dockstore-support

A collection of different projects supporting the dockstore initiative

https://github.com/dockstore/dockstore-support

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

A collection of different projects supporting the dockstore initiative

Basic Info

Host: GitHub
Owner: dockstore
License: apache-2.0
Language: Java
Default Branch: develop
Homepage: https://dockstore.org
Size: 901 KB

Statistics

Stars: 1
Watchers: 19
Forks: 1
Open Issues: 1
Releases: 9

Created about 9 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

dockstore-support

This repo is a sandbox for support code for running, testing workflows on Dockstore, and indexing GA4GH tool registries. Send issues to the main dockstore repo.

Prerequisites

Your environment needs to have the following items:

Maven
Docker

Before you can run the script, you must generate the jar files. cd toolbackup && mvn clean install After you have installed Maven and Docker, you may wish to run the tests; in which case, you need S3Proxy. docker pull andrewgaul/s3proxy docker run -d --publish 8080:80 --env S3PROXY_AUTHORIZATION=none andrewgaul/s3proxy

Communicating with OpenStack

Endpoint Configuration

To use the script, you must provide an endpoint in ~/.toolbackup/config.ini token = XXX server-url = https://dockstore.org:443/api endpoint = XXX By default the token is empty. The default value for the server-url is shown above. These two values are for retrieving dockstore tools.Only the endpoint is mandatory. You can set up your config like so: endpoint = XXX

AWS Credentials

If you do not have ~/.aws/credentials, during testing, the script will generate this file with only the default profile. The default profile is necessary for this script's tests. If you have the credentials file but it is missing the default profile, you must add it in. [default] aws_access_key_id=MOCK_ACCESS_KEY aws_secret_access_key=MOCK_SECRET_KEY You must supply the file with a dockstore profile and the proper keys. ``` [default] awsaccesskeyid=MOCKACCESSKEY awssecretaccesskey=MOCKSECRETKEY

[dockstore] awsaccesskeyid=MOCKACCESSKEY awssecretaccesskey=MOCKSECRETKEY ```

Client

This is the script to backup all Dockstore workflows locally. java -jar target/client.jar --bucket-name clientbucket --key-prefix client --local-dir /home/ubuntu/clientEx --test-mode-activate true We are running with test mode activated which means we will not download all dockstore workflows. The dockstore images targeted will be stored on locally in the directory clientbucket and in the key-prefix client within the directory. The bucket and key-prefix need not have been created. The directory, /home/ubuntu/clientEx will act as temporary storage and it need not to have already been created.

How it Works

Client will pull all the GA4GH tools from the server-url and save them locally. This can be used to run prototypes of utilities on all Dockstore content

Downloader

This is the script to download images from OpenStack to the user's local file system. java -jar target/downloader.jar --bucket-name clientbucket --key-prefix client --destination-dir /home/ubuntu/downloaderEx We are downloading everything in the key-prefix client within the bucket clientbucket into a directory that need not have already been created, /home/ubuntu/downloaderEx.

Tests

The tests do not require a configuration file, but if you wish to set up the values yourself, you can add to the aforementioned ~/.toolbackup/config.ini The default values are shown here. ``` bucket = testbucket prefix = testprefix img = docker/whalesay baseDir = /home/ubuntu/dockstore-saver dir = /home/ubuntu/dockstore-saver/dir checkSizeDir = /home/ubuntu/dockstore-saver/checkSize

[nonexistent] bucket = dockstore-saver-gibberish dir = dockstore-saver-gibberish img = dockstore-saver-gibberish ``` - bucket: Amazon bucket you wish to use for testing the client and downloader - prefix: Consider it a "subdirectory" of the bucket - img: A valid image that can be pulled by any environment which has Docker - baseDir: A local directory which will not be deleted - dir: A local directory which will be deleted, if not specified it will be ~/...baseDir.../dir - checkSizeDir: A local directory to test that the calculation of files' sizes is correct - nonexistent.bucket: A non-existent bucket - nonexistent.dir: A non-existent local directory - nonexistent.img: A non-existent Docker image

The tests will clean up everything but the baseDir. It would be best if you specify directories which do not currently exist, even for the baseDir.

Owner

Name: Dockstore
Login: dockstore
Kind: organization
Location: Toronto, Ontario

Website: https://dockstore.org/
Twitter: DockstoreOrg
Repositories: 47
Profile: https://github.com/dockstore

Support organization for dockstore file provisioning plugins and other useful code

Citation (citation.cff)

abstract: "Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute's GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content."
authors: 
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Yuen
    given-names: Denis
    orcid: "https://orcid.org/0000-0002-6130-1021"
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Cabansay
    given-names: Louise
    orcid: "https://orcid.org/0000-0002-1475-5979"
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Duncan
    given-names: Andrew
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Luu
    given-names: Gary
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Hogue
    given-names: Gregory
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Overbeck
    given-names: Charles
  -
    family-names: Perez
    given-names: Natalie
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Shands
    given-names: Walt
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Steinberg
    given-names: David
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Reid
    given-names: Chaz
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Olunwa
    given-names: Nneka
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Hansen
    given-names: Richard
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Sheets
    given-names: Elizabeth
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: "O'Farrell"
    given-names: Ash
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Cullion
    given-names: Kim
  -
    affiliation: "Data Sciences Platform, Broad Institute"
    family-names: "O'Connor"
    given-names: Brian
    name-particle: D
  -
    affiliation: "UC Santa Cruz Genomics Institute"
    family-names: Paten
    given-names: Benedict
  -
    affiliation: "Ontario Institute for Cancer Research"
    family-names: Stein
    given-names: Lincoln
cff-version: "1.1.0"
date-released: 2021-05-12
doi: "10.1093/nar/gkab346"
license: "Apache 2.0"
message: "If you use this software, please cite it in general using this paper, particularly for Dockstore 1.10 and above"
repository-code: "https://github.com/dockstore/dockstore"
title: "The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols "
version: "1.11"


references:
  - type: article
    scope: "Cite this paper to reference Dockstore up to version 1.9"
    title: "The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows"
    year: 2017-01-18
    journal: F1000Research
    volume: "6"
    issue: "52"
    doi: "10.12688/f1000research.10137.1"
  - type: software-code
    scope: "Cite Zenodo when citing the source code"
    title: "dockstore/dockstore"
    doi: "10.5281/zenodo.592056"
    version: "1.11"

GitHub Events

Total

Release event: 6
Delete event: 25
Member event: 1
Issue comment event: 64
Push event: 101
Pull request event: 28
Pull request review comment event: 22
Pull request review event: 53
Create event: 40

Last Year

Release event: 6
Delete event: 25
Member event: 1
Issue comment event: 64
Push event: 101
Pull request event: 28
Pull request review comment event: 22
Pull request review event: 53
Create event: 40

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 12
Average time to close issues: N/A
Average time to close pull requests: 1 day
Total issue authors: 0
Total pull request authors: 4
Average comments per issue: 0
Average comments per pull request: 1.5
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 2

Past Year

Issues: 0
Pull requests: 12
Average time to close issues: N/A
Average time to close pull requests: 1 day
Issue authors: 0
Pull request authors: 4
Average comments per issue: 0
Average comments per pull request: 1.5
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 2

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Top Authors

Issue Authors

kathy-t (1)

Pull Request Authors

kathy-t (23)
denis-yuen (9)
coverbeck (3)
hyunnaye (3)
dependabot[bot] (3)
svonworl (2)

Top Labels

Issue Labels

Pull Request Labels

dependencies (3) github_actions (3)

Dependencies

toolbackup/pom.xml maven

org.slf4j:slf4j-api compile
ch.qos.logback:logback-classic 1.1.10
com.amazonaws:aws-java-sdk-core 1.11.83
com.amazonaws:aws-java-sdk-s3 1.11.83
com.fasterxml.jackson.core:jackson-annotations 2.11.0
com.fasterxml.jackson.core:jackson-core 2.11.0
com.fasterxml.jackson.core:jackson-databind 2.11.0
com.fasterxml.jackson.jaxrs:jackson-jaxrs-base 2.11.0
com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider 2.11.0
com.google.code.gson:gson 2.8.0
com.google.guava:guava
com.google.guava:guava 21.0
com.scireum:s3ninja 2.7
com.spotify:docker-client 7.0.2
commons-configuration:commons-configuration 1.10
commons-io:commons-io 2.7
commons-lang:commons-lang 2.6
commons-logging:commons-logging 1.2
io.cwl:cwlavro-generated 1.0.6
io.cwl:cwlavro-tools 1.0.6
io.dockstore:swagger-java-client 1.1
joda-time:joda-time 2.9.7
junit:junit
net.sf.jopt-simple:jopt-simple 5.0.3
org.apache.httpcomponents:httpclient 4.5.2
org.apache.httpcomponents:httpcore 4.4.5
org.gaul:s3proxy 1.5.1
org.glassfish.jersey.connectors:jersey-apache-connector 2.22.2
org.glassfish.jersey.core:jersey-client 2.23.1
org.glassfish.jersey.core:jersey-common 2.23.1
org.glassfish.jersey.media:jersey-media-json-jackson 2.22.2
org.jsoup:jsoup 1.10.2
org.slf4j:slf4j-api 1.7.22
org.slf4j:slf4j-simple 1.7.22
xml-apis:xml-apis 1.4.01
com.github.stefanbirkner:system-rules 1.16.1 test
junit:junit 4.13.1 test

tooltester/pom.xml maven

com.amazonaws:aws-java-sdk-s3 1.11.86 compile
com.google.code.gson:gson 2.8.0 compile
com.amazonaws:aws-java-sdk-core 1.11.86
com.beust:jcommander 1.60
com.fasterxml.jackson.core:jackson-annotations 2.12.2
com.fasterxml.jackson.core:jackson-core 2.12.2
com.fasterxml.jackson.core:jackson-databind
com.fasterxml.jackson.core:jackson-databind 2.12.2
com.fasterxml.jackson.jaxrs:jackson-jaxrs-base 2.12.2
com.offbytwo.jenkins:jenkins-client 0.3.8
commons-configuration:commons-configuration 1.10
commons-io:commons-io 2.7
commons-lang:commons-lang 2.6
commons-logging:commons-logging 1.2
de.vandermeer:asciitable 0.2.5
io.cwl:cwlavro-generated 1.0.6
io.cwl:cwlavro-tools 1.0.6
io.dockstore:swagger-java-client 1.9.0
javax.activation:activation 1.1.1
javax.ws.rs:javax.ws.rs-api 2.0.1
javax.xml.bind:jaxb-api 2.2.11
org.apache.httpcomponents:httpclient 4.5.2
org.apache.httpcomponents:httpcore 4.4.4
org.glassfish.jersey.core:jersey-client 2.25.1
org.hamcrest:hamcrest-core 1.3
org.slf4j:slf4j-api 1.7.21
org.slf4j:slf4j-simple 1.7.21
xml-apis:xml-apis 1.4.01
com.github.stefanbirkner:system-rules 1.19.0 test
junit:junit 4.11 test
org.hamcrest:hamcrest-all 1.3 test

.github/workflows/maven.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-java v3 composite

.github/workflows/deploy_tagged.yml actions

metricsaggregator/docker-compose.yml docker

docker.elastic.co/elasticsearch/elasticsearch 7.10.1
localstack/localstack 1.3.1
postgres 13.7

toolbackup/docker-compose.yml docker

andrewgaul/s3proxy sha-ba0fd6d

dockstore-support-reports/pom.xml maven

io.dockstore:metricsaggregator ${project.version}
io.dockstore:toolbackup ${project.version}
io.dockstore:tooltester ${project.version}

jira_automation/pom.xml maven

com.google.code.gson:gson 2.10.1
org.kohsuke:github-api

metricsaggregator/pom.xml maven

com.beust:jcommander
io.dockstore:dockstore-common ${dockstore-core.version}
io.dockstore:openapi-java-client ${dockstore-core.version}
javax.money:money-api
org.apache.commons:commons-configuration2
org.glassfish.jersey.inject:jersey-hk2
org.javamoney.moneta:moneta-core
org.slf4j:slf4j-api
software.amazon.awssdk:s3
cloud.localstack:localstack-utils test
io.dockstore:dockstore-integration-testing ${dockstore-core.version} test
io.dockstore:dockstore-webservice ${dockstore-core.version} test
io.dropwizard:dropwizard-testing test
org.junit.jupiter:junit-jupiter-api test
uk.org.webcompere:system-stubs-core test
uk.org.webcompere:system-stubs-jupiter test

pom.xml maven

io.dockstore:bom-internal 1.15.0-alpha.5 import
org.glassfish.jersey.inject:jersey-hk2 3.0.9
ro.fortsoft.pf4j:pf4j 1.1.1
xml-apis:xml-apis 1.4.01
io.dropwizard:dropwizard-migrations test

topicgenerator/pom.xml maven

ch.qos.logback:logback-classic
com.beust:jcommander
com.knuddels:jtokkit 0.6.1
com.theokanning.openai-gpt3-java:api 0.16.1
com.theokanning.openai-gpt3-java:service 0.16.1
io.dockstore:openapi-java-client ${dockstore-core.version}
io.dockstore:utils ${revision}${changelist}
org.apache.commons:commons-configuration2
org.apache.commons:commons-csv 1.10.0
org.glassfish.jersey.inject:jersey-hk2
org.slf4j:slf4j-api

utils/pom.xml maven

ch.qos.logback:logback-classic
commons-beanutils:commons-beanutils
org.apache.commons:commons-configuration2
org.slf4j:slf4j-api

topicgenerator/docker-compose.yml docker

docker.elastic.co/elasticsearch/elasticsearch 7.10.1
postgres 16.1

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

dockstore-support

Science Score: 44.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

dockstore-support

Prerequisites

Communicating with OpenStack

Endpoint Configuration

AWS Credentials

Client

How it Works

Downloader

Tests

Owner

Citation (citation.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies