Add files via upload

INSTALL.md

@@ -0,0 +1,176 @@
+## Install the latest version of iSeq
+
+```bash
+wget https://github.com/BioOmics/iSeq/releases/download/v1.0.0/iseq-1.0.0.tar.gz
+tar -zvxf iseq-1.0.0.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](https://github.com/madler/pigz) (>=2.8), compressing FASTQ files into gzip format by multiple threads
+- [wget](https://www.gnu.org/software/wget/) (>=1.16), downloading files by ftp or http
+- [axel](https://github.com/axel-download-accelerator/axel) (>=2.17), downloading files by multiple threads
+- [aspera](https://github.com/IBM/aspera-cli) (>=4.4.2.550), downloading files by Aspera
+- [sra-tools](https://github.com/ncbi/sra-tools) (>=2.11.0), fetching SRA download links
+
+```{bash}
+# 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 $3}'
+# Use the following command to check whether dependent software is installed
+iseq --version
+```
+
+## Here is a tutorial on how to install dependencies from source 
+
+### 1. pigz
+
+- Source install (non-Root)
+
+```bash
+wget https://zlib.net/pigz/pigz.tar.gz
+tar -zvxf pigz.tar.gz
+cd pigz
+make
+echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
+source ~/.bashrc
+# Check sotfware version
+pigz --version | awk 'NR==1{print $2}'
+```
+
+- apt install for Ubuntu (Root permission required)
+
+```bash
+sudo apt install pigz
+```
+
+- yum install for Centos (Root permission required)
+
+```bash
+sudo yum install pigz
+```
+
+### 2. wget 
+
+**`wget` is generally included in most Linux distributions and does not need to be installed by ourselves**
+
+- Source install (non-Root)
+
+```bash
+wget https://ftp.gnu.org/gnu/wget/wget-latest.tar.gz
+tar -zvxf wget-latest.tar.gz
+cd wget-1.24.5 # change software version
+./configure --prefix=$(pwd)
+make
+cd src
+echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
+source ~/.bashrc
+# Check sotfware version
+wget --version | awk 'NR==1{print $3}'
+```
+
+- apt install for Ubuntu (Root permission required)
+
+```bash
+sudo apt install wget
+```
+
+- yum install for Centos (Root permission required)
+
+```bash
+sudo yum install wget
+```
+
+### 3. axel
+
+- Source install (non-Root)
+
+```bash
+# see "https://github.com/axel-download-accelerator/axel/releases" to fetch the latest version of axel
+wget https://github.com/axel-download-accelerator/axel/releases/download/v2.17.14/axel-2.17.14.tar.gz
+tar -zvxf axel-2.17.14.tar.gz # change software version
+cd axel-2.17.14 # change software version
+./configure --prefix=$(pwd)
+make && make install
+echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
+source ~/.bashrc
+# Check sotfware version
+axel --version | awk 'NR==1{print $2}'
+```
+
+- apt install for Ubuntu (Root permission required)
+
+```bash
+sudo apt install axel
+```
+
+- yum install for Centos (Root permission required)
+
+```bash
+sudo yum install axel
+```
+
+### 4. aspera
+
+- Source install (only support non-Root)
+
+```bash
+# see "https://www.ibm.com/aspera/connect" to fetch the latest version of aspera
+wget https://d3gcli72yxqn2z.cloudfront.net/downloads/connect/latest/bin/ibm-aspera-connect_4.2.8.540_linux_x86_64.tar.gz
+tar -zvxf ibm-aspera-connect_4.2.8.540_linux_x86_64.tar.gz # change software version
+bash ibm-aspera-connect_4.2.8.540_linux_x86_64.sh # change software version
+echo 'export PATH=$PATH:~/.aspera/connect/bin' >> ~/.bashrc
+source ~/.bashrc
+# Check sotfware version
+ascp --version | awk 'NR==2{print $3}'
+```
+
+### 5. sra-tools
+
+- Source install (non-Root)
+
+```bash
+# see "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current" to choose the appropriate platform
+# e.g. for Ubuntu
+wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
+tar -zvxf sratoolkit.current-ubuntu64.tar.gz
+cd sratoolkit.3.1.0-ubuntu64/bin/ # change software version
+echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
+source ~/.bashrc
+# Check sotfware version
+srapath --version | awk 'NR==2{print $3}'
+```
+
+## Check iSeq version finally
+
+```bash
+iseq --version
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 BioOmics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.