit/
+  - seqkit
+  # FASTA files manipulation
+  - biopython
+  # PDB files manipulation
+  - biopandas
+
+
+

binder/environment.yml

@@ -7,28 +7,10 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - python=3.9
-  # Data analysis
-  - pandas
-  - scipy
-  - matplotlib
-  - jupyterlab
+  - python=3.10
   # Snakemake
   - snakemake-minimal
   # Build DAG with Snakemake
   - graphviz
-  # Code formating
-  - black
-  - flake8
-  - pydocstyle
-  # FASTQ file manipulation
-  # https://anaconda.org/bioconda/seqkit
-  # https://bioinf.shenwei.me/seqkit/
-  - seqkit
-  # FASTA files manipulation
-  - biopython
-  # PDB files manipulation
-  - biopandas
-