Lovely environment management with conda and mamba🥰

Presentation in Tsukuba Bioinfo Assembly at 2022-06-14.
URL: https://tinyurl.com/tba-2022-06-14

Transcript

1. Lovely environment management with conda and mamba🥰 condaとmambaで快適！環境構築🥰
2. Who am I? Akihiro Kuno MD,Ph.D 久野 朗広 👪 Child-rearing and houseworking 💼 Assist Prof at Anatomy and Embryology 🖥 Shellscript😍, R😊, Python😑 💡 Software development, Nanopore, Genome editing https:!/github.com/akikuno あなた誰よ?
3. Today's contents Lovely environment management with conda and mamba
4. Today's contents Lovely environment management with conda and mamba
5. One day, you find an awesome tool ある日、あなたは良さげなソフトウェアを見つけました • This plot looks cool😍 • The tool is available on GitHub https:!/github.com/shenlab-sinai/ngsplot • Install and try it! https:!/doi.org/10.1186/1471-2164-15-284
6. Error!!.😱 なんで動かんの？？（ガチギレ） Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'xrange' is not defined. Did you mean: 'range'?
7. Python 2.7 is required!!. 開発終わっとるやんけ… ＊Python 2 is no longer supported as of Jan 1st, 2020. https:!/github.com/shenlab-sinai/ngsplot
8. You need multiple Python versions 同じソフトウェアで複数のバージョンを持ちたい！ Daily usage🙂 Deep learning🤖 Legacy tools👻 Py2.7 Py3.8 Py3.10 → → → You have three environments in this example
9. Virtual environment 仮想環境 🚫 One machine, One environment Py3.10 Py3.8 Py2.7 🆗 Virtual environment Py3.8 Py2.7 Py3.10 →
10. Today's contents Lovely environment management with conda and mamba
11. conda creates multiple environments!! condaで複数の環境が作れる！ Py2.7 Py3.8 Py3.10 → → → conda create -n env1 python=3.10 conda create -n env2 python=3.8 conda create -n env3 python=2.7
12. Why I love conda?😻 1. Easy and simple commands 2. Bioinformatics tools are available 3. R and Bioconductor are supproted 4. Jupyter compatibility なぜconda推し？😻
13. 1. Easy and simple commands condaでよく使うコマンド # create environment named as tba conda create !-name tba # activate the environment conda activate tba # install packages into the environment conda install wget # delete environment conda deactivate !& conda remove !-name tba !-all 👉 Short hands-on
14. 2. Bioconda provides bioinfo tools Biocondaでバイオインフォツールのインストール conda config !-add channels defaults conda config !-add channels bioconda conda config !-add channels conda-forge # install bioinformatics tools conda install fastqc bwa samtools (https:!/bioconda.github.io/user/install.html) Bioconda's paper 👉 https:!/www.nature.com/articles/s41592-018-0046-7
15. 3. R and Bioconductor packages R関係のパッケージもインストールできます # install R conda install r-base r-essentials # install R packages conda install r-tidyverse r-seurat # install Bioconductor packages conda install bioconductor-biostrings
16. 4. Jupyter compatibility Jupyterの起動も可能 conda create -n tba_jpy3.8 python=3.8 jupyterlab conda create -n tba_jpy3.10 python=3.10 jupyterlab conda activate tba_jpy3.8 !& jupyter lab & conda activate tba_jpy3.10 !& jupyter lab 👉 Short hands-on
17. mamba is a superior alternative conda's drawback is too SLOW😭 mamba is an ultra-fast conda🚅💨 https:!/github.com/mamba-org/mamba mambaはcondaの上位互換（＊個人の感想です）
18. mamba's main commands mambaでよく使うコマンド mamba create -n tba # create environment mamba install wget # install pkgs mamba remove -n tba !-all ※ Use {conda activate} to activate environment
19. Speed comparison between conda and mamba mambaとcondaで速度対決 👉Google Colab
20. If you are interested in conda/mamba お試しくださいませ • Install conda • https:!/docs.conda.io/en/latest/miniconda.html • Windows User: WSL2 is highly recommended • https:!/docs.microsoft.com/en-us/windows/wsl/install • Install mamba (and bioconda) conda config !-add channels defaults conda config !-add channels bioconda conda config !-add channels conda-forge conda install mamba # !> Enjoy your coding!!🍻
21. Thanks for listening!! Any Questions?😋