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pip install biopython==1.78
sudo apt install -y prodigal

# PATH need contain diamond, blast, kma, samtools, bamtools, bedtools2

git clone https://github.com/arpcard/rgi.git -b 6.0.1

cd rgi

# app/Diamond.py

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cd ~
git clone https://github.com/DerrickWood/kraken2.git -b v2.1.2
cd kraken2/

./install_kraken2.sh bin

~/kraken2/bin/kraken2-build --download-taxonomy --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library human --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library archaea --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library bacteria --protein --db db_protein

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import re
import urllib.request
import pandas as pd
from io import BytesIO
from zipfile import ZipFile
from IPython.display import display
import matplotlib.pyplot as plt
import numpy as np

datas = pd.DataFrame(columns=[

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wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_15/gencode.v15.annotation.gtf.gz
wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_21/gencode.v21.chr_patch_hapl_scaff.annotation.gtf.gz

gunzip gencode.v15.annotation.gtf.gz
gunzip gencode.v21.chr_patch_hapl_scaff.annotation.gtf.gz

grep exon gencode.v15.annotation.gtf \
 |awk '{printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |sort -T . -k1,1 -k2,2n | bedtools merge > gencode.37.bed
grep exon gencode.v21.chr_patch_hapl_scaff.annotation.gtf \
 |awk '{printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |sort -T . -k1,1 -k2,2n | bedtools merge > gencode.38.bed

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https://repo.msys2.org/distrib/x86_64/

msys2-x86_64-20150916 5.2.0-3

msys2-x86_64-20160205 5.3.0-1

msys2-x86_64-20160921 6.1.0-1

msys2-x86_64-20161025 6.2.0-2

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git clone https://github.com/seppinho/mutserve.git -b v1.3.4
wget https://github.com/seppinho/mutserve/releases/download/v1.3.4/mutserve-1.3.4.jar

export ref=mutserve/files/rCRS.fasta

bwa index $ref

bwa mem -M -t 4 $ref mt_R1.fq.gz mt_R2.fq.gz \
| samtools view -@ 4 -1 -o mt.bam

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cd ~
git clone https://github.com/fo40225/cdh5-hadoop-mrv1.git
sudo docker build -t seppinho/cdh5-hadoop-mrv1 cdh5-hadoop-mrv1
git clone https://github.com/fo40225/cloudgene-docker.git
sudo docker build -t seppinho/cloudgene-docker cloudgene-docker
git clone https://github.com/fo40225/cloudgene-apps-docker.git
sudo docker run --privileged -it -p 8082:8082 -p 50030:50030 -p 50060:50060 -v ~/cloudgene-apps-docker:/opt/cloudgene/applications/cloudgene-apps-docker seppinho/cloudgene-docker start-cloudgene.sh
# browser localhost:8082 login: admin pw: admin1978

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for /f "skip=1 tokens=3" %%s in ('query user %USERNAME%') do (
  %windir%\System32\tscon.exe %%s /dest:console
)

Rundll32.exe user32.dll, LockWorkStation

"D:\SomeOpenGL.exe"

#### Accelerate Windows Remote Desktop
## Game developers and content creators all over the world are working from home and asking us to help them use Windows Remote Desktop streaming with the tools they use.

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# change power limit
sudo nvidia-smi -pm 1
sudo nvidia-smi -pl 320

# monitor
nvidia-smi dmon -s pucvmt

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mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release && cmake --build . --config Release -v