Installation#
Installation Java and nextflow#
It is highly recommend to install java using SDKMAN
curl -s https://get.sdkman.io | bash # install sdkman
sdk install java 17.0.10-tem # install java 17
java -version # confirm the correct version of java is installed
After then install nextflow with the command-line
curl -s https://get.nextflow.io | bash # donwload nextflow
chmod +x nextflow # make nextflow excutable
sudo mv nextflow /usr/local/bin # move to an executable path (in $PATH)
nextflow info # confirm the installation is done.
Running AIM#
Use following command-line to run AIM.
Install Required Data Dependencies#
AIM utilizes various databases for variant annotation, all of which have been compiled and are available for download. We use AWS S3 for data access, and the data can be downloaded by following these steps:
Install the AWS CLI: Follow the instructions provided in the AWS CLI Installation Guide
Navigate to Your Desired Directory: Change to the directory where you want your data dependencies downloaded. For example, in Ubuntu, use:
cd <desired/folder/path>
Use the following command to sync the S3 bucket to your local directory:
aws s3 sync s3://aim-data-dependencies-2.4-public . --no-sign-request
Warning
Due to licensing restrictions, the HGMD-related database is not included in the public download. To prepare HGMD database, see below.