Taiwan Server2 update history

Update log

• 20231103

  • Install metaphlan4 within miniconda environment

• 20230928

  • Install Docker & Illumina TELL seq

• 20221208

  • Install Miniconda & QIIME2

Install CentOS

Partition assignment

Disk	Parition	MountPoint	Size	Descriptions
sda	sda1	/boot/efi	200MB	開機磁區
sda	sda2	/boot	500MB	開機磁區
sdc	swap	swap	128GB	記憶體交換區
sdc	home	/home	3TB	家目錄
sdc	root	/	4TB	根目錄
sdc	pkg	/pkg	4TB	公用程式
sdc	work	/work	16TB+	工作目錄

• /home

User specific space, which stores tools, references and etc. for their own use.

• /pkg

Public tools share among users.
Always install packages by root.

• /pkg/source

Downloaded packages.

• /work

Working space, stores references and working directory for each projects seperately.

• /work/reference

Stores references for projects.

Install HTOP

#install EPEL library
sudo yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
sudo yum update
sudo yum install htop

Install sysbench

系統測試工具，也可用來測試DataBase效率

sudo yum -y install sysbench

sysbench測試指令

#CPU測試
#透過尋找質數的方式檢測CPU速度，設定在數字10萬的範圍內尋找質數
sudo sysbench –test=cpu –cpu-max-prime=100000 run

#記憶體測試
#測試記憶體扇區設定為8K，總記憶體設定為200G，執行測試。
sudo sysbench –test=memory –memory-block-size=8k –memory-total-size=200G run

#硬碟測試(檔案讀寫與同步效率測試)
#準備階段
sudo sysbench –test=fileio –num-threads=15 –file-total-size=4G –file-test-mode=rndrw prepare
#執行階段
sudo sysbench –test=fileio –num-threads=15 –file-total-size=4G –file-test-mode=rndrw run

#執行緒測試
#測定500個執行緒，每個執行序測試100次，其中每個執行緒有四個共享執行階段。
sudo sysbench –test=threads –num-threads=500 –thread-yields=100 –thread-locks=4 run

Install Miniconda & QIIME2

Source

Miniconda download page
QIIME2 official doc

Miniconda

cd /pkg/source
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
    - Do you accept the license terms? [yes|no]
        yes
    - Miniconda3 will now be installed into this location: /root/miniconda3
      - Press ENTER to confirm the location
      - Press CTRL-C to abort the installation
      - Or specify a different location below
        /pkg/miniconda3  #Change install path to /pkg/
    - Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] 
        no
vi ~/.bash_profile
    -insert: PATH=$PATH:/pkg/miniconda3/bin 在export PATH之前
# 不重新登入就使設定生效
source ~/.bash_profile
conda update conda -y
conda install wget -y

QIIME2

cd /pkg/source

#安裝2021.11版本
wget https://data.qiime2.org/distro/core/qiime2-2021.11-py38-linux-conda.yml
conda env create -n qiime2-2021.11 --file qiime2-2021.11-py38-linux-conda.yml

# Initialize conda shell, activate when login
conda init bash
exit # Re-login
# Cancel activate when login
conda config --set auto_activate_base false
# Activate indicated environment when user login
vi ~/.bash_profile
    -insert: conda activate qiime2-2021.11
# 不重新登入就使設定生效
source ~/.bash_profile

Install XAMPP

Source

XAMPP official

Commands

cd /pkg/source
wget https://downloadsapachefriends.global.ssl.fastly.net/8.1.6/xampp-linux-x64-8.1.6-0-installer.run
chmod +x xampp-linux-x64-8.1.6-0-installer.run
./xampp-linux-x64-8.1.6-0-installer.run
/opt/lampp/lampp start

Error: libnsl not found

XAMPP: SELinux is activated. Making XAMPP fit SELinux…
chcon: 無法存取 '/opt/lampp/lib/mysql/*.so': 沒有此一檔案或目錄
Starting XAMPP for Linux 8.1.1-2…
XAMPP: Starting Apache…fail.
httpd: Syntax error on line 522 of /opt/lampp/etc/httpd.conf: Syntax error on line 6 of /opt/lampp/etc/extra/httpd-xampp.conf: Cannot load modules/mod_perl.so into server: libnsl.so.1: cannot open shared object file: No such file or directory
XAMPP: Starting MySQL…ok.
XAMPP: Starting ProFTPD…ok.

## Do Repo update first if redhat licence expired.
#Install libnsl
dnf upgrade --refresh
sudo dnf install libnsl
#Activate XAMPP again
/opt/lampp/lampp start

XAMPP: Starting Apache…ok.
XAMPP: Starting MySQL…already running.
XAMPP: Starting ProFTPD…already running.

Install Docker & Illumina TELL seq

https://docs.docker.com/engine/install/rhel/ #failed
https://linuxconfig.org/how-to-install-docker-in-rhel-8 #success

Docker

# Uninstall old versions
yum remove docker \
                  docker-client \
                  docker-client-latest \
                  docker-common \
                  docker-latest \
                  docker-latest-logrotate \
                  docker-logrotate \
                  docker-engine \
                  podman \
                  runc
yum install -y yum-utils
# Add repo
dnf config-manager --add-repo=https://download.docker.com/linux/centos/docker-ce.repo
dnf repolist -v
# Find the latest docker version and install
dnf list docker-ce --showduplicates
dnf install docker-ce-3:24.0.6-1.el8
# Start docker
systemctl start docker
systemctl enable docker
# Create docker group and add MacGyver to cocker group
groupadd docker
usermod -aG docker MacGyver

TellSeq

tar xzvf tellread.tar.gz
cd tellread-release
docker load -i docker-tellread
cd ../
tar zxvf tellsort.tar.gz
tar zxvf tellink.tar.gz

sh /pkg/TellSeq/releases_v1.1.1_package/tellread-release/run_tellread.sh \
  -i /work/NGS_DATA/TellSeq_230310_M07490_0026_000000000-KPCC2 \
  -o /work/TellSeqTest/T504-T508 \
  -s T504,T505,T506,T507,T508 \
  -g NONE,NONE,NONE,NONE,NONE
    
docker load -i /pkg/TellSeq/releases_v1.1.1_package/tellink-release/docker-tellink

sh /pkg/TellSeq/releases_v1.1.1_package/tellink-release/run_tellink.sh \
  -r1 /work/TellSeqTest/T504-T508/Full/T504-T508_R1_T506.fastq.gz.corrected.err_barcode_removed.fastq \
  -r2 /work/TellSeqTest/T504-T508/Full/T504-T508_R2_T506.fastq.gz.corrected.err_barcode_removed.fastq \
  -i1 /work/TellSeqTest/T504-T508/Full/T504-T508_I1_T506.fastq.gz.corrected.err_barcode_removed.fastq \
  -d metagenomics \
  -o /work/TellSeqTest/Tellink \
  -k 100 \
  -lc 70 \
  -p T506 \
  -j 30 

Install metaphlan4 within miniconda environment

https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#installation

# add the conda-forge channel to conda

conda install -c conda-forge -c bioconda metaphlan
conda create --name metaphlan4 -c conda-forge -c bioconda r-base
conda activate metaphlan4
pip install metaphlan

tags: Server