TGFAM-Finder

http://tgfam-finder.snu.ac.kr
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A web-based bioinformatics tool for finding and analyzing target gene families with integrated...
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### Run TGFam-Finder Installation Script

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&page=1&sod=asc&sop=and&sst=wr_hit&wr_id=9

Execute the installation script by providing the absolute path where TGFam-Finder should be installed. This script handles the automatic installation of prerequisite tools.

```bash
$perl install_TGFam-Finder.pl absolute_installation_path
(ex. $perl install_TGFam-Finder.pl /home/TGFam-Finder/TGFam)
```

--------------------------------

### Run TGFam-Finder

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&page=1&sod=desc&sop=and&sst=wr_datetime&wr_id=11

Execute the Run_TGFam-Finder.sh script to start the TGFam-Finder analysis. Ensure to use the '.' (dot) command for execution.

```bash
$. Run_TGFam-Finder.sh
(ex. $. Run_TGFam-Finder.sh)
```

--------------------------------

### Navigate to Output Directory

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&page=1&sod=desc&sop=and&sst=wr_datetime&wr_id=11

Change the current directory to the location where annotation results will be saved.

```bash
$cd folder_name_saving_output_of_annotation.
(ex. $cd /home/TGFam-Finder/TGFam/test_sample)
```

--------------------------------

### Build TGFam-Finder Output Directories

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&page=1&sod=desc&sop=and&sst=wr_datetime&wr_id=11

Execute the Build_TGFam-Finder.pl script to construct necessary output directories. This script verifies configuration files and checks for existing directories.

```bash
$perl Build_TGFam-Finder.pl absolute_path_containing_config_files RESOURCE.config PROGRAM_PATH.config
(ex. $perl /home/TGFam-Finder/TGFam/scripts/Build_TGFam-Finder.pl /home/TGFam-Finder/TGFam/test_sample PROGRAM_PATH_test.config RESOURCE_test.config)
```

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### Download TGFam-Finder for Ubuntu

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&page=1&sod=asc&sop=and&sst=wr_hit&wr_id=9

Use wget to download the TGFam-Finder archive for Ubuntu systems. Alternatively, clone the scripts repository from GitHub.

```bash
$wget http://tgfam-finder.snu.ac.kr/download/TGFam-Finder_Ubuntu_v1.01.tar.gz
```

```bash
$git clone https://github.com/tgfam-finder/scripts_ubuntu.git
```

--------------------------------

### Build TGFam-Finder Script

Source: http://tgfam-finder.snu.ac.kr/bbs/board.php?bo_table=Manual&wr_id=11

Execute the Build_TGFam-Finder.pl script to check configuration files and create necessary output directories. Ensure PROGRAM_PATH.config and RESOURCE.config are correctly set.

```perl
perl Build_TGFam-Finder.pl absolute_path_containing_config_files RESOURCE.config PROGRAM_PATH.config
(ex. $perl /home/TGFam-Finder/TGFam/scripts/Build_TGFam-Finder.pl /home/TGFam-Finder/TGFam/test_sample PROGRAM_PATH_test.config RESOURCE_test.config)
```
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