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

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

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

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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

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#! /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

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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

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

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

#!/usr/bin/env nextflow

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

params.outdir = "results"

abhi18av

(use srfi-27)
(use srfi-42)

(define-macro (swap! a b)
  (let1 t (gensym)
    `(let1 ,t ,a
       (set! ,a ,b)
       (set! ,b ,t))))

(define (bubble-sort v)