denis-yuen

### Highlighted new features
- public [preview](https://docs.dockstore.org/en/stable/getting-started/getting-started-with-notebooks.html) for notebooks, get in touch if you wish to integrate with us for notebooks or have suggestions!
- public [preview](https://docs.dockstore.org/en/stable/advanced-topics/metrics.html) for metrics, as above get in touch if you're interested!
- New dashboard provides a cleaner and (we think!) more elegant look at your workflows and tools
  - Also monitor your favourite (starred) workflows for new versions and changes
  - Keep an eye on your favourite or your own organizations and collections
  - A better onboarding experience for new users to register workflows
- initial GA4GH [TRS 2.0.1](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/2.0.1) support
- Dockstore now parses and enables search for language versions (think searching for Nextflow DSL2, CWL v1.1, WDL 1.1, or Galaxy gxformat2 specifically)
- Dockstore also parses and makes a best effort to allow s

denis-yuen

Denis

Charles

Ben

denis-yuen

Keybase proof

I hereby claim:

• I am denis-yuen on github.
• I am mucous (https://keybase.io/mucous) on keybase.
• I have a public key ASCrEL7_Y2Y1UodVzhKNrufLGeIEyFfh4dOYBqnRERl3Cgo

To claim this, I am signing this object:

denis-yuen

git clone https://github.com/CancerCollaboratory/dockstore-tool-bamstats.git
cd dockstore-tool-bamstats/

docker build -t foo .
grep "dockerPull" Dockstore.cwl
docker build -t quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 .
docker run -ti quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 /bin/bash
java -jar /opt/BAMStats-1.25/BAMStats-1.25.jar --help

denis-yuen

Fixes include

• DAG and usability fixes
• hosted workflows delete
• search layout fix
• updated logos
• added terms of service

See a full list of our changes on GitHub

denis-yuen

{
  "run-id": "run_id",
  "tumor-bam":
  {
    "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143.bam",
    "class":"File"
  },
  "normal-bam":
  {
    "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143_BL.bam",

denis-yuen

{
  "input_normal": {
    "path": "normal.bam",
    "class": "File"
  },
  "input_tumour": {
    "path": "tumour.bam",
    "class": "File"
  },
  "index": {

denis-yuen

{
  "reads": [
  {
  "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal.bam",
  "class":"File"
  },
  {"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal2.bam",
  "class":"File"
  }
  ],

denis-yuen

mkdir dnastack_testing
cd dnastack_testing
git clone https://github.com/ga4gh/dockstore-ui.git
cd dockstore-ui/
vim app/scripts/services/webservice.js 
gvim README.md 
npm update
grunt serve
bower update
grunt serve

denis-yuen

#!/bin/bash
set -x

CONFIG_FILE=/mnt/datastore/workflow_data/workflow.ini

# source in the configuration file:
[[ ! -f ${CONFIG_FILE} ]] && "There is no valid workflow.ini set!" && exit 0

source ${CONFIG_FILE}