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Tags: pipeline
1, Export the Conda Environment
On the original computer, you can export the environment to a YAML file. This file will contain all the necessary details about the environment, including the packages and versions.
Open a terminal and activate the environment you want to copy:
conda activate bengal3_ac3
conda env export > bengal3_ac3.yml
conda activate spandx
conda env export > spandx.yml
conda activate chipseq
conda env export > chipseq.yml
conda activate rnaseq
conda env export > rnaseq.yml
conda activate homer
conda env export > homer.yml
conda activate qiime1
conda env export > qiime1.yml
conda activate trycycler
conda env export > trycycler.yml
conda activate vrap
conda env export > vrap.yml
#--------
conda activate chipseq2
conda env export > chipseq2.yml
conda activate r
conda env export > r.yml
conda activate rnaseq_2021
conda env export > rnaseq_2021.yml
conda activate rnaseq_old
conda env export > rnaseq_old.yml
conda activate snippy_env
conda env export > snippy_env.yml
conda activate spandx2
conda env export > spandx2.yml
#--------
conda activate rnaseq
conda env export > rnaseq_sage.yml
conda activate rnaseq2
conda env export > rnaseq2_sage.yml
#--------
TODO: export the yml files from notebook
2, Transfer the YAML File
Copy the environment.yml file from the original computer to the new computer. You can use methods such as USB drives, cloud storage, or direct file transfer over the network (e.g., using SCP if both machines are accessible over a network):
rsync -a -P jhuang@hamm:/home/jhuang/*.yml ./
3, Create the Environment on the New Computer
conda env create -f bengal3_ac3.yml
conda env create -f spandx.yml
#or conda env update --name spandx --file spandx.yml
conda env create -f chipseq.yml
conda env create -f rnaseq.yml
conda env create -f homer.yml
conda env create -f qiime1.yml
conda env create -f trycycler.yml
conda env create -f vrap.yml
# -- for viral variant calling
/home/jhuang/Tools/viral-ngs/bin/easy-deploy-script/viral-ngs-etc/conda-env
viral-ngs
# -- The results can be confirmed by the bacterial variant calling pipelines
spandx
bengal3_ac3 # for the env, we need snakemake_4_3_1.
conda update -n base conda
conda create -n snakemake_4_3_1 snakemake=4.3.1
/home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds
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