📝 seqera hints from chats and notes

index.md

@@ -42,4 +42,14 @@ python/best_practices
 hpc_dtu/setup_user_env
 ```
 
+```{toctree}
+:maxdepth: 2
+:hidden:
+:caption: Seqera
+
+seqera/index
+seqera/debugging
+seqera/setup_infrastructure
+seqera/quantms
+```
 

seqera/debugging.md

@@ -0,0 +1,12 @@
+# Debugging jobs
+
+If a job fails on seqera an intermediate files are lost as the VM state is not saved back
+to the associated blob storage container. This makes debugging a bit more challenging,
+although all relevant inputs are still normally found in the respective working directory
+for a single job.
+
+## Debugging on local machine (or any VM or HPC)
+
+- download the relevant files
+- install the required software using preferrably the method used on Seqera (docker, conda, etc.)
+- run the command that failed and debug

seqera/index.md

@@ -0,0 +1,47 @@
+## Overview
+
+## Pipeline parameters in Seqera
+
+How can directories be set by a browse button? 
+
+[`nf-schema`](https://github.com/nextflow-io/nf-schema) sets this up saving it in a autogenerated `nextflow_schema.json` which 
+is part of the root directory of a pipeline repository.
+
+## Lauching pipelines
+
+Make sure to use a batch account with priority VMs to launch a pipeline and have cheaper
+ephermal (non-priority) VMs for the actual pipeline execution of single jobs.
+
+Each [pool only has one VM size and type](https://learn.microsoft.com/en-us/azure/batch/nodes-and-pools).
+For for complicated setups with different VM
+sizes and types, multiple pools need to be specified (e.g. using process labels using `withLabel`).
+However, as more than one job can run on a big node (which is a single VM) defining 
+non too extensive resources for a process is a good way to economically distribute jobs
+on few nodes. This is very similar to computerome2 if you are familiar with that HPC.
+
+Overview of what happens when you launch a pipeline on Seqera:
+
+- Seqera Platform authenticates to Azure Batch and Storage as a service principal 
+- It adds a task to Azure Batch which runs Nextflow 
+- Nextflow starts on a compute node with an attached managed identity, 
+  this is used by Nextflow to authenticate and start adding jobs and tasks to Azure Batch 
+- An Azure Storage Container bucket is used 
+  as an intermediate working directory for the pipeline
+  - ⚠️ unclear if a job fails how the local storage is handled of the node (VM). Intermediate
+    data might not be copied back to the storage container.
+- Each task on Azure Batch (including the Nextflow task) will pull a Docker container from a registry as well as remote storage which might be located  
+- The node communicates back to Seqera Platform with the current status of the pipeline including completion 
+- Seqera Platform will access the logs and results located on Azure Storage, using the service principal for authentication 
+
+## Using seqera from the command line - tower cli
+
+Check out if you the `tw` cli tool if you want to automate runs without using the 
+web interface at [github.com/seqeralabs/tower-cli](https://github.com/seqeralabs/tower-cli)
+
+
+## Online Resources
+
+- [Nextflow](https://www.nextflow.io/docs/latest/azure.html)
+- [Platform](https://docs.seqera.io/platform/24.2/compute-envs/azure-batch)
+- [Service Principal](https://docs.seqera.io/platform/24.2/compute-envs/azure-batch#entra-service-principal)
+- [Managed Identity](https://docs.seqera.io/platform/24.2/compute-envs/azure-batch#managed-identity)

seqera/quantms.md

@@ -0,0 +1,4 @@
+# QuantMS on Seqera
+
+- using [azure batch compute environments](https://docs.seqera.io/platform/24.2/troubleshooting_and_faqs/azure_troubleshooting#batch-compute-environments)
+-  

seqera/setup_infrastructure.md

@@ -0,0 +1,33 @@
+# Setup Azure batch compute environments
+
+Based on our discussion and the 
+[documentation](https://docs.seqera.io/platform/24.2/enterprise/advanced-topics/manual-azure-batch-setup)
+and [FAQ](https://docs.seqera.io/platform/24.2/troubleshooting_and_faqs/azure_troubleshooting#batch-compute-environments)
+
+
+## Setup Permissions
+
+Here are the key points with setting up Azure Infrastructure using 
+a Managed Identity and Batch Pool.
+
+### On Azure
+
+- Create a service principal
+- Create a managed identity
+- Assign roles to the service principal and managed identity
+- Increase quota for the Azure Batch Account
+- Create Azure Batch pools in the Batch account
+- Attach nodes to the virtual network in the right subnet
+- Whitelist internet access on the subnet.
+
+### On Seqera Platform within a workspace:
+
+- Admin permissions to add credentials, compute environment(s) and pipelines to a workspace 
+
+
+## On VMs as nodes in a pool
+Nodes in a pool are described based on the VM naming convention:
+
+![Name breakdown VM](https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/media/size-series-breakdown.png)
+
+See also [Azure Batch documentation](https://learn.microsoft.com/en-us/azure/batch/nodes-and-pools).