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View GitHub Profile
View gist:87fc34a13eed60179447729cdf7f9ac7
### Editing this command? Also update https://ci.commonwl.org/job/cwl-spec-pr/configure
venv() {
if ! test -d $1 ; then
virtualenv $1
fi
. $1/bin/activate
}
venv venv
(. venv/bin/activate && pip install -U setuptools wheel pip)
(. venv/bin/activate && pip install --ignore-installed --verbose -U cwltest cwltool)
View domain-mapping.csv
We can make this file beautiful and searchable if this error is corrected: Unclosed quoted field in line 6.
output name,Data Format,Data Concept,relationship
assembly,edam:format_1929 (FASTA),"http://edamontology.org/data_0925
""Sequence assembly""","derived from $(inputs.{forward,reverse,interleaved,single}_reads)"
assembly_log,iana:text/plain,"http://edamontology.org/data_3181
""Sequence assembly report""",describes $(outputs.assembly)
samtools_index,edam:format_2572 (BAM) + index,"alignment of reads to assembled contigs
http://edamontology.org/data_1383 is multiple sequence alignment, need a data concept for the result of http://edamontology.org/operation_0523 ""Mapping assembly""","derives from both $(inputs.{forward,reverse,interleaved,single}_reads) & $(outputs.assembly)"
coverage_tab,iana:text/tab-separated-values,"""contig by bam depth matrix"", and evidence report and quality metric",derives from $(outputs.samtools_index)
trimmed_sequences,gz-compressed edam:format_1929 (FASTA) ,"Contigs over a certain minimal length
Need an EDAM concept for the result of http://edamontology.org/operation_3192 ""Sequence t
View a.md
View license-in-svg.xml
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
View gist:d331abfa5900b92ad047bdac13885818
2019-04-18T12:36:44.978016564Z 2019-04-18 12:36:44 cwltool INFO: /usr/bin/arvados-cwl-runner 1.3.1, arvados-python-client 1.3.1, cwltool 1.0.20181116032456
2019-04-18T12:36:44.978518764Z 2019-04-18 12:36:44 cwltool INFO: Resolved '/var/lib/cwl/run/workflows/rp2-to-rp2path.cwl' to 'file:///var/lib/cwl/run/workflows/rp2-to-rp2path.cwl'
2019-04-18T12:36:46.332686764Z 2019-04-18 12:36:46 cwltool INFO: ../../lib/cwl/run/workflows/rp2-to-rp2path.cwl:40:3: Unknown hint http://commonwl.org/cwldep#Dependencies
2019-04-18T12:36:46.810698664Z 2019-04-18 12:36:46 cwltool ERROR: Workflow error, try again with --debug for more information:
2019-04-18T12:36:46.810698664Z ../../lib/cwl/run/tools/RetroPath2/RetroPath2.cwl:9:5: While trying to get Docker image
2019-04-18T12:36:46.810698664Z 'ibisba/retropath2:latest', failed to
2019-04-18T12:36:46.810698664Z execute 'docker': [Errno 2] No such file or
2019-04-18T12:36:
@stain
stain / .notmuch-config
Last active Mar 27, 2019
NotMuch hooks for selectively sorting to inbox, moving archived messages to other folder. offlineimap syncs to /home/USER/mail/company and /home/USER/mail/org1
View .notmuch-config
[database]
path=/home/USER/mail
[user]
name=MyName MySurname
primary_email=me@example.com
other_email=me@example.org
View manifest.jsonld
{
"@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"],
View manifest.jsonld
{
"@context": [
"https://w3id.org/bundle/context",
{
"schema": "http://schema.org/",
"name": "schema:name",
"schema:image": {
"@type": "@id"
},
"schema:isPartOf": {
View manifest.jsonld
{
"@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": {
View linkset.jsonld
{
"@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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