QBiC technical documentation pages

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Summary for all QBiC technical documentation

View the Project on GitHub qbicsoftware/docs

QBiC Documentation

Welcome to QBiC’s technical documentation pages.

Project reports are generated automatically during builds, while this summary is generated daily. So come back often to get the latest reports.

List of projects (by repository name)

1. attachi-cli

No description available for attachi-cli.

GitHub link: https://github.com/qbicsoftware/attachi-cli

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2. barcode-creation

Scripts to create barcodes for tagging samples

GitHub link: https://github.com/qbicsoftware/barcode-creation

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3. barcode-dragon-portlet

No description available for barcode-dragon-portlet.

GitHub link: https://github.com/qbicsoftware/barcode-dragon-portlet

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4. cookiecutter-templates-cli

Collection of cookiecutter templates to generate new portlets, libraries, utilities, etc., using our parent POM structure.

GitHub link: https://github.com/qbicsoftware/cookiecutter-templates-cli

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5. core-utils-lib

Library containing core classes and utilities that are independent of a portal.

GitHub link: https://github.com/qbicsoftware/core-utils-lib

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6. data-model-lib

Libraries providing functionality for the QBiC/openBIS data model

GitHub link: https://github.com/qbicsoftware/data-model-lib

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7. dropboxhandler

No description available for dropboxhandler.

GitHub link: https://github.com/qbicsoftware/dropboxhandler

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8. dropboxreporter

Reports stuff that has happened on a particular day, based on the logs.

GitHub link: https://github.com/qbicsoftware/dropboxreporter

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9. dync-cli

TCP-based python data transfer client and server using ZeroMQ

GitHub link: https://github.com/qbicsoftware/dync-cli

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10. etl-scripts

ETL scripts written in Jython 2.7 for openBIS dropboxes.

GitHub link: https://github.com/qbicsoftware/etl-scripts

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11. example-osgi-library

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GitHub link: https://github.com/qbicsoftware/example-osgi-library

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12. example-osgi-portlet

No description available for example-osgi-portlet.

GitHub link: https://github.com/qbicsoftware/example-osgi-portlet

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13. experiment-creation-portlet

Prototype of new experiment creation and import portlet

GitHub link: https://github.com/qbicsoftware/experiment-creation-portlet

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14. experiment-graph-gui

Stand alone version of the d3 experiment graph

GitHub link: https://github.com/qbicsoftware/experiment-graph-gui

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15. experimental-design-lib

Parsers, writers for experimental design formats etc.

GitHub link: https://github.com/qbicsoftware/experimental-design-lib

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16. geo-uploader-cli

Extracts data from openBIS and (semi-)automizes the data upload

GitHub link: https://github.com/qbicsoftware/geo-uploader-cli

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17. groovydoc-maven-plugin

Maven plugin to allow for inclusion of Gmavenplus generated Groovydocs in project-reports.html

GitHub link: https://github.com/qbicsoftware/groovydoc-maven-plugin

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18. html2pdf-cli

html2pdf. A proof-of-concept HTML to PDF conversion tool.

GitHub link: https://github.com/qbicsoftware/html2pdf-cli

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19. icgc-features

No description available for icgc-features.

GitHub link: https://github.com/qbicsoftware/icgc-features

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20. isa-creator-lib

ISAcreator is a Java desktop application which allows for the creation and editing of ISA-Tab files. Originally developed by Eamonn Maguire, with further contributions by Alejandra Gonzalez-Beltran, David Johnson and Philippe Rocca-Serra (Uni. of Oxford).

GitHub link: https://github.com/qbicsoftware/isa-creator-lib

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21. javafx-d3-lib

Provides a Java API to use the JavaScript library d3.js with the JavaFx WebView

GitHub link: https://github.com/qbicsoftware/javafx-d3-lib

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22. javafx-utils-lib

JavaFX-related utilities

GitHub link: https://github.com/qbicsoftware/javafx-utils-lib

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23. metadata-doc

Collection of metadata sheets for QBiC projects

GitHub link: https://github.com/qbicsoftware/metadata-doc

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24. metadata-model-specification

QBiC’s metadata model specification

GitHub link: https://github.com/qbicsoftware/metadata-model-specification

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25. metastats-cli

Creates a metadata table for an openBIS project for statistical analysis

GitHub link: https://github.com/qbicsoftware/metastats-cli

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26. metastats-object-model

Describes the properties of a QBiC MetaStats object model

GitHub link: https://github.com/qbicsoftware/metastats-object-model

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27. micronaut-utils-lib

A small util library for shared objects in Micronaut-based projects at QBiC.

GitHub link: https://github.com/qbicsoftware/micronaut-utils-lib

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28. mtb-converter-cli

A Python command line tool that parses and converts diagnostic variant data for the Molecular Tumor Board at UKT Tübingen.

GitHub link: https://github.com/qbicsoftware/mtb-converter-cli

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29. mtb-parser-lib

A simple module for diagnostic variant information parsing

GitHub link: https://github.com/qbicsoftware/mtb-parser-lib

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30. nanopore-parser-cli

A command-line application for validating Oxford Nanopore folder structures.

GitHub link: https://github.com/qbicsoftware/nanopore-parser-cli

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31. ncct-style

No description available for ncct-style.

GitHub link: https://github.com/qbicsoftware/ncct-style

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32. nextflow-logger-service

Consumes Nextflow weblog payloads via Http REST and stores them in a database.

GitHub link: https://github.com/qbicsoftware/nextflow-logger-service

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33. omero-importer-cli

A description how to build a slim JAVA omero-importer CLI, without installing OMERO.server

GitHub link: https://github.com/qbicsoftware/omero-importer-cli

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34. omero-importer-recipe

Conda recipe for the Java omero importer cli

GitHub link: https://github.com/qbicsoftware/omero-importer-recipe

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35. omero-lib

Java-based library to connect to the OMERO server

GitHub link: https://github.com/qbicsoftware/omero-lib

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36. omero-portlet

Vaadin portlet for qPortal that displays image (meta)data.

GitHub link: https://github.com/qbicsoftware/omero-portlet

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37. omero-py-lib

Python bindings for OMERO server API 5.4.6

GitHub link: https://github.com/qbicsoftware/omero-py-lib

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38. oncostore-proto-project

The Variantstore is a Java/Groovy-based service application implemented using the Micronaut framework and enables storage and access to information on genomic variants and metadata from a connected database via a RESTful API.

GitHub link: https://github.com/qbicsoftware/oncostore-proto-project

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39. openbis-client-lib

No description available for openbis-client-lib.

GitHub link: https://github.com/qbicsoftware/openbis-client-lib

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40. openbis_connection_tester

Small portlet to test connection problems

GitHub link: https://github.com/qbicsoftware/openbis_connection_tester

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41. parent-poms

We keep all parent POMs under this single repository.

GitHub link: https://github.com/qbicsoftware/parent-poms

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42. portal-utils-lib

Liferay and Vaadin utilities that are quite handy to have when doing portal development.

GitHub link: https://github.com/qbicsoftware/portal-utils-lib

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43. postman-cli

A client software for dataset request and download from openBIS

GitHub link: https://github.com/qbicsoftware/postman-cli

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44. postman-core-lib

Core libraries providing utilities for the download of OpenBIS files and datasets

GitHub link: https://github.com/qbicsoftware/postman-core-lib

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45. power-analysis-portlet

Support power analysis and sample size estimation of DNA microarray and RNA-Seq experimental designs

GitHub link: https://github.com/qbicsoftware/power-analysis-portlet

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46. printer-garden-portlet

Maintaining and updating printer project associations and label printer locations

GitHub link: https://github.com/qbicsoftware/printer-garden-portlet

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47. project-manager

No description available for project-manager.

GitHub link: https://github.com/qbicsoftware/project-manager

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48. project-manager-portlet

A project manager portlet

GitHub link: https://github.com/qbicsoftware/project-manager-portlet

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49. projectbrowser-portlet

QBiC Project Browser enables users to browse and manage their projects. Further, users can run analysis pipelines on registered data.

GitHub link: https://github.com/qbicsoftware/projectbrowser-portlet

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50. projectwizard-portlet

QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

GitHub link: https://github.com/qbicsoftware/projectwizard-portlet

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51. python-data-lib

Python-based library for data processing operations

GitHub link: https://github.com/qbicsoftware/python-data-lib

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52. qbic-docs

QBiC technical documentation, such as API docs.

GitHub link: https://github.com/qbicsoftware/qbic-docs

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53. qbic-pipeline-integration-testing

A repository to hold the code used for pipeline integration testing for nf-core/rnaseq and scilifelab/Sarek at QBIC.

GitHub link: https://github.com/qbicsoftware/qbic-pipeline-integration-testing

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54. qbic-portlet-userdbtools

The existing portlet https://github.com/qbicsoftware/UserDBTools is migrated to our portlet-templaet structure based on maven.

GitHub link: https://github.com/qbicsoftware/qbic-portlet-userdbtools

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55. qbic-pwresetd

Password reset daemon for QBiC services

GitHub link: https://github.com/qbicsoftware/qbic-pwresetd

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56. qbic-setup-doc

Documentation collection and resources about setup guides of application servers

GitHub link: https://github.com/qbicsoftware/qbic-setup-doc

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57. qflow

Portlet for workflow functionality containing admin panel and workflow monitor

GitHub link: https://github.com/qbicsoftware/qflow

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58. qoffer-2-portlet

qOffer assists in managing and creating offers

GitHub link: https://github.com/qbicsoftware/qoffer-2-portlet

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59. qoffer-portlet

QBiC offer generator aims to fulfill quotation preparation processes in a fully automatised fashion.

GitHub link: https://github.com/qbicsoftware/qoffer-portlet

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60. qube-cli

Collection of QBiC’s internal project templates

GitHub link: https://github.com/qbicsoftware/qube-cli

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61. r-container-lib

A collection of project-related Dockerfiles for a controlled R environment with defined R packages

GitHub link: https://github.com/qbicsoftware/r-container-lib

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62. r-container-template

A collection of project-related R scripts with defined package lists and Dockerfiles for reproducible R environments

GitHub link: https://github.com/qbicsoftware/r-container-template

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63. reporting-scripts

No description available for reporting-scripts.

GitHub link: https://github.com/qbicsoftware/reporting-scripts

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64. repowiz-cli

Repository wizard RepoWiz helps to make your data publicly available

GitHub link: https://github.com/qbicsoftware/repowiz-cli

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65. rmageddon-cli

A small linting command line tool for R container evaluation

GitHub link: https://github.com/qbicsoftware/rmageddon-cli

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66. sample-status-updater-cli

Performs post registration tasks after samples have been registered in openBIS, using the openBIS API. To be used as a cron job.

GitHub link: https://github.com/qbicsoftware/sample-status-updater-cli

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67. sample-tracking-helper-lib

An easy to use interface providing sample tracking update functions for ETL scripts

GitHub link: https://github.com/qbicsoftware/sample-tracking-helper-lib

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68. sample-tracking-service

Service that implements a sample tracking interface.

GitHub link: https://github.com/qbicsoftware/sample-tracking-service

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69. sample-tracking-status-portlet

Portlet to query satus, location and general information of samples

GitHub link: https://github.com/qbicsoftware/sample-tracking-status-portlet

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70. sample-tracking-update-portlet

Portlet to update sample status, location and general information

GitHub link: https://github.com/qbicsoftware/sample-tracking-update-portlet

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71. sarek-starter-cli

Various python scripts for bioinformatics data analysis and pre-processing

GitHub link: https://github.com/qbicsoftware/sarek-starter-cli

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72. scark-cli

No description available for scark-cli.

GitHub link: https://github.com/qbicsoftware/scark-cli

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73. services-testing-portlet

A portlet to test services related libraries

GitHub link: https://github.com/qbicsoftware/services-testing-portlet

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74. spark-service

No description available for spark-service.

GitHub link: https://github.com/qbicsoftware/spark-service

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75. statistics-cli

This tools is responsible for data retrieval and formatting, in order to visualize data on our homepage.

GitHub link: https://github.com/qbicsoftware/statistics-cli

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76. statistics-plugin

This repo contains shared classes between the qbic-statistics portlet and the statistics-data-retrieval repo

GitHub link: https://github.com/qbicsoftware/statistics-plugin

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77. statistics-portlet

No description available for statistics-portlet.

GitHub link: https://github.com/qbicsoftware/statistics-portlet

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78. trello-script

This repository holds a collection of scripts, which use the Trello API to easily access the information stored on a Trello Board

GitHub link: https://github.com/qbicsoftware/trello-script

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79. ukt-diagnostics-id-portlet

A portlet that generates patient and sample IDs per request for UKT diagnostics purposes

GitHub link: https://github.com/qbicsoftware/ukt-diagnostics-id-portlet

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80. user-db-portlet

User DB Tools Portlet enables users to add people and affiliations to the SQL user database.

GitHub link: https://github.com/qbicsoftware/user-db-portlet

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81. vaccine-designer-portlet

A portlet for the interactive design of individualized vaccines

GitHub link: https://github.com/qbicsoftware/vaccine-designer-portlet

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82. workflow-dashboard-portlet

Live visualisation of Nextflow workflows in qPortal

GitHub link: https://github.com/qbicsoftware/workflow-dashboard-portlet

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83. workflow-sarek

This is an archived version for a paper, please use https://github.com/nf-core/sarek for new projects!

GitHub link: https://github.com/qbicsoftware/workflow-sarek

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84. xml-manager-lib

Reading and writing of specific openBIS xml properties

GitHub link: https://github.com/qbicsoftware/xml-manager-lib

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Last update: 14 January 2021, 4:26 hrs.