abhi18av

#!/usr/bin/env nextflow

/*
################
NEXTFLOW Global Config
################
*/

params.outdir = "results"

abhi18av

About

Example on how to run locally an AWS Lambda via API Gateway using localstack.

Based on...

1. https://stackoverflow.com/questions/44547574/create-api-gateway-in-localstack/48682628
2. https://ig.nore.me/2016/03/setting-up-lambda-and-a-gateway-through-the-cli/

Usage

abhi18av

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

abhi18av

Keybase proof

I hereby claim:

• I am abhi18av on github.
• I am abhi18av (https://keybase.io/abhi18av) on keybase.
• I have a public key ASDMWQdFu718vj6Kq7l8j79EkpSrqWXsOgxMZmg7b2FHEgo

To claim this, I am signing this object:

abhi18av

#! /usr/bin/env nextflow
import groovy.json.JsonSlurper
import groovy.text.SimpleTemplateEngine
import groovy.util.FileNameByRegexFinder
import java.nio.file.Path
import java.nio.file.Paths
import nextflow.util.SysHelper
PROGRAM_NAME = workflow.manifest.name
VERSION = workflow.manifest.version

abhi18av

curl \
    --retry 5 --continue-at - --max-time 1200 \
    -L ftp.sra.ebi.ac.uk/vol1/fastq/SRR870/008/SRR8703878/SRR8703878_1.fastq.gz \
    -o SRX5499459_SRR8703878_1.fastq.gz

abhi18av

So, it has been an interesting journey, but time to remove git-lfs. Here follows a summary of the approach I used to safely remove git-lfs,

• commit & push everything
• create a branch, something like fix/remove-lfs
• remove hooks git lfs uninstall
• remove lfs stuff from .gitattributes (open file, delete content - don't delete the file!)
• list all lfs files, git lfs ls-files
• run git rm --cached for each file
  • if your list is big, copy the contents into a file.txt
• make sure you remove the number and asterik on each line, you only want the paths to the files

abhi18av

from azure.identity import DefaultAzureCredential
from azure.mgmt.batch import BatchManagementClient
import os
from dotenv import load_dotenv
import sys

load_dotenv()

AZURE_SUBSCRIPTION_ID = os.getenv('AZURE_SUBSCRIPTION_ID')
AZURE_BATCH_RESOURCE_GROUP_NAME = os.getenv('AZURE_BATCH_RESOURCE_GROUP_NAME')

abhi18av

// Dont know why but it requires java 17 fx

// sdk install 17.0.8.fx-zulu
// sdk use java 17.0.8.fx-zulu

@Grapes([
        @Grab(group='org.scalamolecule', module='datomic-client-api-java-scala_2.13', version='1.0.3'),
        @Grab(group='com.datomic', module='local', version='1.0.267'),
        @Grab(group='com.cognitect', module='http-client', version='1.0.126'),
])

abhi18av

~/dev/scala/cljrepl $ cat build.sbt
scalaVersion := "2.11.8"

libraryDependencies ++= Seq(
  "org.clojure" % "clojure" % "1.8.0"
)

~/dev/scala/cljrepl $ cat src/main/scala/foo.scala
import clojure.java.api.Clojure
import clojure.java.api.Clojure.{`var` => cvar}