From b82a1a6339de5ee6d33d80a95ef579de74c3bd07 Mon Sep 17 00:00:00 2001 From: Gervaise Henry <gervaise.henry@utsouthwestern.edu> Date: Fri, 19 Feb 2021 17:58:10 -0600 Subject: [PATCH] Update README.md --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7b715d4..04f49d7 100644 --- a/README.md +++ b/README.md @@ -75,7 +75,8 @@ nextflow run workflow/rna-seq.nf --repRID Q-Y5JA --source production --deriva ./ Cloud Compatibility: -------------------- -This pipeline is also capable of being run on AWS. To do so: +This pipeline is also capable of being run on AWS and DNAnexus. To do so: +### [AWS](https://aws.amazon.com/) * Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml) * Edit one of the aws configs in workflow/config/ * Replace workDir with the S3 bucket generated @@ -83,6 +84,14 @@ This pipeline is also capable of being run on AWS. To do so: * Change queue to the aws batch queue generated * The user must have awscli configured with an appropriate authentication (with `aws configure` and access keys) in the environment which nextflow will be run * Add `-profile` with the name aws config which was customized +### DNAnexus (utilizes the [DNAnexus extension package for Nextflow (XPACK-DNANEXUS)](https://github.com/seqeralabs/xpack-dnanexus)) +* Follow the istructions from [XPACK-DNANEXUS](https://github.com/seqeralabs/xpack-dnanexus) about installing and authenticating (a valid license must be available for the extension package from Seqera Labs, as well as a subsription with DNAnexus) +* Follow the instructions from [XPACK-DNANEXUS](https://github.com/seqeralabs/xpack-dnanexus) about launching runs. A template *json* file has been included ([dnanexusExample.json](docs/dnanexusExample.json)) + * `[version]` should be replaced with the pipeline version required (eg: `v2.0.0`) + * `[credential.json]` should be replaced with the location of the credential file outpted by authentification with Deriva + * `[cookies.txt]` should be replaced with the location of the cookies file outpted by authentification with Deriva for BDBag + * `[repRID]` should be replaced with the replicate RID to be analized (eg: `Q-Y5F6`) + * `[outDir]` should be replaced with the location to save local outputs of the pipeline To generate you own references or new references: ------------------------------------------ -- GitLab