From 3f534c154ea30152983865d10e6d8d13f68c8cf8 Mon Sep 17 00:00:00 2001 From: arontommi Date: Wed, 6 Nov 2019 13:10:09 +0100 Subject: [PATCH 1/8] documentation on how to fix bianca cluster configuration problem --- docs/uppmax.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/uppmax.md b/docs/uppmax.md index 07a7f14..d5bba37 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -26,6 +26,12 @@ If running on Bianca, you will have no internet connection and these configs wil Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca. This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available. +Please note that Bianca only allocates 7 GB memory per core so max memory needs to be configured: + +```bash +--max_memory "112GB" +``` + ## Getting more memory If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags: From 06469901fe1aac666878353cfc848fd5b5e54f4e Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 11:24:29 +0100 Subject: [PATCH 2/8] typo --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index e7d5327..170d618 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -82,7 +82,7 @@ For security reasons, there is no internet access on Bianca so you can't downloa You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use) Note that you will have to download the singularity images as well. -After transfering the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : +After transffering the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : `export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.` From 5726ef3456210e4244aeb01a5eed776dbddadf89 Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 11:26:08 +0100 Subject: [PATCH 3/8] typo --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 170d618..1823408 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -79,7 +79,7 @@ To use it, submit with `-profile uppmax,devel`. For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your bianca project. -You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use) Note that you will have to download the singularity images as well. +You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. After transffering the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : From e6bb7a48521da14b2ca783e9af56fc655aa4a670 Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 11:37:59 +0100 Subject: [PATCH 4/8] capital names --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 1823408..24dcf20 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -77,7 +77,7 @@ To use it, submit with `-profile uppmax,devel`. ## Running on Bianca -For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your bianca project. +For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project. You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. From f84fbb8f890d87ef25b3197ca5e4bdcf8adae4cd Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 11:39:51 +0100 Subject: [PATCH 5/8] typo --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 24dcf20..680feab 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -82,7 +82,7 @@ For security reasons, there is no internet access on Bianca so you can't downloa You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. -After transffering the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : +After transferring the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : `export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.` From 6480aef1db757943b09608212fcad01f16687a47 Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 11:41:33 +0100 Subject: [PATCH 6/8] typo --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 680feab..f4e66cb 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -82,7 +82,7 @@ For security reasons, there is no internet access on Bianca so you can't downloa You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. -After transferring the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : +Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : `export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.` From c2c726551811ffdcb69f0d6906e0d1f65f7ccda6 Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 13:47:47 +0100 Subject: [PATCH 7/8] fix linting errors --- docs/uppmax.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index f4e66cb..43c6282 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -74,14 +74,12 @@ It is not suitable for use with real data. To use it, submit with `-profile uppmax,devel`. - ## Running on Bianca For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project. You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. - Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : `export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.` From ac108379cd02ee9ca9c611f516e23a38b3f68b44 Mon Sep 17 00:00:00 2001 From: arontommi Date: Thu, 26 Nov 2020 13:58:16 +0100 Subject: [PATCH 8/8] trailing spaces --- docs/uppmax.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 43c6282..d9ac5ce 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -76,9 +76,9 @@ To use it, submit with `-profile uppmax,devel`. ## Running on Bianca -For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project. +For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project. -You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. +You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` :