Name: secotrec
Owner: Hammer Lab
Description: Setup Coclobas/Ketrew Clusters
Created: 2017-02-13 21:49:12.0
Updated: 2017-11-15 18:20:16.0
Pushed: 2017-11-13 16:06:46.0
Homepage: null
Size: 197
Language: OCaml
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secotrec
is a library, it provides a bunch of hacks to create more or less
generic deployments.
It comes with 3 preconfigured ?examples?. You should pick one.
secotrec-gke
:nginx
basic-auth HTTP
proxy.secotrec-local
: sets up Postgresql, Ketrew, and Coclobas (in local docker
mode) running locally or on a fresh GCloud box.seotrec-aws
: still experimental, sets up a similar deployment as
secotrec-gke
based on AWS-Btatch.The examples have the option of preparing the default biokepi-work directory
with
b37decoy_20160927.tgz
and
b37_20161007.tgz
.
For other administration purposes, we also provide secotrec-make-dockerfiles
,
as Dockerfile
generation tool.
This file provides detailed usage information, for high-level
tutorial-oriented documentation please check-out the
hammerlab/wobidisco
project. A good
starting point is the ?Running Local?
tutorial.
You can install secotrec either from Opam or from a Docker image.
If you have an opam
environment, for now we need a few packages pinned:
opam pin -n add ketrew https://github.com/hammerlab/ketrew.git
opam pin -n add biokepi https://github.com/hammerlab/biokepi.git
opam pin -n add secotrec https://github.com/hammerlab/secotrec.git
opam upgrade
opam install tls secotrec biokepi
Notes:
tls
to submit jobs to the deployed Ketrew server (prepare
and
test-biokepi-machine
sub-commands).biokepi
is only used by generated code (biokepi machine and its test).# Get the docker image
docker pull hammerlab/keredofi:secotrec-default
# Enter the container for GKE use case
docker run -e KETREW_CONFIGURATION -it hammerlab/keredofi:secotrec-default
If you've chosen to use secotrec-local:
# Enter the container for local use case
docker run \
-v /var/run/docker.sock:/var/run/docker.sock \
-e KETREW_CONFIGURATION \
-it hammerlab/keredofi:secotrec-default \
bash
If you do use secotrec-local
, please mind that we cannot access the Ketrew
server from the current container (which is in a different network). We can jump
to another container which is in the right network:
secotrec-local docker-compose exec coclo opam config exec bash
Once you are inside the container, you first need to configure your gcloud utilities for proper access to GCloud services:
# Login to your acount
gcloud auth login
# Set your GKE project
gcloud config set project YOUR_GKE_PROJECT
Generate a template configuration file:
trec-gke generate-configuration my-config.env
Edit the nicely documented my-config.env
file
until . my-config.env ; secotrec-gke print-configuration
is happy and you are
too.
Note: if you decide to use HTTP-Basic-Auth (htpasswd
option), you will
need to append a user-name and password to some of the commands below
(see the optional --username myuser --password mypassword
arguments).
Then just bring everything up (can take about 15 minutes):
-config.env
trec-gke up
Check:
trec-gke status
Output should say that all services are up:
Name Command State Ports
---------------------------------------------------------------------------------
otest_coclo_1 opam config exec -- /bin/b ... Up 0.0.0.0:8082->8082/tcp
otest_kserver_1 opam config exec -- dash - ... Up 0.0.0.0:8080->8080/tcp
otest_pg_1 /docker-entrypoint.sh postgres Up 0.0.0.0:5432->5432/tcp
otest_tlstun_1 opam config exec -- sh -c ... Up 0.0.0.0:443->8443/tcp
It should show some more interesting information (incl. Ketrew WebUI URL(s)), if there is no display like:
TREC: Getting Ketrew Hello:
ketrew/hello says: ''
0",
"Server_status",
{
...
/* A few lines of JSON */
it means that Ketrew is not (yet) ready to answer (depending on Opam-pins and configuration; the server may not be up right away).
The deployment is usable as is, but to use it with Biokepi more efficiently one can start the ?preparation? Ketrew workflow:
trec-gke prepare [--username myuser --password mypassword]
and go baby-sit the Ketrew workflow on the WebUI.
There is also a test of the Biokepi-Machine (for now, it can be run concurrently to the preparation workflow):
trec-gke test-biokepi-machine [--username myuser --password mypassword]
the workflow uses Coclobas/Kubernetes.
Generate a Ketrew client configuration:
trec-gke ketrew-configuration /tmp/kc.d [--username myuser --password mypassword]
(then you can use export KETREW_CONFIG=/tmp/kc.d/configuration.ml
).
Generate a Biokepi Machine.t
:
trec-gke biokepi-machine /tmp/bm.ml [--username myuser --password mypassword]
We can have a top
-like display:
trec-gke top
We can talk directly to the database used by Ketrew and Coclobas:
trec-gke psql
The subcommand docker-compose
(alias dc
) forwards its arguments to
docker-compose
on the node, with the configuration, e.g.:
trec-gke dc ps
trec-gke dc logs coclo
trec-gke dc exec kserver ps aux
trec-gke get-coclobas-logs somewhere.tar.gz
e:
trec-gke --help
Take down everything (including the Extra-NFS server and its storage) with the following command:
trec-gke down --confirm
Note that this action requires the additional --confirm
argument
to prevent destroying the secotrec setup accidentally. -y
, --yes
,
--really
, and --please
are other alternatives that can be
used to confirm the destroy procedure.
Configuration is all optional (the gcloud
version adds some constrains;
cf. the generated config-file), but it works the same way as Secotrec-GKE:
trec-local generate-configuration my-config.env
it my-config.env
ce my-config.env
trec-local print-configuration
trec-local up
trec-local status
Other commands work as well:
trec-local top # top-like display of the containers
trec-local prepare # submits the preparation workflow to Ketrew (get `b37decoy`)
trec-local ketrew-configuration /path/to/config/dir/ # generate a Ketrew config
trec-local biokepi-machine /path/to/biokepi-machine.ml # generate a Biokepi config/machine
trec-local test biokepi-machine
trec-local down
secotrec-make-dockerfiles
is designed to update the Docker-Hub images
at hammerlab/keredofi
.
The README.md
and the corresponding branches of GitHub
repository hammerlab/keredofi
are
also updated for convenience by this tools (but we do not use Docker-Hub
automated builds any more).
Display all the Dockerfiles on stdout:
secotrec-make-dockerfiles view
Write the Dockerfile
s in their respective branches and commit if something
changed:
secotrec-make-dockerfiles write --path=/path/to/keredofi
when done, the tool displays the Git graph of the Keredofi repo; if you're
happy, just go there and git push --all
.
Submit a Ketrew workflow that builds and runs some tests on all the
Dockerfiles
(for now this expects a secotrec-local
-like setup):
eval `secotrec-local env`
secotrec-make-dockerfiles test
See secotrec-make-dockerfiles test --help
for more options, you can for
instance push to the Docker-Hub:
secotrec-make-dockerfiles test \
--repo hammerlab/keredofi-test-2 --push agent-cooper,black-lodge
When in the environment WITH_AWS_NODE
is true
, and application
secotrec-aws-node
is built, see:
secotrec-aws-node --help
For now the this uses the AWS API to setup a ?ready-to-use? EC2 server.
The build requires master
versions of: aws
and aws-ec2
:
all () {
local tmpdir=$HOME/tmp/
rm -fr $tmpdir/ocaml-aws
cd $tmpdir
git clone https://github.com/inhabitedtype/ocaml-aws.git
cd ocaml-aws
opam pin add -y -n aws .
for lib in $(find libraries/ -type d -name opam) ; do
echo "Do $lib"
opam pin add -y -n aws-$(basename $(dirname $lib)) ./$(dirname $lib)/
done;
alls () {
local all="aws aws-ec2"
opam remove -y $all
for lib in $all ; do
ocamlfind remove $lib
done
opam install -y $all
Usage:
# Set your AWS credentials:
export AWS_KEY_ID=AKSJDIEJDEIJDEKJJKXJXIIEJDIE
export AWS_SECRET_KEY=dliejsddlj09823049823sdljsd/sdelidjssleidje
# Configure once:
secotrec-aws-node config --path /path/to/store/config-and-more/ \
--node-name awsuser-dev-0 \
--ports 22,443 \
--region us-east-1 \
--pub-key-file ~/.ssh/id_rsa.pub
# Then play as much as needed:
secotrec-aws-node show-configuration --path /path/to/store/config-and-more/
secotrec-aws-node up --path /path/to/store/config-and-more/ [--dry-run]
secotrec-aws-node down --path /path/to/store/config-and-more/ [--dry-run]
secotrec-aws-node ssh --path /path/to/store/config-and-more/
Everything should be idempotent (but some ?Waiting for? functions may timeout for now).
More to come?