Installing miARma in Windows using docker.
Docker allows you to package an application with all of its dependencies into a standardized unit for software development called containers. miARmaSeq is available in four different cointainers from four different linux Flavours:
To use miARmaSeq from a docker container, you need to follow these two steps:
- Install Docker for Windows. A detailed installation instruction guide is provided in docker's webpage.
- Download a miARmaSeq container using three simple steps:
1. Once docker has been installed, you will be able to download the latest miARma docker image, but invoking the following command:
$>docker search miarmaseq
You will see something like:
NAME DESCRIPTION STARS OFFICIAL AUTOMATED
miarmaseq/fedora miARma software ready to use in latest Fedora 0
miarmaseq/debian miARma software ready to use in latest Debian 0
miarmaseq/ubuntu miARma software ready to use in latest Ubuntu 0
miarmaseq/centos miARma software ready to use in latest Centos 0
2. Download the image for the Linux you prefer, we will use Ubuntu for this example:
$>docker run -t -i -u miARma miarmaseq/Ubuntu /bin/bash
The output of the above command will print the following:
Unable to find image 'miarmaseq/ubuntu:latest' locally
latest: Pulling from miarmaseq/ubuntu
5a132a7e7af1: Pull complete
fd2731e4c50c: Pull complete
28a2f68d1120: Pull complete
a3ed95caeb02: Pull complete
e65fc194676d: Pull complete
4b9388360b01: Pull complete
f52ea2e105b0: Pull complete
9b542f69b796: Pull complete
b4404181ac75: Pull complete
3565047a5ad2: Pull complete
6486f53a2d11: Pull complete
aa0334d9aaab: Pull complete
eeca8bd80007: Pull complete
Digest: sha256:823c4dfed917d9ad69ea42e8f90cd481c695d1842317e6ad89f2c1cd0063ce5f
Status: Downloaded newer image for miarmaseq/ubuntu:latest
miARma@Ubuntu:~$
3. Once you are login in the Ubuntu machine, you can try miARmaSeq by executing the miARma binary:
[miARma@Ubuntu ~]$ cd miARma/
[miARma@Ubuntu miARma]$ ./miARma
#########################################################################
# miARma, miRNA and RNASeq Multiprocess Analysis #
# miARma v 1.7 (Aug-2017) #
# #
# Created at Computational Biology and Bioinformatics Group (CbBio) #
# Institute of Biomedicine of Seville. IBIS (Spain) #
# Modified and Updated at Bioinformatics Unit at IPBLN-CSIC #
# Institute for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC). #
# Granada (Spain) #
# Copyright (c) 2017 IBIS & IPBLN. All rights reserved. #
# mail : miARma-devel@cbbio.es #
#########################################################################
Usage:
perl ./miARma file.ini [options]
Options:
-check Instead of running the analysis contained in file.ini, it checks that parameters are correct and then quits.
-help Print this help.
[miARma@Ubuntu miARma]$
Installing miARma in Windows from a image:
miARmaSeq is also available in windows using a virtualized system. It contais miARmaSeq itselfs and provides a virtualized linux operative system. To use miARmaSeq from a image, you need to follow these three steps:
- 1. Install a virtualizer (we recommend the following free softwares):
- 2. Download the image file from this link.
- 3. Import the downloaded file with your virtualizer software.
| a) Use this video to import a ova file using VirtualBox. |
b) Use this video to import a ova file using VMWare. |
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Once the ova file has been imported, you can use it pressing the start button. You will see a virtualized linux where you need to:
| a) Press Log In. |
b) Change to miARmaSeq directory and execute the binary. |
c) You will see miARmaSeq help. |
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Once miARmaSeq has been correctly installed using any of the proposed method, continue to next section to see how miARmaSeq works.
