Merge pull request #277 from marcmtk/computerome

Computerome

.github/workflows/main.yml

@@ -30,6 +30,7 @@ jobs:
             - 'ccga_med'
             - 'cfc'
             - 'cfc_dev'
+            - 'computerome'
             - 'crick'
             - 'denbi_qbic'
             - 'ebc'

README.md

@@ -102,6 +102,7 @@ Currently documentation is available for the following systems:
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
 * [CFC](docs/cfc.md)
+* [Computerome](docs/computerome.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [DENBI_QBIC](docs/denbi_qbic.md)

conf/computerome.config

@@ -0,0 +1,29 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Computerome 2.0 cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
+  config_profile_url = 'https://www.computerome.dk/'
+  project = null
+  cache_dir = "/home/projects/$params.project/scratch"
+  schema_ignore_params = "project,cache_dir"
+  
+  //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
+  max_memory = 1500.GB 
+  max_cpus = 40
+  
+  //There is no max walltime on the cluster, but a week seems sensible if not directly specified
+  max_time = 168.h 
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = params.cache_dir
+}
+
+process {
+  beforeScript = "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir"
+  executor = 'pbs'
+  queueSize = 2000
+  clusterOptions = "-A $params.project -W group_list=$params.project"
+} 

docs/computerome.md

@@ -0,0 +1,38 @@
+# nf-core/configs: Computerome 2.0 Configuration
+
+To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
+
+## Using the Computerome config profile
+
+Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
+
+To use, run the pipeline with `-profile computerome` (one hyphen).
+This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome servers.
+It will enable `Nextflow` to manage the pipeline jobs via the `Torque` job scheduler.
+Using this profile, `Singularity` image(s) containing required software(s) will be downloaded before execution of the pipeline.
+
+Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. The computerome configuration uses your project's scratch folder as the cachedir if not specified.
+
+In addition to this config profile, you will also need to specify a Computerome project id.
+You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
+For example:
+
+```bash
+# Launch a nf-core pipeline with the computerome profile for the project id ab00002
+$ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]
+```
+
+> NB: If you're not sure what your Computerome project ID is, try running `groups`.
+
+Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
+Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
+
+## About Computerome 2.0
+
+The Danish National Supercomputer for Life Sciences (a.k.a. Computerome) is installed at the DTU National Lifescience Center at Technical University of Denmark.
+
+The computer hardware is funded with grants from Technical University of Denmark (DTU), University of Copenhagen (KU) and Danish e-infrastructure Cooperation (DeiC) - also, it is the official Danish ELIXIR Node.
+
+Computerome 1.0 was opened in November 2014 at #121 on TOP500 Supercomputing Sites.
+
+The current setup, Computerome 2.0, was opened in 2019. It's compute resources consists of 31760 CPU cores with 210 TeraBytes of memory, connected to 17 PetaBytes of High-performance storage,

nfcore_custom.config

@@ -23,6 +23,7 @@ profiles {
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
+  computerome  { includeConfig "${params.custom_config_base}/conf/computerome.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }