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View gist:87fc34a13eed60179447729cdf7f9ac7
### Editing this command? Also update
venv() {
if ! test -d $1 ; then
virtualenv $1
. $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),"
""Sequence assembly""","derived from $(inputs.{forward,reverse,interleaved,single}_reads)"
""Sequence assembly report""",describes $(outputs.assembly)
samtools_index,edam:format_2572 (BAM) + index,"alignment of reads to assembled contigs is multiple sequence alignment, need a data concept for the result of ""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 ""Sequence t
View license-in-svg.xml
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
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
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
name=MyName MySurname
View manifest.jsonld
"@context": [
"name": ""
"@id": "",
"@type": ["DataCatalog", "ro:ResearchObject"],
View manifest.jsonld
"@context": [
"schema": "",
"name": "schema:name",
"schema:image": {
"@type": "@id"
"schema:isPartOf": {
View manifest.jsonld
"@context": "",
"@id": "",
"@type": ["DataCatalog", ""],
"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": "",
"anchor": "@id",
"href": "@id",
"dct": "",
"link": "",
"title": {
"@id": ""
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