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Tazro Inutano Ohta inutano

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View bsplus.example.ttl
@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" ;
View Dockerfile
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 \
View virtuoso.log
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 }
View cwl-stat.rb
require 'yaml'
require 'json'
require 'pp'
module CWL
class Workflow
def initialize(fpath)
@workflow = YAML.load(open(fpath))
end
@inutano
inutano / wtdbg2.console.txt
Created Jul 25, 2019
wtdbg2 genome assembly: output in console
View wtdbg2.console.txt
$ 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
View download.go
// https://golangcode.com/download-a-file-with-progress/
package main
import (
"fmt"
"io"
"net/http"
"os"
"strings"
View SAMD00000345.ttl
@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."
View SAMD00000345.jsonld
{"@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
View SAMEA1652233.jsonld
{
"@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",
{
View SAMEA1652233.jsonld
{
"@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",
{