mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
82a9972be7
- Add .DEFAULT_GOAL := all to Makefile for consistent default target - Document -j/--jobs option in README.md to allow parallel compilation - Add JOBS variable and -j/--jobs argument to install script (default: 1) - Replace fragile mkdir/cp commands with robust error handling and clear diagnostics - Add build directory preservation on copy failure for manual recovery - Pass -j option to make during compilation to enable parallel builds
73 lines
3.2 KiB
Markdown
73 lines
3.2 KiB
Markdown
# obitools V4
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*OBITools V4* is the new version of *OBITools*. They are closer to *OBITools2* than to *OBITools3*.
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They are implemented in *GO* and are tens of times faster than OBITools2.
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The git for *OBITools4* is available at :
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> https://github.com/metabarcoding/obitools4
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## Installing *OBITools V4*
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An installation script that compiles the new *OBITools* on your Unix-like system is available online.
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The easiest way to run it is to copy and paste the following command into your terminal
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```{bash}
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
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```
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By default, the script installs the latest version of *OBITools* commands and other associated files into the `/usr/local` directory.
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### Installation Options
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The installation script offers several options:
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> -l, --list List all available versions and exit.
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>
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> -v, --version Install a specific version (e.g., `-v 4.4.3`).
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> By default, the latest version is installed.
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>
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> -i, --install-dir Directory where obitools are installed
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> (as example use `/usr/local` not `/usr/local/bin`).
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>
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> -p, --obitools-prefix Prefix added to the obitools command names if you
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> want to have several versions of obitools at the
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> same time on your system (as example `-p g` will produce
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> `gobigrep` command instead of `obigrep`).
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>
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> -j, --jobs Number of parallel jobs used for compilation
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> (default: 1). Increase this value to speed up
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> compilation on multi-core systems (e.g., `-j 4`).
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### Examples
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List all available versions:
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```{bash}
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
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```
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Install a specific version:
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```{bash}
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version 4.4.3
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```
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Install in a custom directory with command prefix:
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```{bash}
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
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bash -s -- --install-dir test_install --obitools-prefix k
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```
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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`.
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### Note on Version Compatibility
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The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
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Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be
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available on your system, use the `--install-dir` and `--obitools-prefix` options as shown above.
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## Continuing the analysis...
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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](https://git.metabarcoding.org/obitools/obitools4/robireadfasta) R module.
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