tar -xzf bbtoolsflver-*.tar.gz cd bbtoolsflver/ cat version.txt | grep FILTER_VER Expected output: FILTER_VER=bbtools_fl_2.1 SDMs require structured packages ( .deb , .rpm , or .msi ). If you only have the source tarball, you must convert it. Option A: Convert to .deb (For APT-based SDM) Use checkinstall or create a manual DEB structure.
sudo gem install fpm fpm -s tar -t rpm -n bbtoolsflver -v 1.0.0 --prefix /opt/bbtoolsflver bbtoolsflver-1.0.0.tar.gz # Install via SDM sudo rpm -ivh bbtoolsflver-1.0.0-1.x86_64.rpm For SCCM, convert the folder to an MSI using Advanced Installer or WiX Toolset . bbtoolsflver to sdm install
sudo apt install checkinstall cd bbtoolsflver/ # Create a custom install script mkdir -p debian/DEBIAN cat > debian/DEBIAN/control << EOF Package: bbtoolsflver Version: 1.0.0 Section: science Priority: optional Architecture: amd64 Depends: openjdk-11-jre-headless Description: BBTools with filter version flver for SDM EOF mkdir -p debian/usr/local/bbtoolsflver cp -r * debian/usr/local/bbtoolsflver/ Build DEB dpkg-deb --build debian bbtoolsflver_1.0.0_amd64.deb Deploy via SDM sudo dpkg -i bbtoolsflver_1.0.0_amd64.deb Option B: Convert to .rpm (For YUM/DNF SDM) Use fpm (Effing Package Management) to simplify the conversion. tar -xzf bbtoolsflver-*
Remember: always verify the filter version with --help after installation. If the SDM still fails to recognize the flag, you likely need to symlink the old filter binary to a standard name (e.g., ln -s /opt/bbtoolsflver/filter_fl /usr/local/bin/filter ). sudo gem install fpm fpm -s tar -t rpm -n bbtoolsflver -v 1
chmod +x /usr/local/bin/bbtoolsflver-sdm Now, within your SDM workflow, call:
After installation, create an SDM wrapper script:
| Requirement | Specification | | --- | --- | | | Ubuntu 20.04/22.04 LTS, CentOS 7+, or Windows Server 2019+ | | SDM Type | YUM/DNF (RHEL), APT (Debian), or SCCM (Windows) | | Java | OpenJDK 11 or 17 (BBTools requires Java) | | Disk Space | Minimum 5 GB (for reference genomes + filters) | | Network | Access to GitHub, SourceForge, or internal artifact repo | Step 1: Locate the “bbtoolsflver” Artifact The bbtoolsflver identifier is rarely available in standard repositories. You will likely find it as a tarball or a ZIP file in a legacy repository. For Linux/macOS: wget https://sourceforge.net/projects/bbmap/files/BBMap_38.90_flver.tar.gz # or an internal mirror curl -O http://internal-repo/tools/bbtoolsflver-1.0.0.tar.gz Verification: Extract the contents to inspect the filter version: