From 2afb4f0ad6674546b320baeb52f360733f6c69f4 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 13 Apr 2021 14:37:54 +0200 Subject: [PATCH 1/3] Don't recommend setting --custom_config_base manually --- README.md | 29 ++++++++++++----------------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 7637725..613ee05 100644 --- a/README.md +++ b/README.md @@ -39,27 +39,22 @@ You should be able to get a good idea as to how other people are customising the ### Offline usage -If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. -Then run the pipeline with `--custom_config_base` or `params.custom_config_base` set to the location of the directory containing the repository files: +To use nf-core pipelines offline, we recommend using the `nf-core download` helper tool. This will download both the pipeline files and also the config profiles from `nf-core/configs`. The pipeline files are then edited to load the configs from their relative file path correctly. ```bash -## Download and unzip the config files -cd /path/to/my/configs -wget https://github.com/nf-core/configs/archive/master.zip -unzip master.zip - -## Run the pipeline -cd /path/to/my/data -nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/ +# Download the workflow + transfer to offline cluster +nf-core download rnaseq +scp nf-core-rnaseq-3.0.tar.gz me@myserver.com:/path/to/workflows # or however you prefer to transfer files to your offline cluster +ssh me@myserver.com +# Extract workflow files +cd /path/to/workflows +tar -xzf nf-core-rnaseq-3.0.tar.gz +# Run workflow +cd /path/to/data +nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile mycluster ``` -Alternatively, instead of using the configuration profiles from this repository, you can run your pipeline directly calling the single institutional config file that you need with the `-c` parameter. - -```bash -nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config -``` - -> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier. +If you prefer, you can download these config profiles yourself and customise the `--custom_config_base` / `params.custom_config_base` parameter in each pipeline to to set to the location of the configs directory. ## Adding a new config From 2f343868adf18aed131194082230fd84ac210fef Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 13 Apr 2021 22:52:31 +0200 Subject: [PATCH 2/3] Apply suggestions from code review Co-authored-by: Maxime Garcia --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 613ee05..4ccc10a 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,7 @@ To use nf-core pipelines offline, we recommend using the `nf-core download` help # Download the workflow + transfer to offline cluster nf-core download rnaseq scp nf-core-rnaseq-3.0.tar.gz me@myserver.com:/path/to/workflows # or however you prefer to transfer files to your offline cluster +# Connect to offline cluster ssh me@myserver.com # Extract workflow files cd /path/to/workflows From c7e4ea25f5b2618d3ba6e7efd18146ba45d25113 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 14 Apr 2021 23:30:17 +0200 Subject: [PATCH 3/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4ccc10a..5feb3cc 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ cd /path/to/data nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile mycluster ``` -If you prefer, you can download these config profiles yourself and customise the `--custom_config_base` / `params.custom_config_base` parameter in each pipeline to to set to the location of the configs directory. +If required, you can instead download the nf-core/configs files yourself and customise the `--custom_config_base` / `params.custom_config_base` parameter in each pipeline to to set to the location of the configs directory. ## Adding a new config