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Add docs on producing binaries with GA4GH support #20

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Aug 11, 2020
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Add docs on producing binaries with GA4GH support #20

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Add docs on producing binaries with GA4GH support
tskir Jul 28, 2020
2369129
Reflect that the name of Nextflow pod is subject to change
tskir Aug 11, 2020
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8 changes: 5 additions & 3 deletions nextflow_TES/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Instructions below have been tested for CSC Rahti cloud running on RedHat OpenSh
# Cloud parameters
export CLOUD_BASE_URL=c03.k8s-popup.csc.fi:8443
export CLOUD_NAMESPACE=tesk-cineca
export NEXTFLOW_POD=nextflow-dockerhub-7-9bdlm
export NEXTFLOW_POD=nextflow-dockerhub-10-gcdt8
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This pod name will keep changing whenever pod is rebuild by user or is involuntary build up by OpenShift cluster due to pod rescue, load balancing etc..Shall we mention it in readme so that reader doesn't get confused that it is related to hardcoded Nextflow container name/tags

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Good point. I reflected it here: 2369129


# OpenShift command line tools release
export OC_RELEASE_URL=https://github.com/openshift/origin/releases/download/v3.11.0/openshift-origin-client-tools-v3.11.0-0cbc58b-linux-64bit.tar.gz
Expand All @@ -20,7 +20,7 @@ Instructions below have been tested for CSC Rahti cloud running on RedHat OpenSh
| tar --extract --gzip --wildcards --strip-components 1 --file=/dev/stdin '*/oc'

1. In your browser, go to https://${CLOUD_BASE_URL}/console/command-line. Copy and execute the `./oc login ...` command.
1. Switch to the necessary namespace: `./oc project ${CLOUD_NAMESPACE}`
1. Switch to the necessary namespace: `./oc project ${CLOUD_NAMESPACE}`. To list all pods, use the command: `./oc get pods`
1. RSH to the required pod: `./oc rsh ${NEXTFLOW_POD}`

## Run the workflow
Expand Down Expand Up @@ -56,10 +56,12 @@ Build from source (make sure to substitute the correct fork and branch names):
git clone https://github.com/tskir/nextflow
cd nextflow
git checkout master
make -j `nproc` pack
make packGA4GH
cd ..
```

Note that the default `make pack` will produce a binary which does **not** include GA4GH support, so you have to run `make packGA4GH` instead. This command is introduced in a PR https://github.com/nextflow-io/nextflow/pull/1666, and is yet to be merged.

There are two ways to run this installation instead of system-wide Nextflow:
* You can run `bash nextflow/launch.sh [flags]`, but it has do be done on the same machine where you compiled it, otherwise the different baked-in paths will not match.
* You can transfer the self-contained binary generated in the `build/releases/` directory to the Kubernetes pod and run it there.
Expand Down