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"

inutano

@base <http://schema.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<http://identifiers.org/biosample/SAMD00000345> a <DataRecord>,
    <BioChemEntity>,
    <http://purl.obolibrary.org/obo/OBI_0000747>;
  <additionalProperty> [
    a <PropertyValue>;
    <name> "broad-scale environmental context";
    <value> "n.a."

inutano

{"@context":{"@base":"http://schema.org/","@vocab":"http://schema.org/","url":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"dateCreated":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"dateModified":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"Sample":{"@id":"http://purl.obolibrary.org/obo/OBI_0000747"},"name":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"value":{"@type":"http://www.w3.org/2001/XMLSchema#string"}},"@type":["DataRecord","BioChemEntity","Sample"],"identifier":"SAMD00000345","dateCreated":"2014-07-30T00:00:00Z","dateModified":"2019-02-18T00:01:52.977Z","isPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"datasetPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"@id":"http://identifiers.org/biosample/SAMD00000345","name":"SAMD00000345","description":"type strain of Lactobacillus oryzae","url":"https://www.ebi.ac.uk/biosamples/sample/SAMD00000345","additionalProperty":[{"@type":"PropertyValue","name":"INSDC cente

inutano

{
  "@context": "http://schema.org",
  "@type": "DataRecord",
  "identifier": "biosamples:SAMEA1652233",
  "dateCreated": "2012-12-31T00:00:00Z",
  "dateModified": "2018-01-20T06:06:51.993Z",
  "mainEntity": {
    "@context": [
      "http://schema.org",
      {

inutano

{
  "@context": "http://schema.org",
  "@type": "DataRecord",
  "identifier": "biosamples:SAMEA1652233",
  "dateCreated": "2012-12-31T00:00:00Z",
  "dateModified": "2018-01-20T06:06:51.993Z",
  "mainEntity": {
    "@context": [
      "http://schema.org",
      {