cleaned v1.0 commit

.gitignore

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+*.log
+/log

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Ivan William Harsono
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the disclaimer
+below) provided that the following conditions are met:
+
+     * Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+
+     * Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+
+     * Neither the name of the copyright holder nor the names of its
+     contributors may be used to endorse or promote products derived from this
+     software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

Prerequisite.md

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+## Download latest Docker 
+Source :  https://docs.docker.com/engine/install/ubuntu/
+### Add Docker's official GPG key:
+```bash
+sudo apt-get update
+sudo apt-get install ca-certificates curl
+sudo install -m 0755 -d /etc/apt/keyrings
+sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+sudo chmod a+r /etc/apt/keyrings/docker.asc
+```
+
+### Add the repository to Apt sources:
+```bash
+echo \
+  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
+  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
+  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo apt-get update
+```
+
+### Install latest version
+```bash
+sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+```
+
+### Dry run using Hello World
+```bash
+sudo docker run hello-world
+```
+
+
+## Download Latest Anaconda 2023.09 (Recommended for cleaner python environment, and some subtools require Python support)
+Latest version on 14-02-2024 is 23.09
+
+### Download and follow instructions from bash script
+Note : choose yes for option adding Anaconda to PATH
+```bash
+wget https://repo.anaconda.com/archive/Anaconda3-2023.09-0-Linux-x86_64.sh
+chmod a+x ./Anaconda3-2023.09-0-Linux-x86_64.sh
+bash Anaconda3-2023.09-0-Linux-x86_64.sh
+```

README.md

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+# IDeRare
+
+IDeRare or *"Indonesia Exome Rare Disease Variant Discovery Pipeline"* is simple and ready to use variant discovery pipeline to discover rare disease variants from exome sequencing data.
+
+**Note:** currently IDeRare paper is being considered journal submission.
+
+## Description
+- This pipeline is designed to be used in Linux environment
+- Original paper may used different version of tools, and the prerequisite used in this pipeline is the latest version of the tools
+- This pipeline is designed and tested with Indonesia rare disease trio patient, but it should be also usable for general cases of rare disease variant discovery from Exome Sequences data given paired end .fq.gz file and HPO data(s)
+- Ensure you have at least 250GB free for database and application setup, and 100GB free for each Trio family exome set
+- The .yaml file path are assuming all the folder are stored in ```Downloads``` folder with subfolder of ```Database``` (for RefSeq, dbNSFP, dbSNP, ClinVar), ```Sandbox``` (for application and its database), ```IDeRare``` (git cloned folder)
+
+## Quick Install
+1. Clone this repository
+```bash
+git clone https://github.com/ivanwilliammd/IDeRare
+```
+2. Have a Linux environment (Ubuntu or Ubuntu-like 22.04 LTS distro is recommended)
+3. Install [Docker](https://docs.docker.com/engine/install/ubuntu/) and [Anaconda - optional](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)- see [Prerequisite.md](Prerequisite.md) for more details
+4. Run dependency installation script and database script
+```bash
+source install_dependencies.sh
+source download_database.sh
+```
+2. Set the data, directory file reference and trio information on ```iderare.yml```.<br><br> 
+**Note** : all exome files should be located in the ```input/A_FASTQ``` folder of absolute path setup by ```data_dir``` at ```iderare.yml```
+<br><br>
+![File Structure](picture/01.png)
+![Example File](picture/02.png)
+1. Run the bash script
+```bash
+source iderare.sh
+```