Merge pull request #429 from chriswyatt1/ucl_myriad

Ucl_myriad

.github/workflows/main.yml

@@ -89,6 +89,7 @@ jobs:
           - "sbc_sharc"
           - "seg_globe"
           - "tigem"
+          - "ucl_myriad"
           - "uct_hpc"
           - "unibe_ibu"
           - "uppmax"

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)

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
+}

docs/ucl_myriad.md

@@ -0,0 +1,51 @@
+# 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 <YOUR_ID> 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/<YOUR_ID>/.bashrc):
+
+```bash
+# Set all the Singularity cache dirs to Scratch
+export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
+export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
+export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
+export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
+
+# Bind your Scratch directory so it is accessible from inside the container
+export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
+```
+
+### 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:
+
+```bash
+export PATH=$PATH:/home/<YOUR_ID>/bin
+```

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" }