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## 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

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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

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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:

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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

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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

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$ fio --loops=5 --size=1g --runtime=5 --time_based=1 --stonewall --direct=1 --group_reporting \
>     --name=SeqQ8T1read --bs=1048576 --iodepth=8 --rw=read \
>     --name=SeqQ8T1write --bs=1048576 --iodepth=8 --rw=write \
>     --name=SeqQ1T1read --bs=1048576 --iodepth=1 --rw=read \
>     --name=SeqQ1T1write --bs=1048576 --iodepth=1 --rw=write \
>     --name=4kQ32T16read --bs=4096 --iodepth=32 --numjobs=16 --rw=randread \
>     --name=4kQ32T16write --bs=4096 --iodepth=32 --numjobs=16 --rw=randwrite \
>     --name=4kQ1T1read --bs=4096 --iodepth=1 --rw=randread \
>     --name=4kQ1T1write --bs=4096 --iodepth=1 --rw=randwrite
SeqQ8T1read: (g=0): rw=read, bs=(R) 1024KiB-1024KiB, (W) 1024KiB-1024KiB, (T) 1024KiB-1024KiB, ioengine=psync, iodepth=8

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$ fio --loops=5 --size=1g --runtime=5 --time_based=1 --stonewall --direct=1 --group_reporting \
>     --name=SeqQ8T1read --bs=1048576 --iodepth=8 --rw=read \
>     --name=SeqQ8T1write --bs=1048576 --iodepth=8 --rw=write \
>     --name=SeqQ1T1read --bs=1048576 --iodepth=1 --rw=read \
>     --name=SeqQ1T1write --bs=1048576 --iodepth=1 --rw=write \
>     --name=4kQ32T16read --bs=4096 --iodepth=32 --numjobs=16 --rw=randread \
>     --name=4kQ32T16write --bs=4096 --iodepth=32 --numjobs=16 --rw=randwrite \
>     --name=4kQ1T1read --bs=4096 --iodepth=1 --rw=randread \
>     --name=4kQ1T1write --bs=4096 --iodepth=1 --rw=randwrite
SeqQ8T1read: (g=0): rw=read, bs=(R) 1024KiB-1024KiB, (W) 1024KiB-1024KiB, (T) 1024KiB-1024KiB, ioengine=psync, iodepth=8

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git clone https://github.com/alexdobin/STAR.git -b 2.7.9a
cd STAR/source
# edit Makefile:L35 CXXFLAGS_SIMD ?= -mavx2
# to CXXFLAGS_SIMD ?= -march=native
make STAR -j $(nproc)
sudo make install

cd ~
mkdir Gencode_human
cd Gencode_human

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sudo mount /dev/sda2 /mnt
sudo mkdir /mnt/boot/efi
sudo mount /dev/sda1 /mnt/boot/efi
sudo mount --bind /dev /mnt/dev
sudo mount --bind /proc /mnt/proc
sudo mount --bind /sys /mnt/sys
sudo cp /etc/resolv.conf /mnt/etc/resolv.conf
#### after reboot, ubuntu 18.04, sudo ln -s ../run/systemd/resolve/stub-resolv.conf /etc/resolv.conf
sudo chroot /mnt
apt install -y grub-efi-amd64-bin

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lscpu
Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
CPU(s):              36
On-line CPU(s) list: 0-35
Thread(s) per core:  1
Core(s) per socket:  18
Socket(s):           2
NUMA node(s):        2