From a2dbb9971e6e7fdf4c56b7add06562481dc7d079 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 30 Sep 2024 14:42:57 +0200 Subject: [PATCH] Update nextflow install docs (#5198) [ci skip] Signed-off-by: christopher-hakkaart Signed-off-by: Christopher Hakkaart Co-authored-by: Paolo Di Tommaso --- docs/install.md | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/docs/install.md b/docs/install.md index 2fbccc207ca..75dc3bb5138 100644 --- a/docs/install.md +++ b/docs/install.md @@ -60,12 +60,21 @@ Nextflow is distributed as a self-installing package, in order to make the insta chmod +x nextflow ``` -3. Move Nextflow into an executable path: +3. Move Nextflow into an executable path. For example: ```bash - sudo mv nextflow /usr/local/bin + mkdir -p $HOME/.local/bin/ + mv nextflow $HOME/.local/bin/ ``` + :::{tip} + Ensure the directory `$HOME/.local/bin/` is included in your `PATH` variable. Temporarily add this directory to `PATH` by setting `export PATH="$PATH:$HOME/.local/bin"`. Add the directory to `PATH` permanently by adding the export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`. Alternatively, move the `nextflow` executable to a directory already in your `PATH`. + ::: + + :::{warning} + Nextflow will update its executable during the self update process, therefore the update can fail if the executable is placed in a directory with restricted permissions. + ::: + 4. Confirm that Nextflow is installed correctly: ```bash @@ -83,7 +92,7 @@ nextflow self-update You can also temporarily switch to a specific version of Nextflow with the `NXF_VER` environment variable. For example: ```bash -NXF_VER=23.10.0 nextflow run hello +NXF_VER=23.10.0 nextflow info ``` ## Stable and edge releases @@ -98,10 +107,10 @@ To use the latest edge release, set `NXF_EDGE=1` when updating: NXF_EDGE=1 nextflow self-update ``` -You can also use `NXF_VER` to switch to any edge release: +You can also use `NXF_VER` to temporarily switch to any edge release. For example: ```bash -$ nextflow info +NXF_VER=24.06.0-edge nextflow info ``` ## Standalone distribution