af213ab446
This release focuses on improving build reliability, memory efficiency for large datasets, and portability of Linux binaries. ### Static Linux Binaries - Linux binaries are now built with static linking using musl, eliminating external runtime dependencies and ensuring portability across distributions. ### Memory-Aware Batching - Users can now control memory usage during processing with the new `--batch-mem` option, specifying limits such as 128K, 64M, or 1G. - Batching logic now respects both size and memory constraints: batches are flushed when either threshold is exceeded. - Conservative memory estimation for sequences helps avoid over-allocation, and explicit garbage collection after large batch discards reduces memory spikes. ### Build System Improvements - Upgraded to Go 1.26 for improved performance and toolchain stability. - Fixed cross-compilation issues by replacing generic include paths with architecture-specific ones (x86_64-linux-gnu and aarch64-linux-gnu). - Streamlined macOS builds by removing special flags, using standard `make` targets. - Enhanced error reporting during build failures: logs are now shown before cleanup and exit. - Updated install script to correctly configure GOROOT, GOPATH, and GOTOOLCHAIN, with visual progress feedback for downloads. All batching behavior is non-breaking and maintains backward compatibility while offering more predictable resource usage on large datasets.
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.