Merge branch 'master' of https://github.com/BackofenLab/docker-galaxy-graphclust

Author: bgruening

Dockerfile

@@ -9,7 +9,8 @@ ENV ENABLE_TTS_INSTALL True
 
 # Enable Conda dependency resolution
 ENV GALAXY_CONFIG_CONDA_AUTO_INSTALL=True \
-    GALAXY_CONFIG_CONDA_AUTO_INIT=True
+    GALAXY_CONFIG_CONDA_AUTO_INIT=True \
+    GALAXY_CONFIG_USE_CACHED_DEPENDENCY_MANAGER=True    
 
 # Install tools
 ADD graphclust.yml $GALAXY_ROOT/tools.yaml

README.md

@@ -1,28 +1,39 @@
 [![DOI](https://zenodo.org/badge/5466/bgruening/docker-galaxy-stable.svg)](https://zenodo.org/badge/latestdoi/5466/bgruening/docker-galaxy-stable)
 [![Build Status](https://travis-ci.org/BackofenLab/docker-galaxy-graphclust.svg?branch=master)](https://travis-ci.org/BackofenLab/docker-galaxy-graphclust)
-[![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)
+[![Docker Repository on Quay](https://quay.io/repository/bgruening/galaxy-graphclust/status "Docker Repository on Quay")](https://quay.io/repository/bgruening/galaxy-graphclust)
 
 Galaxy GraphClust Flavor
 ========================
 
 :whale: Galaxy Docker repository for GraphClust
 
-# Requirements
+# Requirements:
 
- - [Docker](https://docs.docker.com/installation/) for Linux / Windows / OSX
- - [Kitematic](https://kitematic.com/) for Windows / OS-X (Optional)
+ - [Docker](https://docs.docker.com/installation/)
+   A Docker client with the necessary user permissions is required for running the Galaxy GraphClust. Docker supports the three major desktop operating systems  Linux, Windows and Mac OSX. Please refer to Docker [installation guideline](https://docs.docker.com/installation/) for details.
 
-# Usage
+- For Windows and Mac systems it is additinally possible to use [Kitematic](https://kitematic.com/) and launch Galaxy GraphClust Flavor from the OS graphical user interface.
 
-To launch:
+- Alternative to launch the docker, having access to a Galaxy instance server preconfigured with the set of tools included in 'graphclust.yml' would be enough to run GraphClust Galaxy pipeline. (TODO: clarify this option) (TODO: mention Freiburg galaxy server?)
+
+# Setup:
+
+## To run the Galaxy server:
 
 ```
-docker run -i -t -p 8080:80 bgruening/galaxy-graphclust
+docker run -i -t -p 8080:80 backofenlab/docker-galaxy-graphclust
 ```
 
 For more details about this command line or specific usage, please consult the
 [`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.
 
+# Usage:
+
+## To launch the Galaxy GraphClust pipeline:
+* Inside your browser goto [http://localhost:8080/](http://localhost:8080/)
+
+TODO
+
 # Contributers
 
  - Milad Miladi

graphclust.yml

@@ -94,3 +94,87 @@ tools:
   tool_shed_url: https://toolshed.g2.bx.psu.edu
   install_resolver_dependencies: True
   install_tool_dependencies: False
+
+- name: fasta_compute_length
+  owner: devteam
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: fasta_formatter
+  owner: devteam
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: fasta_nucleotide_changer
+  owner: devteam
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: fasta_to_tabular
+  owner: devteam
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: tabular_to_fasta
+  owner: devteam
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: find_subsequences
+  owner: bgruening
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: fasta_merge_files_and_filter_unique_sequences
+  owner: galaxyp
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: get_orfs_or_cdss
+  owner: peterjc
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: seq_filter_by_id
+  owner: peterjc
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: seq_select_by_id 
+  owner: peterjc
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: seq_rename
+  owner: peterjc
+  tool_panel_section_label: "FASTA manipulation tools"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: True
+  install_tool_dependencies: False
+
+- name: infernal
+  owner: bgruening
+  tool_panel_section_label: "GraphClust"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  install_resolver_dependencies: False
+  install_tool_dependencies: True