From 195819c2e18dca6f46239320d2e0c888a580c664 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 15:49:55 +0200 Subject: [PATCH 1/9] add a capability matrix --- README.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/README.md b/README.md index b2892650d..239b2cc45 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,28 @@ [![Gitter](https://badges.gitter.im/bgruening/docker-galaxy-stable.svg)](https://gitter.im/bgruening/docker-galaxy-stable?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) ![docker pulls](https://img.shields.io/docker/pulls/bgruening/galaxy-stable.svg) ![docker stars](https://img.shields.io/docker/stars/bgruening/galaxy-stable.svg) + +Capability matrix +================= + +Galaxy is a powerful framework with sheer endless possibilities of deployment methods and features. +This is often overwhelming and makes the choise for the correct deployment harder. +In the following matrix we will try to give you an overview about the feature we do +offer with the Galaxy Docker project, which features are constantly tested under different deployments. +Please note this can only cover a small spectrum but is actually possible with Galaxy. +We are aiming to fill this matrix step by step. + +| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io)* | [SWARM](https://docs.docker.com/engine/swarm) | +| -------------- |:-------------:| :-------:|:----:|:----:| +| SLURM | x | x |- |- | +| HT-Condor | x | x |- |- | +| IE | x | x |- |- | +| Conda resolver | x | x |- |- | +| TS resolver | x | - |- |- | + + + + Galaxy Docker Image =================== From bc8f01d7938da035bb1fba6d1c0a1464acb1b64b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 15:53:59 +0200 Subject: [PATCH 2/9] add pgadmin --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 239b2cc45..e9d2c1331 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,7 @@ We are aiming to fill this matrix step by step. | IE | x | x |- |- | | Conda resolver | x | x |- |- | | TS resolver | x | - |- |- | +| pgadmin | - | x |- |- | From ef7d905caf3e7c2279dc6a83fd96e350540ff78b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 7 May 2017 00:23:22 +0200 Subject: [PATCH 3/9] htcondor + docker --- README.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index e9d2c1331..c31848e8e 100644 --- a/README.md +++ b/README.md @@ -15,14 +15,15 @@ offer with the Galaxy Docker project, which features are constantly tested under Please note this can only cover a small spectrum but is actually possible with Galaxy. We are aiming to fill this matrix step by step. -| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io)* | [SWARM](https://docs.docker.com/engine/swarm) | -| -------------- |:-------------:| :-------:|:----:|:----:| -| SLURM | x | x |- |- | -| HT-Condor | x | x |- |- | -| IE | x | x |- |- | -| Conda resolver | x | x |- |- | -| TS resolver | x | - |- |- | -| pgadmin | - | x |- |- | +| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io)* | [SWARM](https://docs.docker.com/engine/swarm) | +| ------------------- |:-------------:| :-------:|:----:|:----:| +| SLURM | x | x |- |- | +| HT-Condor | x | x |- |- | +| HT-Condor + Docker | - | x |- |- | +| IE | x | x |- |- | +| Conda resolver | x | x |- |- | +| TS resolver | x | - |- |- | +| pgadmin | - | x |- |- | From 578897f0374559606bf34cce9f4d8fde45e9e932 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 8 May 2017 10:22:31 +0200 Subject: [PATCH 4/9] [ci skip] work more on the capability matrix --- README.md | 32 ++++++++++++++++++-------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index c31848e8e..4780ec30b 100644 --- a/README.md +++ b/README.md @@ -11,22 +11,26 @@ Capability matrix Galaxy is a powerful framework with sheer endless possibilities of deployment methods and features. This is often overwhelming and makes the choise for the correct deployment harder. In the following matrix we will try to give you an overview about the feature we do -offer with the Galaxy Docker project, which features are constantly tested under different deployments. -Please note this can only cover a small spectrum but is actually possible with Galaxy. +offer with the Galaxy Docker project and which features are constantly tested under different deployments. +Please note this can only cover a small spectrum what is actually possible with Galaxy. We are aiming to fill this matrix step by step. -| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io)* | [SWARM](https://docs.docker.com/engine/swarm) | -| ------------------- |:-------------:| :-------:|:----:|:----:| -| SLURM | x | x |- |- | -| HT-Condor | x | x |- |- | -| HT-Condor + Docker | - | x |- |- | -| IE | x | x |- |- | -| Conda resolver | x | x |- |- | -| TS resolver | x | - |- |- | -| pgadmin | - | x |- |- | - - - +| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io):hatching_chick: | [Swarm](https://docs.docker.com/engine/swarm) | [Rancher](http://rancher.com/rancher-os) | +| ----------------------- |:-------------:| :-------:|:----:|:----:|:----:| +| SLURM Job Runner (JR) | x | x |- |- |+ | +| HT-Condor JR | x | x |- |- |+ | +| HT-Condor JR + Docker | - | x |- |- |+ | +| Kubernetes JR | - | x |- |- |+ | +| Interactive Environments| | x | x |- |- |+ | +| Conda resolver | x | x |- |- |+ | +| TS resolver :koala: | x | - |- |- |- | +| compute auto scale | - | + |- |- |+ | +| pgadmin4 support | - | x |- |- |+ | + +:koala: For the composed versions, the Tool Shed (TS) resolver were left out on purpose to keep the image sizes small. +It simply means that we do not ship the [requirements](https://galaxyproject.org/toolshed/package-recipes/) needed to compile traditional TS dependencies. This feature can be enabled by simply installing all requirements into the galaxy-web container. However, we recommend to use [Conda packages](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). + +:hatching_chick: The kubernetes (k8s) setup is based on [kompose](https://github.com/kubernetes-incubator/kompose) to convert the needed YAML files. Galaxy Docker Image =================== From b513abcb17f76c8bf1f4b6fb1744ae5a01addf8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 May 2017 22:20:55 +0200 Subject: [PATCH 5/9] Update README.md --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 4780ec30b..dea25b03d 100644 --- a/README.md +++ b/README.md @@ -17,15 +17,15 @@ We are aiming to fill this matrix step by step. | Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io):hatching_chick: | [Swarm](https://docs.docker.com/engine/swarm) | [Rancher](http://rancher.com/rancher-os) | | ----------------------- |:-------------:| :-------:|:----:|:----:|:----:| -| SLURM Job Runner (JR) | x | x |- |- |+ | -| HT-Condor JR | x | x |- |- |+ | -| HT-Condor JR + Docker | - | x |- |- |+ | -| Kubernetes JR | - | x |- |- |+ | -| Interactive Environments| | x | x |- |- |+ | -| Conda resolver | x | x |- |- |+ | +| SLURM Job Runner (JR) | x | x |- |- |x | +| HT-Condor JR | x | x |- |- |x | +| HT-Condor JR + Docker | - | x |- |- |x | +| Kubernetes JR | - | x |- |- |x | +| Interactive Environments| x | x |- |- |x | +| Conda resolver | x | x |- |- |x | | TS resolver :koala: | x | - |- |- |- | -| compute auto scale | - | + |- |- |+ | -| pgadmin4 support | - | x |- |- |+ | +| compute auto scale | - | + |- |- |x | +| pgadmin4 support | - | x |- |- |x | :koala: For the composed versions, the Tool Shed (TS) resolver were left out on purpose to keep the image sizes small. It simply means that we do not ship the [requirements](https://galaxyproject.org/toolshed/package-recipes/) needed to compile traditional TS dependencies. This feature can be enabled by simply installing all requirements into the galaxy-web container. However, we recommend to use [Conda packages](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). From d10b41069ecf3a8ba8552da8782fadaafca8c592 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 May 2017 22:22:50 +0200 Subject: [PATCH 6/9] use checkmark --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index dea25b03d..e529c64f5 100644 --- a/README.md +++ b/README.md @@ -17,15 +17,15 @@ We are aiming to fill this matrix step by step. | Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io):hatching_chick: | [Swarm](https://docs.docker.com/engine/swarm) | [Rancher](http://rancher.com/rancher-os) | | ----------------------- |:-------------:| :-------:|:----:|:----:|:----:| -| SLURM Job Runner (JR) | x | x |- |- |x | -| HT-Condor JR | x | x |- |- |x | -| HT-Condor JR + Docker | - | x |- |- |x | -| Kubernetes JR | - | x |- |- |x | -| Interactive Environments| x | x |- |- |x | -| Conda resolver | x | x |- |- |x | -| TS resolver :koala: | x | - |- |- |- | -| compute auto scale | - | + |- |- |x | -| pgadmin4 support | - | x |- |- |x | +| SLURM Job Runner (JR) | ✔ | ✔ |- |- |✔ | +| HT-Condor JR | ✔ | ✔ |- |- |✔ | +| HT-Condor JR + Docker | - | ✔ |- |- |✔ | +| Kubernetes JR | - | ✔ |- |- |✔ | +| Interactive Environments| ✔ | ✔ |- |- |✔ | +| Conda resolver | ✔ | ✔ |- |- |✔ | +| TS resolver :koala: | ✔ | - |- |- |- | +| compute auto scale | - | ✔ |- |- |✔ | +| pgadmin4 support | - | ✔ |- |- |✔ | :koala: For the composed versions, the Tool Shed (TS) resolver were left out on purpose to keep the image sizes small. It simply means that we do not ship the [requirements](https://galaxyproject.org/toolshed/package-recipes/) needed to compile traditional TS dependencies. This feature can be enabled by simply installing all requirements into the galaxy-web container. However, we recommend to use [Conda packages](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). From 32af1d0586be6da741c57290fb8e2132968be46f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 May 2017 22:44:20 +0200 Subject: [PATCH 7/9] adding more ideas to the matrix --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e529c64f5..8a12938d4 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,10 @@ We are aiming to fill this matrix step by step. | SLURM Job Runner (JR) | ✔ | ✔ |- |- |✔ | | HT-Condor JR | ✔ | ✔ |- |- |✔ | | HT-Condor JR + Docker | - | ✔ |- |- |✔ | -| Kubernetes JR | - | ✔ |- |- |✔ | +| Kubernetes JR | - | - |- |- |- | +| Kubernetes JR | - | - |- |- |- | +| Chronos JR | - | - |- |- |- | +| Pulsar JR | - | - |- |- |- | | Interactive Environments| ✔ | ✔ |- |- |✔ | | Conda resolver | ✔ | ✔ |- |- |✔ | | TS resolver :koala: | ✔ | - |- |- |- | From 675e399a1055d9395a71c248cd0bf4b17688ce4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 May 2017 22:46:52 +0200 Subject: [PATCH 8/9] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 8a12938d4..0f9396e83 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,6 @@ We are aiming to fill this matrix step by step. | HT-Condor JR | ✔ | ✔ |- |- |✔ | | HT-Condor JR + Docker | - | ✔ |- |- |✔ | | Kubernetes JR | - | - |- |- |- | -| Kubernetes JR | - | - |- |- |- | | Chronos JR | - | - |- |- |- | | Pulsar JR | - | - |- |- |- | | Interactive Environments| ✔ | ✔ |- |- |✔ | From 77fa7690392a0e44bda401965a50ca4101950419 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 May 2017 22:51:10 +0200 Subject: [PATCH 9/9] move the cap_matrix further down --- README.md | 59 ++++++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index 0f9396e83..b06297de2 100644 --- a/README.md +++ b/README.md @@ -5,35 +5,6 @@ ![docker pulls](https://img.shields.io/docker/pulls/bgruening/galaxy-stable.svg) ![docker stars](https://img.shields.io/docker/stars/bgruening/galaxy-stable.svg) -Capability matrix -================= - -Galaxy is a powerful framework with sheer endless possibilities of deployment methods and features. -This is often overwhelming and makes the choise for the correct deployment harder. -In the following matrix we will try to give you an overview about the feature we do -offer with the Galaxy Docker project and which features are constantly tested under different deployments. -Please note this can only cover a small spectrum what is actually possible with Galaxy. -We are aiming to fill this matrix step by step. - -| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io):hatching_chick: | [Swarm](https://docs.docker.com/engine/swarm) | [Rancher](http://rancher.com/rancher-os) | -| ----------------------- |:-------------:| :-------:|:----:|:----:|:----:| -| SLURM Job Runner (JR) | ✔ | ✔ |- |- |✔ | -| HT-Condor JR | ✔ | ✔ |- |- |✔ | -| HT-Condor JR + Docker | - | ✔ |- |- |✔ | -| Kubernetes JR | - | - |- |- |- | -| Chronos JR | - | - |- |- |- | -| Pulsar JR | - | - |- |- |- | -| Interactive Environments| ✔ | ✔ |- |- |✔ | -| Conda resolver | ✔ | ✔ |- |- |✔ | -| TS resolver :koala: | ✔ | - |- |- |- | -| compute auto scale | - | ✔ |- |- |✔ | -| pgadmin4 support | - | ✔ |- |- |✔ | - -:koala: For the composed versions, the Tool Shed (TS) resolver were left out on purpose to keep the image sizes small. -It simply means that we do not ship the [requirements](https://galaxyproject.org/toolshed/package-recipes/) needed to compile traditional TS dependencies. This feature can be enabled by simply installing all requirements into the galaxy-web container. However, we recommend to use [Conda packages](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). - -:hatching_chick: The kubernetes (k8s) setup is based on [kompose](https://github.com/kubernetes-incubator/kompose) to convert the needed YAML files. - Galaxy Docker Image =================== @@ -50,6 +21,7 @@ The Image is based on [Ubuntu 14.04 LTS](http://releases.ubuntu.com/14.04/) and # Table of Contents +- [Capability matrix](#cap_matrix) - [Usage](#Usage) - [Upgrading images](#Upgrading-images) - [Enabling Interactive Environments in Galaxy](#Enabling-Interactive-Environments-in-Galaxy) @@ -77,6 +49,35 @@ The Image is based on [Ubuntu 14.04 LTS](http://releases.ubuntu.com/14.04/) and - [Support & Bug Reports](#Support-Bug-Reports) +# Capability matrix [[toc]](#toc) + +Galaxy is a powerful framework with sheer endless possibilities of deployment methods and features. +This is often overwhelming and makes the choise for the correct deployment harder. +In the following matrix we will try to give you an overview about the feature we do +offer with the Galaxy Docker project and which features are constantly tested under different deployments. +Please note this can only cover a small spectrum what is actually possible with Galaxy. +We are aiming to fill this matrix step by step, get in [contact](https://gitter.im/bgruening/docker-galaxy-stable) if you want to help! + +| Feature | Monolithic | [Compose](https://docs.docker.com/compose) | [Kubernetes](https://kubernetes.io):hatching_chick: | [Swarm](https://docs.docker.com/engine/swarm) | [Rancher](http://rancher.com/rancher-os) | +| ----------------------- |:-------------:| :-------:|:----:|:----:|:----:| +| SLURM Job Runner (JR) | ✔ | ✔ |- |- |✔ | +| HT-Condor JR | ✔ | ✔ |- |- |✔ | +| HT-Condor JR + Docker | - | ✔ |- |- |✔ | +| Kubernetes JR | - | - |- |- |- | +| Chronos JR | - | - |- |- |- | +| Pulsar JR | - | - |- |- |- | +| Interactive Environments| ✔ | ✔ |- |- |✔ | +| Conda resolver | ✔ | ✔ |- |- |✔ | +| TS resolver :koala: | ✔ | - |- |- |- | +| compute auto scale | - | ✔ |- |- |✔ | +| pgadmin4 support | - | ✔ |- |- |✔ | + +:koala: For the composed versions, the Tool Shed (TS) resolver were left out on purpose to keep the image sizes small. +It simply means that we do not ship the [requirements](https://galaxyproject.org/toolshed/package-recipes/) needed to compile traditional TS dependencies. This feature can be enabled by simply installing all requirements into the galaxy-web container. However, we recommend to use [Conda packages](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). + +:hatching_chick: The kubernetes (k8s) setup is based on [kompose](https://github.com/kubernetes-incubator/kompose) to convert the needed YAML files. + + # Usage [[toc]](#toc) At first you need to install docker. Please follow the [very good instructions](https://docs.docker.com/installation/) from the Docker project.