diff --git a/README.md b/README.md index db486c5..7374a1c 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,7 @@ A preprint is available here https://www.biorxiv.org/content/10.1101/2020.02.08. 3. [Installation](#installation) : - [base installation](#base-installation) - [conda usage](#for-conda-usage) + - [gcloud usage](#for-gcloud-usage) - [containers usage](#for-containers-usage) - [software installe locally](#for-usage-of-software-installed-locally) 4. [Test the pipeline](#test-the-pipeline) @@ -111,6 +112,37 @@ conda deactivate #you need to change the line 3 and 25 to the path of your env (/path/to/install/metawrap-env) ``` +### For gcloud usage +If you use the google lifescience ressources you first need to setup a few parameters. + +In the nextflow.config you need to change the parameters of gcloud to correspond to your project (line 67 to 78). +```sh + gcloud { + //workDir = "/tmp/nextflow-docker_pipelines-$USER" + process.executor = 'google-lifesciences' + process.memory = params.memory + bucketDir = 'gs://bucket/work-dir' // change this to your bucket where you want the workfile to be stored + google { project = 'project-name-111111'; zone = 'europe-north1-a' } // insert your project ID as well as the zone(s) you want to use + // you can also use {region = 'europe-north1'} instead of zone + google.lifeSciences.copyImage = 'google/cloud-sdk:latest' + google.lifeSciences.preemptible = true + google.lifeSciences.bootDiskSize = "10GB" + google.lifeSciences.debug = true + //includeConfig 'configs/preemptible.config' + } +``` +You will also have to change the bucket to store the different database in: + /modules/checkmgetdatabases.nf ; /modules/eggnog_get_databases.nf ; /modules/sourmashgetdatabase.nf + +To do so just edit the line using your bucket. keep the structure for more clarity (e.g. keep the "/databases-nextflow/sourmash" part). + +Example: +```sh +if (workflow.profile.contains('gcloud')) {publishDir 'gs://gcloud_storage/databases-nextflow/sourmash', mode: 'copy', pattern: "genbank-k31.lca.json.gz" } +#becomes +if (workflow.profile.contains('gcloud')) {publishDir 'gs://MY_STORAGE/databases-nextflow/sourmash', mode: 'copy', pattern: "genbank-k31.lca.json.gz" } +``` + ### For containers usage If you use containers either docker or singularity, you don't need extra installations