How do I know which (bio)softwares are available in Taito?
We have listed the installed softwares here: https://research.csc.fi/software. The list can be filtered to show only the softwares relevant to your field (i.e. "Biosciences").
Biosoftwares are also listed topically on our bioscience site ("BioBox"): https://research.csc.fi/bioscience-programs
These links above list only the software that is actively maintained in the CSC servers. However, especially in Taito there are many bioinformatics tools that are installed even though CSC is not actively supporting them. When using these unsupported tool in Taito, remember that CSC does not guarantee that they are properly installed and working correctly.
If you can't find the tool you want to use in the software list, you can use following tricks to check if some version of the tool is available in Taito.
Use module spider command to check if there is a module for the tool you wish to use. For example:
module spider gatkIf you are looking for a biosoftware, try loading biokit module and check if software works after that. Many bioinformatics tools are actually workflows that contain several pieces of software. Some of the modules within biokit may include the tool you wish to use. Note also that there now are two biokit collections: default version and biokit/4.9.3. Remember to check both of them as some tools may be available in only one of the biokits.
module load biokit
module load biokit/4.9.3
- In Taito, the bioinformatics tools are installed in directory /appl/bio. In this directory you can check if there is an installation directory for the tool you would like to use. If you know the name of the command or executable you would like to use, you can check if it is found in some of the installation directories, with the command:
find /appl/bio -name "your_tool_name*" 2> /dev/nullFor example to check if any version of TransDecoder is available, you could use command:
find /appl/bio -name "TransDecoder*" 2> /dev/nullNote however that as the find command checks all the files in the /appl/bio directory, running the command may take up to 10 minutes.
- You can install the missing tool yourself to Taito. CSC can support you with the installation.
Feel free to ask for the installation from CSC Servicedesk (firstname.lastname@example.org).