inutano

reference:
  class: File
  path: Homo_sapiens_assembly38.fasta
  format: http://edamontology.org/format_1929
sortsam_max_records_in_ram: 5000000
sortsam_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_MarkDuplicates_java_option: -XX:-UseContainerSupport -Xmx32g -Xms32g
gatk4_BaseRecalibrator_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_ApplyBQSR_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_HaplotypeCaller_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g

inutano

reference:  # type "File"
    class: File
    format: http://edamontology.org/format_1929
    location: http://data.dbcls.jp/~inutano/human-reseq/test/data/human-reseq-test-data/hs37d5.release-20190328/hs37d5.fa
    secondaryFiles:
      - class: File
        location: http://data.dbcls.jp/~inutano/human-reseq/test/data/human-reseq-test-data/hs37d5.release-20190328/hs37d5.dict
      - class: File
        location: http://data.dbcls.jp/~inutano/human-reseq/test/data/human-reseq-test-data/hs37d5.release-20190328/hs37d5.fa.amb
      - class: File

inutano

{
    "$graph": [
        {
            "class": "CommandLineTool",
            "id": "#bwa-mem-SE.cwl",
            "label": "bwa-mem-SE-0.7.12",
            "hints": [
                {
                    "class": "DockerRequirement",
                    "dockerPull": "biocontainers/bwa:v0.7.12_cv3"

inutano

{
  "stanzas": [
    "https://togostanza.github.io/metastanza/hash-table.js",
    "https://togostanza.github.io/metastanza/barchart.js"
  ],
  "templates": {
    "variant": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/variant.hbs",
    "gene": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/gene.hbs",
    "protein": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/protein.hbs",
    "interaction": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/interaction.hbs",

inutano

@base <http://schema.org/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix provo: <http://www.w3.org/ns/prov#> .

<http://identifiers.org/biosample/SAMN03765156>
    <mainEntity> [
        <additionalProperty> [
            <name> "cell line" ;
            <value> "HeLa-229" ;

inutano

ENV DEBIAN_VERSION=buster-20200327
ENV ODGI_COMMIT=5e18490156f08368dae0b25a69e0cf5efa5427ca
ENV SPODGI_COMMIT=84a1af531e5381216eeb5035e284167ed886da21

FROM debian:${DEBIAN_VERSION} as odgi_build
WORKDIR "/tmp"
RUN DEBIAN_FRONTEND=noninteractive \
    && apt-get update -y \
    && apt-get install -y --no-install-recommends \
      build-essential \

inutano

		Sat Feb 08 2020
01:57:36 { Loading plugin 1: Type `plain', file `geos' in `../hosting'
01:57:36   plain version 1.0.3230 from OpenLink Software
01:57:36   GEOS plugin based on Geometry Engine Open Source library from Open Source Geospatial Foundation
01:57:36   SUCCESS plugin 1: loaded from ../hosting/geos.so }
01:57:36 { Loading plugin 2: Type `plain', file `im' in `../hosting'
01:57:36   IM version 0.62 from OpenLink Software
01:57:36   Support functions for Image Magick 6.9.9
01:57:36   SUCCESS plugin 2: loaded from ../hosting/im.so }

inutano

require 'yaml'
require 'json'
require 'pp'

module CWL
  class Workflow
    def initialize(fpath)
      @workflow = YAML.load(open(fpath))
    end

inutano

$ ls ERR2092776_1.fastq
ERR2092776_1.fastq
$ docker run -it --rm -v $(pwd):/work -w /work quay.io/inutano/wtdbg2:v2.2 wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
--
-- total memory       65880284.0 kB
-- available          65173720.0 kB
-- 12 cores
-- Starting program: wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
-- pid                         1
-- date         Wed Jul 17 03:38:08 2019

inutano

// https://golangcode.com/download-a-file-with-progress/
package main

import (
	"fmt"
	"io"
	"net/http"
	"os"
	"strings"