From 8ba35f721c496b081192cd38f3b2c2e4936f259e Mon Sep 17 00:00:00 2001
From: qlr900 <qlr900@dangpu01fl.unicph.domain>
Date: Tue, 5 Jul 2022 12:05:10 +0200
Subject: [PATCH] add ku_sund_dangpu.md

---
 docs/ku_sund_dangpu.md | 58 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 docs/ku_sund_dangpu.md

diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md
new file mode 100644
index 0000000..c2b9454
--- /dev/null
+++ b/docs/ku_sund_dangpu.md
@@ -0,0 +1,58 @@
+# nf-core/configs: PROFILE Configuration
+
+All nf-core pipelines have been successfully configured for use on the dangpu PROFILE CLUSTER at the 
+Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen.
+
+To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the PROFILE CLUSTER.
+
+## Modules
+
+Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 
+```
+
+## How to use the nf-core pipelines on PROFILE CLUSTER
+
+###1. set up .bash_profile
+Add memory restrictions to `.bash_profile`. Use `vim` text editor to edit `.bash_profile` file (or create one if it does not exist in your home directory:
+
+```
+vi ~/.bash_profile
+```
+
+paste the following text within the file:
+```
+# personalising the profile: change the value of the variable $abc123 to your own user id
+abc123=def456 
+
+# In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this
+export NXF_OPTS='-Xms1g -Xmx4g'
+
+# Don't fill up your home directory with cache files
+export NXF_HOME=/projects/dan1/people/${abc123}/cache/nxf-home 
+export NXF_TEMP=${SNIC_TMP:-$HOME/glob/nxftmp}
+
+# Nextflow singularity image cachedir export 
+NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${abc123}/cache/singularity-images  
+```
+
+then save the changes and exit the editor. Now you need to activate the `.bash_profile` by logging out and in again to PROFILE CLUSTER or by typing:
+```
+source .bash_profile
+```
+
+The `$HOME` directory at dangpu has restricted space and should not be used to store cache files. Create those designated cache spaces for nextflow and singularity outside your `$HOME`:
+```
+mkdir $NXF_SINGULARITY_CACHEDIR
+mkdir $NXF_HOME
+```
+
+### 3. choose a nf-core pipeline and test it with your preferred settings
+```
+nextflow run nf-core/rnaseq -profile test -c <myconfig> 
+```
+