Bowtie2

This sub-directory contains:

• The Install Script(Install)
• The Package Config File(bowtie2_package.cfg)
• The Package Dependencies File(bowtie2_dependencies.cfg)

USAGE: ./trigger_tool_install.sh tool_name [tool_version]

After installing the package_downloads repos

See: https://github.com/mdibl/package_downloads/wiki/How-To-Install-This-Repos

cd to package_downloads/ install root directory and run

Example 1: ./trigger_tool_install.sh bowtie2
The above command tells the trigger script to install the current version of bowtie2

Example 2: ./trigger_tool_install.sh bowtie2 v2.3.3.1
The above command tells the trigger script to install version v2.3.3.2

The Install Script

This script is called by the main install script (install_package.sh) to build and install a new version of the package

What it does:

1. sources the main config file to set global path
2. sources the dependencies config file
3. runs the build and copy the executables to /opt/software/bin

Note:

The following environment variables are expected to be set by the caller:

1. GLOBAL_CONFIG (Path to the main Configuration file ${PACKAGE_DOWNLOADS_BASE}/Configuration )
2. PACKAGE_BASE (Path to the new release install directory ${EXTERNAL_SOFTWARE_BASE}/${SHORT_NAME}/${RELEASE_DIR})
3. PACKAGE_DEPENDENCIES_FILE (The dependencies file for this tool PACKAGE_DOWNLOADS_BASE/SHORT_NAME/

The Package Config File

The config file sets environment variables specific to this tool. Some key variables include:

• GIT_ORG
• SHORT_NAME (same as the name of the tool local directory)
• GIT_REPOS
• REMOTE_SITE
• REMOTE_DIR
• REPOS_TAG_PATTERN
• REMOTE_VERSION_FILE
• RELEASE_DIR
• EXPORT_GIT
• CLONE_GIT

The Package Dependencies File

Each tool's dependency file contains the pre-install and post-install sets of dependencies. Bowtie2 only uses few of these variables.

Used for Pre-Install Dependencies Check

• BIN_DEPENDENCIES
• LIB_DEPENDENCIES

Used To Verify the install was a success

• FILE_CHECK
• DIR_CHECK

Used to copy files to ../bin /../lib ../lib64 ../include

• BIN_FILES
• INCLUDE_DIR
• LIB64_DIR
• LIB_DIR

Appendix: