- Permalink: https://gist.github.com/stain/4cd4cb1763a4ac57f1de270aa6f1a996 (this review)
- Authors: Gabriele Scalia, Matteo Pelucchi, Alessandro Stagni, Alberto Cuoci, Tiziano Faravelli, Barbara Pernici
- Title: Scholarly data analysis to aid scientific model development
- Submitted to: Data Science (Research Paper)
- Special issue: Selection of extended papers from SAVE-SD 2017 and Save-SD 2018
- Submitted on: 2018-12-16
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[database] | |
path=/home/USER/mail | |
[user] | |
name=MyName MySurname | |
primary_email=me@example.com | |
other_email=me@example.org | |
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{ | |
"@context": [ | |
"https://schema.org/", | |
"https://w3id.org/bundle/context", | |
{ | |
"name": "http://schema.org/name" | |
} | |
], | |
"@id": "https://data.wholetale.org/api/v1/tale/5c875b6feff2c60001d2810f", | |
"@type": ["DataCatalog", "ro:ResearchObject"], |
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{ | |
"@context": [ | |
"https://w3id.org/bundle/context", | |
{ | |
"schema": "http://schema.org/", | |
"name": "schema:name", | |
"schema:image": { | |
"@type": "@id" | |
}, | |
"schema:isPartOf": { |
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{ | |
"@context": "https://schema.org/", | |
"@id": "https://data.wholetale.org/api/v1/tale/5c875b6feff2c60001d2810f", | |
"@type": ["DataCatalog", "http://purl.org/wf4ever/ro#ResearchObject"], | |
"dataset": [ | |
{ | |
"@id": "doi:10.5065/D6862DM8", | |
"identifier": "doi:10.5065/D6862DM8", | |
"name": "Humans and Hydrology at High Latitudes: Water Use Information", | |
"publisher": { |
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{ | |
"@context": [ | |
{ | |
"@vocab": "https://www.iana.org/assignments/link-relations/", | |
"anchor": "@id", | |
"href": "@id", | |
"dct": "http://purl.org/dc/terms/", | |
"link": "https://www.iana.org/assignments/link-relations#", | |
"title": { | |
"@id": "http://purl.org/dc/terms/title" |
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############################################################################### | |
# Ubuntu 16.04, CUDA 9.0, OpenMPI, and GROMACS. | |
# | |
# Requirements: | |
# * gromacs directory in build directory with source for GROMACS. | |
# | |
# Build with: | |
# sudo nvidia-docker build -t gromacs . \ | |
# --build-arg GROMACS_VERSION=gromacs_version \ | |
# --build-arg JOBS=16 |
- Permalink: https://gist.github.com/stain/30e49363238d5a35e26f9fb1a31ebf8e
- Date: 2018-12-18
- Title: Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
- Authors: Tazro Ohta, Tomoya Tanjo, Osamu Ogasawara
- Call: GigaScience Technical Note
- Submitted preprint:
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stain@biggie:~/dropbox/work/cwlprov/newest-swift/rnaseqwf_0.5.0_mac$ cwlprov run | |
2018-09-24 20:30:12.438801 Flow 6458a48e-fabc-448f-9f17-0a1c6ff9a674 [ Run of workflow/packed.cwl#main | |
2018-09-24 20:30:26.239962 Step 201a6074-031a-4793-8719-863834d78cd9 Run of workflow/packed.cwl#main/run_star (0:02:31.016639) | |
2018-09-24 20:32:57.294541 Step ff48e829-82b5-48fb-a0fb-c7a8cd038bf8 Run of workflow/packed.cwl#main/sort_bam (0:00:02.014422) | |
2018-09-24 20:32:59.318559 Step 0128708d-e2a7-41f6-afe5-1833e4da59bc Run of workflow/packed.cwl#main/index_bam (0:00:01.680102) | |
2018-09-24 20:33:02.074684 Step 44f03c62-2d1b-478b-8f61-bfa1a3824d69 Run of workflow/packed.cwl#main/run_rsem (0:00:14.659971) | |
2018-09-24 20:33:16.748069 Step b5ff0180-5466-4cf5-b9c3-b71bc0542eaa Run of workflow/packed.cwl#main/run_markduplicates (0:00:03.764102) | |
2018-09-24 20:33:20.519469 Step e9a3b636-20d2-43f5-96b1-0cea68b43044 Run of workflow/packed.cwl#main/run_index_markduplicates_bam (0:00:01.502664) | |
2018-09-24 20:33:22.068415 S |
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(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0/ | |
Detected CWLProv research Object: test/revsort-cwlprov-0.4.0/ | |
(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0 validate | |
Valid: test/revsort-cwlprov-0.4.0 | |
(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0 info | |
Research Object of CWL workflow run | |
ID: arcp://uuid,d47d3d43-4830-44f0-aa32-4cda74849c63/ | |
Profile: https://w3id.org/cwl/prov/0.4.0 |