Tazro Inutano Ohta inutano
inutano
/ wf_params.yml
Created
May 26, 2022 06:58
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| 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
/ fastqSE2bam.zenodo.yml
Last active
April 22, 2022 07:03
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| 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
/ fastqSE2bam.packed.cwl
Created
April 22, 2022 06:32
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| { | |
| "$graph": [ | |
| { | |
| "class": "CommandLineTool", | |
| "id": "#bwa-mem-SE.cwl", | |
| "label": "bwa-mem-SE-0.7.12", | |
| "hints": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "biocontainers/bwa:v0.7.12_cv3" |
inutano
/ templates.json
Created
June 11, 2021 05:50
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| { | |
| "stanzas": [ | |
| "https://togostanza.github.io/metastanza/hash-table.js", | |
| "https://togostanza.github.io/metastanza/barchart.js" | |
| ], | |
| "templates": { | |
| "variant": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/variant.hbs", | |
| "gene": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/gene.hbs", | |
| "protein": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/protein.hbs", | |
| "interaction": "https://raw.githubusercontent.com/dbcls/togosite/fix-hbs-render/config/togosite-human/templates/interaction.hbs", |
inutano
/ bsplus.example.ttl
Created
June 16, 2020 23:27
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| @base <http://schema.org/> . | |
| @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | |
| @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | |
| @prefix provo: <http://www.w3.org/ns/prov#> . | |
| <http://identifiers.org/biosample/SAMN03765156> | |
| <mainEntity> [ | |
| <additionalProperty> [ | |
| <name> "cell line" ; | |
| <value> "HeLa-229" ; |
inutano
/ Dockerfile
Created
April 9, 2020 07:32
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| ENV DEBIAN_VERSION=buster-20200327 | |
| ENV ODGI_COMMIT=5e18490156f08368dae0b25a69e0cf5efa5427ca | |
| ENV SPODGI_COMMIT=84a1af531e5381216eeb5035e284167ed886da21 | |
| FROM debian:${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
/ virtuoso.log
Created
April 7, 2020 07:37
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| 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
/ cwl-stat.rb
Last active
September 4, 2019 01:52
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| require 'yaml' | |
| require 'json' | |
| require 'pp' | |
| module CWL | |
| class Workflow | |
| def initialize(fpath) | |
| @workflow = YAML.load(open(fpath)) | |
| end |
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| $ 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
/ download.go
Created
July 9, 2019 00:35
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| // https://golangcode.com/download-a-file-with-progress/ | |
| package main | |
| import ( | |
| "fmt" | |
| "io" | |
| "net/http" | |
| "os" | |
| "strings" |
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