From 7163e8723d7f7011bfb3f6aa225c170848a6c5c1 Mon Sep 17 00:00:00 2001
From: Anthony Underwood <email2ants@gmail.com>
Date: Wed, 21 Apr 2021 20:17:42 +0100
Subject: [PATCH] Create sanger.md

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+# nf-core/configs: Wellcome Sanger Institute Configuration
+
+To use, run the pipeline with `-profile sanger`. This will download and launch the [`sanger.config`](../conf/sanger.config) which has been
+pre-configured with a setup suitable for the Wellcome Sanger Institute LSF cluster.
+Using this profile, either a docker image containing all of the required software will be downloaded, and converted to a Singularity image or 
+a Singularity image downloaded directly before execution of the pipeline.
+
+## Running the workflow on the Wellcome Sanger Institute cluster
+
+The latest version of Nextflow is not installed by default on the cluster. You will need to install it into a directory you have write access to
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
+Nextflow shouldn't run directly on the submission node but on a compute node.
+To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh`
+
+```
+#!/bin/bash
+#BSUB -o /path/to/a/log/dir/%J.o
+#BSUB -e /path/to/a/log/dir//%J.e
+#BSUB -M 8000
+#BSUB -q long
+#BSUB -n 4
+
+export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
+export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
+export NXF_ANSI_LOG=false
+export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
+export NXF_VER=21.03.0-edge
+
+
+/path/to/your/install/nextflow run \
+/path/to/nf-core/pipeline/main.nf \
+-w /path/to/some/dir/work \
+-profile sanger \
+-c my_specific.config \
+-qs 1000 \
+-resume
+
+## clean up on exit 0 - delete this if you want to keep the work dir
+status=$?
+if [[ $status -eq 0 ]]; then
+  rm -r /path/to/some/dir/work
+fi
+```
+