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INSTALL.md

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Install the latest version of iSeq

version="1.0.0"
wget "https://github.com/BioOmics/iSeq/releases/download/v${version}/iSeq-v${version}.tar.gz"
tar -zvxf "iSeq-v${version}.tar.gz"
cd iSeq/bin/
chmod +x iseq
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
source ~/.bashrc

Anyway, as long as you install the following dependencies and add them to the environment variables, iSeq can be used.

  • pigz (>=2.8), compressing FASTQ files into gzip format by multiple threads
  • wget (>=1.16), downloading files by ftp or http
  • axel (>=2.17), downloading files by multiple threads
  • aspera (>=4.4.2.550), downloading files by Aspera
  • sra-tools (>=2.11.0), fetching SRA download links
# Due to the sra-tools >= 3.0 use CMake to build, sometimes it may be downloaded failed by conda, so use sra-tools=2.11.0
conda create -n iseq -c conda-forge -c bioconda pigz wget axel aspera-cli sra-tools=2.11 
# Check sotfware version
pigz --version | awk 'NR==1{print $2}'
wget --version | awk 'NR==1{print $3}'
axel --version | awk 'NR==1{print $2}'
ascp --version | awk 'NR==2{print $3}'
srapath --version | awk 'NR==2{print $3}'
# Use the following command to check whether dependent software is installed
iseq --version

Important

Using Ubuntu on Windows, installing Wget through conda may lead to "unable to resolve host address", which in turn may prevent iSeq from fetching data. You can don't install wget by conda. Or, this issue also can be resolved by following command:

conda activate iseq
# Map the system's built-in wget to the conda environment, ensuring that wget is properly installed.
ln -sf /usr/bin/wget $(which wget)
# Including the 'srapath'. you can install SRA Toolkit and then change the path below to your own.
ln -sf ~/YourPathway/sratoolkit/bin/srapath $(which srapath)

Here is a tutorial on how to install dependencies from source

1. pigz

  • Source install (non-Root)
wget https://zlib.net/pigz/pigz.tar.gz
tar -zvxf pigz.tar.gz
cd pigz
make
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
source ~/.bashrc
# Check sotfware version
pigz --version | awk 'NR==1{print $2}'
  • apt install for Ubuntu (Root permission required)
sudo apt install pigz
  • yum install for Centos (Root permission required)
sudo yum install pigz

2. wget

wget is generally included in most Linux distributions and does not need to be installed by ourselves

  • Source install (non-Root)
wget https://ftp.gnu.org/gnu/wget/wget-latest.tar.gz
tar -zvxf wget-latest.tar.gz
cd wget-1.24.5 # change software version
./configure --prefix=$(pwd)
make
cd src
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
source ~/.bashrc
# Check sotfware version
wget --version | awk 'NR==1{print $3}'
  • apt install for Ubuntu (Root permission required)
sudo apt install wget
  • yum install for Centos (Root permission required)
sudo yum install wget

3. axel

  • Source install (non-Root)
# see "https://github.com/axel-download-accelerator/axel/releases" to fetch the latest version of axel
wget https://github.com/axel-download-accelerator/axel/releases/download/v2.17.14/axel-2.17.14.tar.gz
tar -zvxf axel-2.17.14.tar.gz # change software version
cd axel-2.17.14 # change software version
./configure --prefix=$(pwd)
make && make install
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
source ~/.bashrc
# Check sotfware version
axel --version | awk 'NR==1{print $2}'
  • apt install for Ubuntu (Root permission required)
sudo apt install axel
  • yum install for Centos (Root permission required)
sudo yum install axel

4. aspera

  • Source install (only support non-Root)
# see "https://www.ibm.com/aspera/connect" to fetch the latest version of aspera
wget https://d3gcli72yxqn2z.cloudfront.net/downloads/connect/latest/bin/ibm-aspera-connect_4.2.8.540_linux_x86_64.tar.gz
tar -zvxf ibm-aspera-connect_4.2.8.540_linux_x86_64.tar.gz # change software version
bash ibm-aspera-connect_4.2.8.540_linux_x86_64.sh # change software version
echo 'export PATH=$PATH:~/.aspera/connect/bin' >> ~/.bashrc
source ~/.bashrc
# Check sotfware version
ascp --version | awk 'NR==2{print $3}'

5. sra-tools

  • Source install (non-Root)
# see "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current" to choose the appropriate platform
# e.g. for Ubuntu
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
tar -zvxf sratoolkit.current-ubuntu64.tar.gz
cd sratoolkit.3.1.0-ubuntu64/bin/ # change software version
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
source ~/.bashrc
# Check sotfware version
srapath --version | awk 'NR==2{print $3}'

Check iSeq version finally

iseq --version