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### Memory-Aware Batching - Introduced configurable min/max batch size bounds and memory limits for precise resource control. - Added `--batch-mem` CLI option to enable adaptive batching based on estimated sequence memory footprint (e.g., 128K, 64M, 1G). - Implemented `RebatchBySize()` to handle both byte and count limits, flushing when either threshold is exceeded. - Added conservative memory estimation via `BioSequence.MemorySize()` and enhanced garbage collection for explicit cleanup after large batch discards. - Updated internal batching logic across core modules to consistently apply default memory (128 MB) and size (min: 1, max: 2000) bounds. ### Linux Build Enhancements - Enabled static linking for Linux binaries using musl, producing portable, self-contained executables without external dependencies. ### Build System & Toolchain Improvements - Updated Go toolchain to 1.26.1 with corresponding dependency bumps (e.g., go-getoptions, gval, regexp2, go-json, progressbar, logrus, testify). - Fixed Makefile to safely quote LDFLAGS for paths with spaces. - Improved build error handling: on failure, logs are displayed before cleanup and exit. - Updated install script to correctly set GOROOT, GOPATH, and GOTOOLCHAIN, ensuring GOPATH directory creation. - Added progress bar to curl downloads in the install script for visual feedback during Go and OBITools4 downloads. All batching behavior remains non-breaking, with consistent constraints improving predictability during large dataset processing.
obitools V4
OBITools V4 is the new version of OBITools. They are closer to OBITools2 than to OBITools3. They are implemented in GO and are tens of times faster than OBITools2.
The git for OBITools4 is available at :
Installing OBITools V4
An installation script that compiles the new OBITools on your Unix-like system is available online. The easiest way to run it is to copy and paste the following command into your terminal
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
By default, the script installs the latest version of OBITools commands and other associated files into the /usr/local directory.
Installation Options
The installation script offers several options:
-l, --list List all available versions and exit.
-v, --version Install a specific version (e.g.,
-v 4.4.3). By default, the latest version is installed.-i, --install-dir Directory where obitools are installed (as example use
/usr/localnot/usr/local/bin).-p, --obitools-prefix Prefix added to the obitools command names if you want to have several versions of obitools at the same time on your system (as example
-p gwill producegobigrepcommand instead ofobigrep).-j, --jobs Number of parallel jobs used for compilation (default: 1). Increase this value to speed up compilation on multi-core systems (e.g.,
-j 4).
Examples
List all available versions:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
Install a specific version:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version 4.4.3
Install in a custom directory with command prefix:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
bash -s -- --install-dir test_install --obitools-prefix k
In this last example, the binaries will be installed in the test_install directory and all command names will be prefixed with the letter k. Thus, obigrep will be named kobigrep.
Note on Version Compatibility
The names of the commands in the new OBITools4 are mostly identical to those in OBITools2.
Therefore, installing the new OBITools may hide or delete the old ones. If you want both versions to be
available on your system, use the --install-dir and --obitools-prefix options as shown above.
Continuing the analysis...
Before with OBITools2 to continue the analysis, obitab was used as last command to produce a tab delimited file that was loadable in R or in any spreadsheet. The generated file was huge and required to load the full dataset in memory to be produced. Hereby OBITools4 proposes to substitute the obitab usage by the ROBIFastRead R module.