Commit 410260ce authored by Cameron's avatar Cameron

Merge branch 'docker/update' into 'development'

Docker/update

See merge request !72
parents 0e2761d9 366c70dd
Pipeline #3993 passed with stage
in 11 seconds
......@@ -11,7 +11,7 @@ Released on **January 23, 2017**.
Install
-------
* Docker - `apetkau/snvphyl-galaxy-1.0.1`
* Docker - `phacnml/snvphyl-galaxy-1.0.1`
* Virtual Machine - [snvphyl-galaxy-1.0.1.zip](https://irida.corefacility.ca/downloads/snvphyl-galaxy/snvphyl-galaxy-1.0.1.zip)
* Galaxy Tools - [suite_snvphyl_1_0_1](https://irida.corefacility.ca/galaxy-shed/view/nml/suite_snvphyl_1_0_1/4841b7148c44)
* Galaxy Workflows
......@@ -37,7 +37,7 @@ Released on **May 25, 2016**.
Install
-------
* Docker - `apetkau/snvphyl-galaxy-1.0`
* Docker - `phacnml/snvphyl-galaxy-1.0`
* Virtual Machine - [snvphyl-galaxy-1.0.zip](https://irida.corefacility.ca/downloads/snvphyl-galaxy/snvphyl-galaxy-1.0.zip)
* Galaxy Tools - [suite_snvphyl_1_0_0](https://irida.corefacility.ca/galaxy-shed/view/nml/suite_snvphyl_1_0_0/4e41de612a14)
* Galaxy Workflows
......@@ -67,7 +67,7 @@ Released on **November 13, 2015**.
Install
-------
* Docker - `apetkau/snvphyl-galaxy-0.3`
* Docker - `phacnml/snvphyl-galaxy-0.3`
* Virtual Machine - [snvphyl-galaxy-0.3.zip](https://irida.corefacility.ca/downloads/snvphyl-galaxy/snvphyl-galaxy-0.3.zip)
* Galaxy Tools - [suite_snvphyl_0_3_0](https://irida.corefacility.ca/galaxy-shed/view/nml/suite_snvphyl_0_3_0/bb2e651149da)
* Galaxy Workflow - [SNVPhyl Paired-End 0.3](../workflows/SNVPhyl/0.3/snvphyl-workflow-0.3.ga) and [SNVPhyl Paired-End 0.3 (invalid-positions)](../workflows/SNVPhyl/0.3/snvphyl-workflow-0.3-invalid-positions.ga)
......@@ -89,7 +89,7 @@ Released on **September 21, 2015**.
Install
-------
* Docker - `apetkau/snvphyl-galaxy:0.2-beta-1`
* Docker - `phacnml/snvphyl-galaxy-0.2-beta-1`
* Virtual Machine - [snvphyl-galaxy-0.2-beta-1.zip](https://irida.corefacility.ca/downloads/snvphyl-galaxy/snvphyl-galaxy-0.2-beta-1.zip)
* Galaxy Tools - [suite_snvphyl_0_2_0](https://irida.corefacility.ca/galaxy-shed/repository?repository_id=8cbe70cdff6b156a&changeset_revision=9c9c6f7e0d43)
* Galaxy Workflow - [SNVPhyl Paired-End 0.2](../workflows/SNVPhyl/0.2/snvphyl-workflow-0.2.ga) and [SNVPhyl Paired-End 0.2 (invalid-positions)](../workflows/SNVPhyl/0.2/snvphyl-workflow-0.2-invalid-positions.ga)
......
......@@ -43,7 +43,7 @@ Please see <http://snvphyl.readthedocs.io/en/latest/install/virtualmachine/> for
A [Docker][] image of SNVPhyl and Galaxy can be launched by running:
```bash
docker run -d -p 48888:80 apetkau/snvphyl-galaxy-1.0.1
docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1
```
Galaxy and SNVPhyl can then be access through <http://localhost:48888> with username `admin@galaxy.org` and password `admin`.
......
......@@ -9,7 +9,7 @@ Usage
Before running this image, please make sure [Docker][] is installed. Once Docker is installed, please run:
```bash
docker run -d -p 48888:80 apetkau/snvphyl-galaxy-1.0
docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1
```
This will download an instance of the SNVPhyl Galaxy image from [Docker Hub](https://hub.docker.com/) and run this image. Galaxy will be accessible on your local machine at http://localhost:48888. This will take a while to load, especially if it is the first time running.
......
#Galaxy - SNVPhyl
#
# VERSION 1.0
FROM phacnml/snvphyl-galaxy-0.2-beta-1:0.2-beta-1
MAINTAINER Aaron Petkau, aaron.petkau@gmail.com
# Set `allow_library_path_paste` to allow for linking to files within Docker Galaxy.
RUN sed -i -e 's/^#allow_library_path_paste.*/allow_library_path_paste = True/' /etc/galaxy/galaxy.ini
#Galaxy - SNVPhyl
#
# VERSION 1.0
FROM phacnml/snvphyl-galaxy-0.3:0.3
MAINTAINER Aaron Petkau, aaron.petkau@gmail.com
# Set `allow_library_path_paste` to allow for linking to files within Docker Galaxy.
RUN sed -i -e 's/^#allow_library_path_paste.*/allow_library_path_paste = True/' /etc/galaxy/galaxy.ini
#Galaxy - SNVPhyl
#
# VERSION 1.0
FROM phacnml/snvphyl-galaxy-1.0.1:1.0.1
MAINTAINER Aaron Petkau, aaron.petkau@gmail.com
# Set `allow_library_path_paste` to allow for linking to files within Docker Galaxy. Remove `--shared` so Docker does not oversubscribe jobs.
RUN sed -i -e 's/^#allow_library_path_paste.*/allow_library_path_paste = True/' /etc/galaxy/galaxy.ini && \
sed -i -e 's/ --share//' /etc/galaxy/job_conf.xml
#Galaxy - SNVPhyl
#
# VERSION 1.0
FROM phacnml/snvphyl-galaxy-1.0:1.0
MAINTAINER Aaron Petkau, aaron.petkau@gmail.com
# Set `allow_library_path_paste` to allow for linking to files within Docker Galaxy. Remove `--shared` so Docker does not oversubscribe jobs.
RUN sed -i -e 's/^#allow_library_path_paste.*/allow_library_path_paste = True/' /etc/galaxy/galaxy.ini && \
sed -i -e 's/ --share//' /etc/galaxy/job_conf.xml
This directory contains `Dockerfile`s for minor updates to the snvphyl-galaxy Docker images.
......@@ -20,7 +20,7 @@ This assumes that both Python and [Docker][] are installed. If Docker requires
Alternatively, the Docker instance can be launched directly with:
```bash
docker run -d -p 48888:80 apetkau/snvphyl-galaxy-1.0.1
docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1
```
Once running, SNVPhyl/Galaxy can be accessed from <http://localhost:48888> with username `admin@galaxy.org` and password `admin`. Please see [Usage][] and [Installation][] for more details.
......
......@@ -15,13 +15,13 @@ Running SNVPhyl
Once Docker is installed, the latest version of SNVPhyl can be downloaded and run with:
```bash
docker run -d -p 48888:80 apetkau/snvphyl-galaxy-1.0.1
docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1
```
This will download and run a docker image with SNVPhyl and Galaxy. By default this will **not persist** data run through SNVPhyl after Docker has been shutdown. To permanently store this data, please run:
```bash
docker run -d -p 48888:80 -v /home/user/galaxy_storage/:/export/ apetkau/snvphyl-galaxy-1.0.1
docker run -d -p 48888:80 -v /home/user/galaxy_storage/:/export/ phacnml/snvphyl-galaxy-1.0.1
```
Where `/home/user/galaxy_storage` as a location where files will be persisted between Docker runs. For more information on how this works, see the [Galaxy Docker][] page.
......@@ -45,7 +45,7 @@ This will show a list of all running docker containers, similar to:
```
CONTAINER ID IMAGE ...
0d56c773a972 apetkau/snvphyl-galaxy-1.0.1 ...
0d56c773a972 phacnml/snvphyl-galaxy-1.0.1 ...
```
This shows all running docker containers and a unique container id. To shutdown the docker container, please use this container id and run the below command.
......
......@@ -10,7 +10,7 @@ To both install Docker and get SNVPhyl, please run:
```bash
curl -sSL https://get.docker.com/ | sh # Installs Docker
docker run -t -p 48888:80 apetkau/snvphyl-galaxy-1.0.1 # Downloads and runs SNVPhyl and Galaxy
docker run -t -p 48888:80 phacnml/snvphyl-galaxy-1.0.1 # Downloads and runs SNVPhyl and Galaxy
```
This will install Docker, download the SNVPhyl Galaxy docker image, and run this image in a Docker container. This will take a while to fully download and start up. You may have to start the `docker` service after installation for Docker to work. This should be a command like `sudo service docker start`, or `sudo systemctl start docker` depending on your system. See the [Docker Install][] guide for more details.
......
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