Install SBFS manually

Overview

Install SBFS manually for Linux and macOS. Note that these instructions are meant for advanced users.

Conversely, learn to install SBFS automatically.

Linux

1. Download the SBFS executable file.

curl https://igor.sbgenomics.com/downloads/sbfs/linux-amd64/sbfs -O

2. Change the file permissions so you are able to run the executable

chmod a+x sbfs

The SBFS is now fully installed. See below for optional SBFS operations.

Optional operations

Add SBFS to the PATH

Add SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. path/to/dir/sbfs).

• Move SBFS binary to a directory which is already in the PATH.

sudo mv sbfs /usr/local/bin/

• Add the directory which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary.

Add bash completion for SBFS

Please note that this only works with bash completion version 4, which should be previously installed and enabled.

To add bash completion on Linux, issue the following command:

sudo bash -c "sbfs gen completion > /etc/bash_completion.d/sbfs"

To complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command:

sudo sbfs gen man /usr/local/share/man/man1/

Please note that if /usr/local/share/man is not in your manpath then you should use any other directory from the manpath such as:

• /usr/local/man
• /usr/share/man

macOS

Prerequisite

Before installing SBFS, please install macFUSE. Check if FUSE is installed via your System Preferences.

Procedure

1. Download the SBFS executable file.

curl https://igor.sbgenomics.com/downloads/sbfs/darwin-amd64/sbfs -O

2. Change the file permissions so you are able to run the executable.

chmod a+x sbfs

The SBFS is now fully installed. See below for optional SBFS operations.

Optional operations

Add SBFS to the PATH

Add SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. path/to/dir/sbfs).

• Move SBFS binary to a directory which is already in the PATH.

sudo mv sbfs /usr/local/bin/

• Add the directory which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary.

Add bash completion for SBFS

Please note that this only works with bash completion version 4, which should be previously installed and enabled.

To add bash completion on macOS, issue the following command:

sudo bash -c "sbfs gen completion > /usr/local/etc/bash_completion.d/sbfs

To complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command:

source /usr/local/etc/bash_completion.d/sbfs

Install man pages

To install man pages, use this command:

sudo sbfs gen man /usr/local/share/man/man1/

Please note that if /usr/local/share/man is not in your manpath then you should use any other directory from the manpath such as:

• /usr/local/man
• /usr/share/man