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Kez Cleal edited this page Mar 25, 2023 · 16 revisions

Installing GW on Android

This is a guide to installing GW on your android phone/tablet. Basically we will be adding a Linux desktop environment (DE) to your device so you can potentially use other bioinformatics tools, not just GW!

Prerequisites

  • Termux - a terminal emulator. Get this from the fdroid repository
  • VNC Viewer - this is the screen sharing tool for your Linux DE

Installation

GW can be installed using the package manager

  • Open the termux app
  • Update the package manager and grab GW
pkg update -y # select default options when prompted
pkg install -y x11-repo
pkg install -y gw aterm tigervnc

The following are recommended to use GW interactively, but not essential: 

pkg install -y xfce4 vim kitty

Usage

  • Start the vncserver in termux app. This will enable screen sharing with your VNC Viewer app. You will be asked to set a password!

vncserver -localhost

You should see a message like New 'localhost:1 ()' desktop is localhost:1. This is telling you that the screen is hosted at display :1, so the connection port will (normally) be 5901.

  • Open VNC Viewer. Add a new connection to 127.0.0.1:5901 and type in password.

You will see an aterm terminal window. It is possible to run GW from here, although it's worth going an extra step and starting xfce for a full linux desktop. Type this into the aterm window: 

xfce4-session &

You should now see a Linux desktop environment, with access to kitty - a nicer terminal than aterm (see top-left menu Applications -> System -> Kitty). Kitty also works well for accessing data on remote servers using your Android device.

  • To access files outside of termux on the device, run termux-setup-storage in termux and allow file permissions. You can then connect external hard drives, for example.

Testing

To test gw, you can use any bam file with its reference fasta file. A test bam and fasta can be downloaded by cloning gw from github.

pkg install git
git clone https://github.com/kcleal/gw.git

These files are found in the gw/test directory, and can be viewed with.

cd gw/test
gw -r chr1 -b test.bam test.fa

Next steps

The gw config file currently ends up in an obscure location. To get gw to read it copy it to your home directory using cp $PREFIX/share/doc/gw/gw.ini ~.

You can also save yourself some typing every session by editing .bashrc.

If you dont have .bashrc in your termux home directory, copy the one from cp $PREFIX/etc/bash.bashrc ~/.bashrc.

Add this to your .bashrc:

alias vnc="vncserver -geometry 1920x1080 -localhost"
alias desktop="xfce4-session &"

Now, typing vnc in termux will launch the vncserver. When you open your VNC Viewer, typing desktop will start an xfce4 session.

Debugging

  • Check to see what vncservers are already running using vncserver -list. You can kill a server by using vncserver -kill :1, for example.
  • You may have an x11 lock file located in $PREFIX/tmp, remove this might help rm -rf $PREFIX/tmp/.X*

Useful links to aid with debugging:

https://wiki.termux.com/wiki/Building_packages https://wiki.termux.com/wiki/Termux-setup-storage https://wiki.termux.com/wiki/Graphical_Environment

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