From 9b971c2b7655e661251f5c981c3be14ba1a69177 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Tue, 18 Oct 2022 14:03:07 +0000 Subject: [PATCH] Ucl_myriad --- .github/workflows/main.yml | 1 + README.md | 1 + conf/ucl_myriad.config | 34 +++++++++++++++++++++++++ docs/ucl_myriad.md | 52 ++++++++++++++++++++++++++++++++++++++ nfcore_custom.config | 1 + 5 files changed, 89 insertions(+) create mode 100644 conf/ucl_myriad.config create mode 100644 docs/ucl_myriad.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 55488be..3936468 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -89,6 +89,7 @@ jobs: - "sbc_sharc" - "seg_globe" - "tigem" + - "ucl_myriad" - "uct_hpc" - "unibe_ibu" - "uppmax" diff --git a/README.md b/README.md index 50c34aa..fe38eb9 100644 --- a/README.md +++ b/README.md @@ -143,6 +143,7 @@ Currently documentation is available for the following systems: - [SBC_SHARC](docs/sbc_sharc.md) - [SEG_GLOBE](docs/seg_globe.md) - [TIGEM](docs/tigem.md) +- [UCL_MYRIAD](docs/ucl_myriad.md) - [UCT_HPC](docs/uct_hpc.md) - [UNIBE_IBU](docs/unibe_ibu.md) - [UPPMAX](docs/uppmax.md) diff --git a/conf/ucl_myriad.config b/conf/ucl_myriad.config new file mode 100644 index 0000000..3f9425c --- /dev/null +++ b/conf/ucl_myriad.config @@ -0,0 +1,34 @@ +params { + + config_profile_description = 'University College London Myriad cluster' + config_profile_contact = 'Chris Wyatt (ucbtcdr@ucl.ac.uk)' + config_profile_url = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/' + +} + +process { + executor='sge' + penv = 'smp' +} + +params { + // Defaults only, expecting to be overwritten + max_memory = 128.GB + max_cpus = 36 + max_time = 72.h + // igenomes_base = 's3://ngi-igenomes/igenomes/' +} + +// optional executor settings + +executor { + + queueSize = 10 + submitRateLimit = '1 sec' + +} + +singularity { + enabled = true + autoMounts = true +} \ No newline at end of file diff --git a/docs/ucl_myriad.md b/docs/ucl_myriad.md new file mode 100644 index 0000000..4d32658 --- /dev/null +++ b/docs/ucl_myriad.md @@ -0,0 +1,52 @@ +# nf-core/configs: Myriad Configuration + +All nf-core pipelines have been successfully configured for use on UCL's myriad cluster [University College London](https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/). + +To use, run the pipeline with `-profile ucl_myriad`. This will download and launch the [`ucl_myriad.config`](../conf/ucl_myriad.config) which has been pre-configured with a setup suitable for the myriad cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +## Using Nextflow on Myriad + +Before running the pipeline you will need to install and configure Nextflow and Singularity. + +### Singularity + +This can be done with the following commands: + +```bash +## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also +module add java/openjdk-11/11.0.1 +module add singularity-env/1.0.0 + +``` + +Then set the correct configuration of the cache directories, where is replaced with you credentials which you can find by entering `whoami` into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home//.bashrc): + +``` +# Set all the Singularity cache dirs to Scratch +export SINGULARITY_CACHEDIR=/home//Scratch/.singularity/ +export SINGULARITY_TMPDIR=/home//Scratch/.singularity/tmp +export SINGULARITY_LOCALCACHEDIR=/home//Scratch/.singularity/localcache +export SINGULARITY_PULLFOLDER=/home//Scratch/.singularity/pull + +# Bind your Scratch directory so it is accessible from inside the container +export SINGULARITY_BINDPATH=/scratch/scratch/ +``` + +### Nextflow + +Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`). + +```bash +## Download Nextflow-all +curl -s https://get.nextflow.io | bash +NXF_VER=22.10.0 +nextflow -self-update +chmod a+x nextflow +mv nextflow ~/bin/nextflow +``` + +Then make sure that your bin PATH is executable, by placing the following line in your .bashrc: + +``` +export PATH=$PATH:/home//bin +``` \ No newline at end of file diff --git a/nfcore_custom.config b/nfcore_custom.config index 83390c4..51c1121 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -71,6 +71,7 @@ profiles { sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} tigem { includeConfig "${params.custom_config_base}/conf/tigem.config"} + ucl_myriad { includeConfig "${params.custom_config_base}/conf/ucl_myriad.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }