From 5fe82fe9fd1f4b4ffba467bfad218c17fa3dbdf4 Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 21 Apr 2023 22:56:33 +0200 Subject: [PATCH 1/2] Fix env name --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b4df224..234062e 100644 --- a/README.md +++ b/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 From 581950f5b887fb1f0a1768713f9e3164b37ace62 Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 21 Apr 2023 22:56:53 +0200 Subject: [PATCH 2/2] Create dev env --- binder/environment-dev.yml | 34 ++++++++++++++++++++++++++++++++++ binder/environment.yml | 20 +------------------- 2 files changed, 35 insertions(+), 19 deletions(-) create mode 100644 binder/environment-dev.yml diff --git a/binder/environment-dev.yml b/binder/environment-dev.yml new file mode 100644 index 0000000..df0122d --- /dev/null +++ b/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 + + + \ No newline at end of file diff --git a/binder/environment.yml b/binder/environment.yml index ed10191..2b76364 100644 --- a/binder/environment.yml +++ b/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 - \ No newline at end of file