Install Driver
check if you have GPU(pysical)
lspci | grep -i nvidia
Disable nouveau
vim /etc/modprobe.d/blacklist-nouveau.conf
blacklist nouveau
options nouveau modeset=0
linnil1 changed 2 years agoView mode Like Bookmark
[toc]
Target
I want to setup a DNS server for alias all the server in the internal networks.
It's possible to use ansible to update all /etc/hosts in each server. However it is not a elegant way.
Thus, I setup the coredns and try to figure out the configuration for supporting all commonly used protocols (plain, https, tls) and test them one by one. Finally, I will set this DNS IP:port in our main router.
Setup Coredns
linnil1 changed 3 years agoView mode Like Bookmark
Upload your fastq, we will run HLA pipeline for your in aws.
Github: https://github.com/linnil1/hla-on-aws
Architecture
API
API logic
I deploy my nuxt APP in Cloudflare
APIGateway + lambda as API server
linnil1 changed 3 years agoView mode Like Bookmark
Add logger in iptable
about iptable
https://www.hostinger.com/tutorials/iptables-tutorial
https://help.ubuntu.com/community/IptablesHowTo
show it
sudo iptables --line-numbers -L
sudo iptables --line-numbers -L OUTPUT
linnil1 changed 3 years agoView mode Like Bookmark
1. Create a slack webhook
https://api.slack.com/messaging/webhooks
2. Setup for Synology
Goto > Control Panel > Notification > SMS
2.1 then enable it
2.2 and add SMS service provider
2.3 Skip request Header
linnil1 changed 3 years agoView mode Like Bookmark
1. Find the series name
ESPON-L355
2. Download software
https://www.epson.com.tw/%E6%94%AF%E6%8F%B4%E6%9C%8D%E5%8B%99/%E5%8D%B0%E8%A1%A8%E6%A9%9F/%E5%8E%9F%E5%BB%A0%E9%80%A3%E7%BA%8C%E4%BE%9B%E5%A2%A8%E5%8D%B0%E8%A1%A8%E6%A9%9F/Epson-L355/s/SPT_C11CC86406#drivers
Download ESPONNET from website https://www.epson.com.tw/%E6%94%AF%E6%8F%B4%E6%9C%8D%E5%8B%99/%E5%8D%B0%E8%A1%A8%E6%A9%9F/%E5%8E%9F%E5%BB%A0%E9%80%A3%E7%BA%8C%E4%BE%9B%E5%A2%A8%E5%8D%B0%E8%A1%A8%E6%A9%9F/Epson-L355/s/SPT_C11CC86406?review-filter=Windows+10+64-bit
3.0 Find the device
linnil1 changed 3 years agoView mode Like Bookmark
TL;DR
Backgroud
I have four machines plugged on apcups, include two server, one Synology NAS, one QNAP NAS. Yet the ups has only one USB port, I will try to share the ups status to all machines and notify them whether the power is gone.
Get UPS status via USB
Connect one of the server to APC via USB.
Then, setup apcupsd
linnil1 changed 3 years agoView mode Like Bookmark
Path
Nginx root: /etc/nginx/
Main config: /etc/nginx/nginx.conf
Add SSL
Put your certification in /certs and than
server {
server_name toolmen.bime.ntu.edu.tw;
listen 8080 ssl http2;
linnil1 changed 3 years agoView mode Like Bookmark
VBSeq
Wang, YY., Mimori, T., Khor, SS. et al. HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel. Hum Genome Var 6, 29 (2019). https://doi.org/10.1038/s41439-019-0061-y
http://nagasakilab.csml.org/hla/
Main changed
I tested on 3.42.0
Download specific IMGT/HLA versiongit clone https://github.com/ANHIG/IMGTHLA HLA
cd HLA
linnil1 changed 4 years agoView mode Like Bookmark
Hisat2
Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).
https://daehwankimlab.github.io/hisat2/
https://daehwankimlab.github.io/hisat-genotype/
https://github.com/DaehwanKimLab/hisat2
https://github.com/DaehwanKimLab/hisat-genotype
linnil1 changed 4 years agoView mode Like Bookmark
Kourami
https://github.com/Kingsford-Group/kourami
Lee, H., & Kingsford, C. Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery. Genome Biology 19(16), 2018
I follow this tutorial https://github.com/Kingsford-Group/kourami/blob/master/preprocessing.md#2-creating-kourami-hla-panel-and-merged-msas-from-another-version-release-of-imgthla-db-or-a-custom-version
Prerequested
You can successful run Kourmai for HLA typing.
i.e. The below command should work
linnil1 changed 4 years agoView mode Like Bookmark
HackMD (Recommanded): https://hackmd.io/oTjzyAzFQ9Genk7zsRWq_g
Q0
If you are doing genetic counseling, what is the most frequent question you have been asked. Otherwise, what do you want to ask a certified Genetic Counselor? Why? (20%)
Conseling
I have not been asked ever, but I guess the questions may related to cancer.
Ask
linnil1 changed 4 years agoView mode Like Bookmark
First step, install it
Follow https://hub.docker.com/_/wordpress/ to make sure WordPress can work on your machine.
In this tutorial, wordpress:5.4.0-php7.2-apache are used.
Second, get certification
You can use certbot to get certification files
docker run --rm -it -p 80:80 -p 443:443 -v $PWD/letsencrypt:/etc/letsencrypt certbot/certbot certonly --standalone
linnil1 changed 4 years agoView mode Like 3 Bookmark
Judge Open: 2021/1/19
This is just an exercise. This score is NOT included into our final score.
[toc]
Version
Python: 3.8.5 (Note: no numpy)
Java: openjdk14 (https://openjdk.java.net/projects/jdk/14/)
Platform: Debian
linnil1 changed 4 years agoView mode Like Bookmark
Grub basic operation
Edit in /etc/default/grub
For ubuntu
sudo update-grub2
For centos
sudo grub2-mkconfig -o /boot/efi/EFI/centos/grub.cfg
Cpu Sync Error
linnil1 changed 4 years agoView mode Like Bookmark