From f8a7ee8d5c1accf1ffa0f9afac7a13f0291089a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 10:44:37 +0200 Subject: [PATCH 1/6] Add documentation about running offline --- docs/usage.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 5b7f7aa6..96fa08a4 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -393,3 +393,33 @@ We recommend adding the following line to your environment to limit this (typica ```bash NXF_OPTS='-Xms1g -Xmx4g' ``` + +### Running the pipeline without Internet access + +The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). +Here is an example command to download pipeline version 1.1.0 with singularity images: + +``` +nf-core download \ + --container singularity \ + --compress none \ + --revision 1.1.0 \ + raredisease +``` +For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters). + +Contrary to the paragraph about Nextflow on the nf-core tools page, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: + +``` +./nextflow plugin install nf-validation +``` + +Now you can transfer the `nextflow` binary as well as its directory `$HOME/.nextflow` to the system without Internet access, and use it there. It is necessary to use an explicit version of `nf-validation` offline, or Nextflow will check for the most recent version online. Find the version of nf-validation you downloaded in `$HOME/.nextflow/plugins`, then specify this version for `nf-validation` in your configuration file: + +``` +plugins { + // Set the plugin version explicitly, otherwise nextflow will look for the newest version online. + id 'nf-validation@0.3.1' +} +``` +This should go in your Nexflow confgiguration file, specified with `-c ` when running the pipeline. From d6e7394f209ccbdb6f62da15990a860d98687860 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 12:20:29 +0200 Subject: [PATCH 2/6] Use the correct name for new container system --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 96fa08a4..c6ca7078 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -401,7 +401,7 @@ Here is an example command to download pipeline version 1.1.0 with singularity i ``` nf-core download \ - --container singularity \ + --container-system singularity \ --compress none \ --revision 1.1.0 \ raredisease From 7bdd5d862a0a7c7409b91d3965e24deb8c824538 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 12:29:58 +0200 Subject: [PATCH 3/6] Correct typo --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index c6ca7078..e989218f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -422,4 +422,4 @@ plugins { id 'nf-validation@0.3.1' } ``` -This should go in your Nexflow confgiguration file, specified with `-c ` when running the pipeline. +This should go in your Nextflow confgiguration file, specified with `-c ` when running the pipeline. From f3deb8d979d915007d20106bffd1845ae6d41ae7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 12:35:33 +0200 Subject: [PATCH 4/6] Point to the documentation to download Nextflow --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index e989218f..95ccf5ac 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -408,7 +408,7 @@ nf-core download \ ``` For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters). -Contrary to the paragraph about Nextflow on the nf-core tools page, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: +Contrary to the paragraph about [Nextflow](https://nf-co.re/docs/usage/offline#nextflow) on the page linked above, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: ``` ./nextflow plugin install nf-validation From eaa4ca53174e02185d2f467977be4e5c8c9e7a6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 13:35:10 +0200 Subject: [PATCH 5/6] Removed the example and rephrased for clarity --- docs/usage.md | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 95ccf5ac..06ce8cd6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -396,19 +396,9 @@ NXF_OPTS='-Xms1g -Xmx4g' ### Running the pipeline without Internet access -The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). -Here is an example command to download pipeline version 1.1.0 with singularity images: +The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters). -``` -nf-core download \ - --container-system singularity \ - --compress none \ - --revision 1.1.0 \ - raredisease -``` -For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters). - -Contrary to the paragraph about [Nextflow](https://nf-co.re/docs/usage/offline#nextflow) on the page linked above, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: +Contrary to the paragraph about [Nextflow](https://nf-co.re/docs/usage/offline#nextflow) on the page linked above, it is not possible to use the "-all" packaged version of Nextflow for this pipeline. The online version of Nextflow is necessary to support the necessary nextflow plugins. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: ``` ./nextflow plugin install nf-validation From 6304e718d3c5d9641d6db0cdb31c3c1d9e4ab4cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Wed, 26 Jul 2023 13:58:00 +0200 Subject: [PATCH 6/6] Spelling configuration Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- docs/usage.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/usage.md b/docs/usage.md index 06ce8cd6..70790df4 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -412,4 +412,5 @@ plugins { id 'nf-validation@0.3.1' } ``` + This should go in your Nextflow confgiguration file, specified with `-c ` when running the pipeline.