𝕋his is a guide to configuring a Windows system to utilize many of the tools that the Im Lab uses. […] The native command line options in Windows are not well-integrated for many bioinformatic tools, so an alternative solution is to use Windows Subsystem for Linux (WSL). This allows your … Read more →

𝕋o get access to the servers at ANL, you will need at minimum an account with Argonne’s MCS division, as well as access to specific computing groups. This process is usually handled by one of the researchers at ANL, as they need to serve as a sponsor for external users. […] Once you are … Read more →

𝕋his page is about downloading and decrypting data from NCBI dbGaP. I will split up the instructions into Downloading and Decrypting […] To download, one must be approved in the dbGaP controlled data access system, receive an email that the data is ready, and follow the given instructions. … Read more →

𝕋he same info can be found at this page, https://www.ddbj.nig.ac.jp/jga/download-e.html, but the steps may be slightly different because we applied for Biobank Japan data before they integrated with the D-way system. […] I wrote a batch script and ran the following lines to download all the … Read more →

𝕋his wiki will show you how to set up SSH keys and configure custom connection options for accessing uchicago tarbell. After successful configuration, you can login your tarbell much more simply by running the following command: ssh tarbell […] Reference: Read more →

𝕋his is a guide on how to prepare a Post-Implementation Report for cloud credits, for future reference. This guide is based on the one prepared for the deadline of February 28th 2019. A Post-Implementation Report (PIR) provides data to compare the Cloud Credits model to traditional mechanisms of … Read more →

ℍow to submit data to Zenodo […] See Yanyu’s instructions https://github.com/hakyimlab/Yanyus-misc-tools/tree/master/zenodo_upload Read more →

𝕊top/start your EC2 instances programatically through AWS Command Line Interface (CLI). […] Stop your EC2 instances to avoid incurring charges when not in use. […] Your secret key must be kept very secret. Please store it in a very safe place and don’t include it in your code. … Read more →

𝕙ttps://rcc-uchicago.github.io/user-guide/ […] Please follow the instruction to request your RCC account: General RCC User Account Request PI Account Name: pi-haky Rcc Software: R, RStudio, Python, Python Rcc Research: My main research goal is to perform biomedical big data analysis and … Read more →

#Open RStudio #Type the following: nameproject = “PNPO-Alcohol-Epilepsy” githubuser = “hakyimlab” library(workflowr) setwd("~/Github") wflow_git_config(user.name = “Your Name”, user.email = “email@domain”) wflow_start(nameproject) … Read more →