- Install AWS CLI
pip3 install awscli --upgrade --user
# export PATH=~/.local/bin:$PATH (add into ~/.bashrc)
# source ~/.bashrc
- Configure the CLI
This Gist summarizes my work for the Reactome project "Query Reactome Data in R" during the Google Summer of Code 2020.
I would first like to begin by thanking my mentors Justin Cook, Joel Weiser, and Solomon Shorser for their guidance and support this summer. It was a privilege to learn from such a talented and experienced team.
The main objective was to create an interface in R to query data from the Reactome knowledgebase.
# ------ a python cell ------ | |
%load_ext rpy2.ipython | |
pd_df = pd_df.T | |
# ------ an R cell ------ | |
%%R -i pd_df | |
# `-i pd_df` means access to the global variable pd_df | |
r_df = do.something(pd_df) |
#!/usr/bin/env python | |
# fix t2t gff3 error | |
# now the problem is ids for some start&stop condons/exons are not unique | |
# 11/20/2022 | |
import sys,gzip | |
from collections import defaultdict | |
def sep_info(info): |
# setup | |
gcloud auth list | |
gcloud config set compute/zone us-east1-b | |
gcloud config set compute/region us-east1 | |
# create an instance template | |
cat << EOF > startup.sh | |
#! /bin/bash | |
apt-get update | |
apt-get install -y nginx |