obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2026-03-25 13:30:52 +00:00
Code Issues Packages Projects Releases Wiki Activity

Enhance OBITools4 installation script with version control and documentation

Browse Source 
Update installation script to support specific version installation, list available versions, and improve documentation.

- Add support for installing specific versions with -v/--version flag
- Add -l/--list flag to list all available versions
- Improve help message with examples
- Update README.md to reflect new installation options and examples
- Add note on version compatibility between OBITools2 and OBITools4
- Remove ecoprimers directory
- Improve error handling and user feedback during installation
- Add version detection and download logic from GitHub releases
- Update installation process to use tagged releases instead of master branch
This commit is contained in:
Eric Coissac
2026-02-06 09:52:43 +01:00
parent 9c162459b0
commit aa819618c2
3 changed files with 166 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
README.md
View File

@@ -16,12 +16,17 @@ The easiest way to run it is to copy and paste the following command into your t
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
```
By default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.
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, the installation script offers two options:
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/local` not `/usr/local/bin`).
>
@@ -30,14 +35,31 @@ available on your system, the installation script offers two options:
> same time on your system (as example `-p g` will produce
> `gobigrep` command instead of `obigrep`).
You can use these options by following the installation command:
### Examples
List all available versions:
```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
```
Install a specific version:
```{bash}
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:
```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
bash -s -- --install-dir test_install --obitools-prefix k
```
In this case, 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`.
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...