简体中文 ｜ English
Hi, you can call me John or WindWindLady, the nickname. This README may have lots of grammatical or some weird writing errors, please point them out! I'll appreciate it because you're helping me improve my writing skill.
I'm a graduate student majored in genetics. When deciding to learn this major, I heard that bioinformatic approaches will be needed in the rest of my career and Unix-like OSs such as Linux and macOS has advantages doing the analyses. So I'm using the newest MacBook Pro with M2 Pro chip. Obviously, the choice is not a good idea, for almost every software in bioinformatic is stilled compiled under x86-64 architecture instead of arm64. And macOS does not have the kind of instant translating ability when softwares using x86-based library (not Rosetta 2, it won't work when compiling). So, I've spent lots of time learning how to run the software in need.
I'm not talking about the disadvantages about OS or computing architecture. I just want to say it is VERY IMPORTANT to choose a fitting tool for the work.
All above is the reason I want to open this project. I wanna share my experience to help those who have similar problems whether or not I can really help. For me, it's a pleasure to give other people clues to solve the darn problems (sorry about the language). Also it's my first time using GitHub's project function. I hope we can improve the ability together!
- M2 Pro chip with 12-core CPU & 19-core GPU
- 32 GB of Unified Memory
- macOS 14.0 Sonoma (may update when releasing new version)
- Homebrew (for installing)
- VS Code (IDE sometimes)
- R Studio with R 4.3.0 There is a doc for installing a package Install gradientForest
- CTL for Xcode
- Parallels Desktop (for using some GIS software or software incompatible with macOS)
- Anaconda (for bioinformatic virtual environments)
- bwa 0.7.17 (installed via Homebrew)
- samtools 1.18 (locally compiled and running well)
- gemma 0.97 (openblas and gsl installed but cannot installed 0.98.x via Homebrew or locally complied)
- GenALEx (Excel Macro)
- Bayescan （GUI version which not supported multi-thread) This software now can stably run in my Mac, see this article which is in Chinese Install Bayescan
- Structure
- Arlequin
- Dataformater
- PGDSpider Same with Bayescan
- ArcMap 10.8
I may not list all the softwares and their version using now because of the number, and please make sure you have installed the prerequisite environments or libraries when reading my journals.
You'll be mad when installing R package
Not Now, I'm writing but it needs time.
Maybe I take GitHub as a journal or log website, not a platform sharing the codes. But I want to learn, to study. I think it will be a good way to communicate. There may be not any release in this project but I may share some codes files. With the help from kinds of communities, I may send an article to Cell, Nature or Science one day. Maybe. (LOL)