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add initial version
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‎.travis.yml‎

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sudo: required
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language: python
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python: 2.7
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services:
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- docker
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env:
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- TOX_ENV=py27
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git:
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submodules: false
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before_install:
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- wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
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- make docker_install
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- travis_wait 45 make docker_build
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- make docker_run
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- sleep 300
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install:
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- make install
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script:
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- make test_api
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- make test_ftp
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- make test_bioblend
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- make test_docker_in_docker

‎Dockerfile‎

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# Galaxy - GraphClust
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FROM bgruening/galaxy-stable:16.10
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MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com
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ENV GALAXY_CONFIG_BRAND GraphClust
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ENV ENABLE_TTS_INSTALL True
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# Enable Conda dependency resolution
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ENV GALAXY_CONFIG_CONDA_AUTO_INSTALL=True \
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GALAXY_CONFIG_CONDA_AUTO_INIT=True
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# Install tools
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ADD graphclust.yml $GALAXY_ROOT/tools.yaml
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RUN install-tools $GALAXY_ROOT/tools.yaml && \
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/tool_deps/_conda/bin/conda clean --tarballs

‎README.md‎

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# docker-galaxy-graphclust
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Galaxy flavor for GraphClust
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[![DOI](https://zenodo.org/badge/5466/bgruening/docker-galaxy-stable.svg)](https://zenodo.org/badge/latestdoi/5466/bgruening/docker-galaxy-stable)
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[![Build Status](https://travis-ci.org/BackofenLab/docker-galaxy-graphclust.svg?branch=master)](https://travis-ci.org/BackofenLab/docker-galaxy-graphclust)
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[![Docker Repository on Quay](https://quay.io/repository/bgruening/galaxy-ngs-preprocessing/status "Docker Repository on Quay")](https://quay.io/repository/bgruening/galaxy-ngs-preprocessing)
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Galaxy GraphClust Flavor
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========================
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:whale: Galaxy Docker repository for GraphClust
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# Requirements
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- [Docker](https://docs.docker.com/installation/) for Linux / Windows / OSX
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- [Kitematic](https://kitematic.com/) for Windows / OS-X (Optional)
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# Usage
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To launch:
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```
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docker run -i -t -p 8080:80 bgruening/galaxy-graphclust
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```
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For more details about this command line or specific usage, please consult the
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[`README`](https://github.com/bgruening/docker-galaxy-stable/blob/master/README.md) of the main Galaxy Docker image, on which the current image is based.
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# Contributers
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- Milad Miladi
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- Eteri Sokhoyan
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- Bjoern Gruening
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# History
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- 0.1: Initial release!
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# Support & Bug Reports
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You can file an [github issue](https://github.com/BackofenLab/docker-galaxy-graphclust/issues) or ask us on the [Galaxy development list](http://lists.bx.psu.edu/listinfo/galaxy-dev).

‎graphclust.yml‎

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---
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# This is a sample file to be used as a reference for populating a list of
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# tools that you wish to install into Galaxy from a Tool Shed via the
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# `install_tool_shed_tools.py` script.
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#
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# For each tool you want to install, you must provide the following keys:
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# * name: this is is the name of the tool to install
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# * owner: owner of the Tool Shed repository from where the tools is being
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# installed
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# Further, you need to provide **one** of the following two keys:
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# * tool_panel_section_id: ID of the tool panel section where you want the
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# tool to be installed. The section ID can be found
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# in Galaxy's `shed_tool_conf.xml` config file. Note
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# that the specified section must exist in this file.
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# Otherwise, the tool will be installed outside any
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# section.
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# * tool_panel_section_label: Display label of a tool panel section where
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# you want the tool to be installed. If it does not
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# exist, this section will be created on the target
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# Galaxy instance (note that this is different than
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# when using the ID).
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# Multi-word labels need to be placed in quotes.
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# Each label will have a corresponding ID created;
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# the ID will be an all lowercase version of the
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# label, with multiple words joined with
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# underscores (e.g., 'BED tools' -> 'bed_tools').
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#
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# Tou can also specify the following optional keys to further define the
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# installation properties:
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# * tool_shed_url: the URL of the Tool Shed from where the tool should be
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# installed. (default: https://toolshed.g2.bx.psu.edu)
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# * revisions: a list of revisions of the tool, all of which will attempt to
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# be installed. (default: latest)
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# * install_tool_dependencies: True or False - whether to install tool
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# dependencies or not. (default: True)
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# * install_repository_dependencies: True or False - whether to install repo
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# dependencies or not. (default: True)
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api_key: admin
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galaxy_instance: http://localhost:8080
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tools:
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- name: graphclust_cmfinder
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_postprocessing
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_fasta_to_gspan
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_mlocarna
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_nspdk
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_prepocessing_for_mlocarna
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: graphclust_preprocessing
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owner: rnateam
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tool_panel_section_label: "GraphClust"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False
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- name: text_processing
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owner: bgruening
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tool_panel_section_id: "textutil"
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tool_shed_url: https://toolshed.g2.bx.psu.edu
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install_resolver_dependencies: True
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install_tool_dependencies: False

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