fo40225

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

fo40225

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

fo40225

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.

fo40225

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

# monitor
nvidia-smi dmon -s pucvmt

fo40225

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

fo40225

## first, STAR
## second, RemoveDuplicates

cd ~
mkdir CICERO-reference
cd CICERO-reference
mkdir GRCh37-lite
cd  GRCh37-lite
wget -O reference.tar.gz https://zenodo.org/record/3839940/files/reference.tar.gz?download=1
tar axvf reference.tar.gz

fo40225

sudo apt install -y libdb-dev axel
sudo cpan DB_File URI::Escape Set::IntervalTree Carp::Assert JSON::XS PerlIO::gzip

cd ~
axel -n 50 -q https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
axel -n 50 -q https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz
tar axvf GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
tar axvf GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz

git --recursive https://github.com/STAR-Fusion/STAR-Fusion.git -b v1.10.0

fo40225

user@ubuntu:~$ sudo docker run -it -v $HOME:/data --privileged --rm \
>  --device=/dev/kfd --device=/dev/dri --group-add video \
>  rocm/pytorch:rocm3.3_ubuntu16.04_py3.6_pytorch
root@4373d0a3dd33:/# apt install cabextract
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  libmspack0
The following NEW packages will be installed:

fo40225

sudo apt update
sudo apt install libnuma-dev
wget -q -O - http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key | sudo apt-key add -
echo 'deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main' | sudo tee /etc/apt/sources.list.d/rocm.list
sudo apt update
sudo apt install rocm-dkms
sudo usermod -a -G video $LOGNAME
sudo reboot

export PATH=/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64:$PATH

fo40225

user@ubuntu:~/Flops/version3/binaries-linux$ ./2006-Core2
Running Core 2 tuned binary with 1 thread...

Single-Precision - 128-bit SSE - Add/Sub
    GFlops = 34.624
    Result = 4.33405e+06

Double-Precision - 128-bit SSE2 - Add/Sub
    GFlops = 17.312
    Result = 2.18144e+06