SPRING for Windows
The SPRING software (Release 13.12.01) for Windows (both 32-bit and 64-bit) is available free of charge for academic usage. You can follow the steps specified below to install the software:
| 1. | Open a command prompt | # This is a console version. |
| 2. | C: | # Switch to hard drive C:. |
| 3. | CD \ | # Switch to the root. |
| 4. | MD spring | # Create the install directory named "spring". |
| 5. | download setup-windows.exe | # Save the downloaded file in C:\spring. |
| 6. | setup-windows.exe | # Run the setup program. |
It will take a while for the setup program to automatically download all necessary files (about 4.5G) for the SPRING software. You can also download a single zip file containing everything from Our server, Google drive, or Baidu cloud.
After installation, you can use SPRING to prioritize candidate variants, as:
| 1. | spring.exe -p -o results.txt -s seedgene.txt candidate.txt | ||
| Prioritize SNVs in candidate.txt using seed genes in seedgene.txt. Save results to results.txt. | |||
| 2. | spring.exe -p -s seedgene.txt candidate.vcf | ||
| Prioritize SNVs in candidate.vcf. Save results to a default file named spring.out. | |||
| 3. | spring.exe -r -o results.txt 100800 | ||
| Recommend seed genes for disease with MIM number 100800 and save to results.txt. | |||
The SPRING software has been tested in Windows 8.1 (64-bit), 8 (64-bit), 7 (32-bit and 64-bit), Vista (32-bit) and XP (32-bit). If you have any bug reports, comments, suggestions, and questions, please do not hesitate to send us an email.
SPRING for Mac OS X
The SPRING software (Release 13.12.01) for Mac OS X (64-bit) is available free of charge for academic usage. You can follow the steps specified below to install the software:
| 1. | cd | # Change to your home directory $HOME. |
| 2. | mkdir spring | # Create the install directory named "spring". |
| 3. | cd spring | # Change to the install directory. |
| 4. | download setup-macos | # Save the downloaded file in $HOME/spring. |
| 5. | chmod +x setup-macos | # Make the setup program executable. |
| 6. | ./setup-macos | # Run the setup program. |
| 7. | chmod +x spring | # Make the spring program executable. |
It will take a while for the setup program to automatically download all necessary files (about 4.5G) for the SPRING software. You can also download a single tgz file containing everything from Our server, Google drive, or Baidu cloud.
After installation, you can use SPRING to prioritize candidate variants, as:
| 1. | ./spring -p -o results.txt -s seedgene.txt candidate.txt | ||
| Prioritize SNVs in candidate.txt using seed genes in seedgene.txt. Save results to results.txt. | |||
| 2. | ./spring -p -s seedgene.txt candidate.vcf | ||
| Prioritize SNVs in candidate.vcf. Save results to a default file named spring.out. | |||
| 3. | ./spring -r -o results.txt 100800 | ||
| Recommend seed genes for disease with MIM number 100800 and save to results.txt. | |||
The SPRING software has been tested in Mac OS X 10.9 Mavericks and 10.8 Mountain Lion. If you have any bug reports, comments, suggestions, and questions, please do not hesitate to send us an email.
SPRING for Linux
The SPRING software (Release 13.12.01) for Linux (both 32-bit and 64-bit) is available free of charge for academic usage. You can follow the steps specified below to install the software:
| 1. | cd | # Change to your home directory $HOME. |
| 2. | mkdir spring | # Create the install directory named "spring". |
| 3. | cd spring | # Change to the install directory. |
| 4. | download setup-linux | # Save the downloaded file in $HOME/spring. |
| 5. | chmod +x setup-linux | # Make the setup program executable. |
| 6. | ./setup-linux | # Run the setup program. |
| 7. | chmod +x spring | # Make the spring program executable. |
It will take a while for the setup program to automatically download all necessary files (about 4.5G) for the SPRING software. You can also download a single tar.gz file containing everything from Our server, Google drive, or Baidu cloud.
After installation, you can use SPRING to prioritize candidate variants, as:
| 1. | ./spring -p -o results.txt -s seedgene.txt candidate.txt | ||
| Prioritize SNVs in candidate.txt using seed genes in seedgene.txt. Save results to results.txt. | |||
| 2. | ./spring -p -s seedgene.txt candidate.vcf | ||
| Prioritize SNVs in candidate.vcf. Save results to a default file named spring.out. | |||
| 3. | ./spring -r -o results.txt 100800 | ||
| Recommend seed genes for disease with MIM number 100800 and save to results.txt. | |||
The SPRING software has been tested in Ubuntu 12.04 (64-bit), Mint 16 (32-bit) and Mageia 3 (32-bit). If you have any bug reports, comments, suggestions, and questions, please do not hesitate to send us an email.