SeqGrapheR

SeqGrapheR is a program for vizualization and exploration of sequence based graphs generated in RepeatExplorer output. More information about RepeatExplorer can be found on http://repeatexplorer.org/

Introduction to SeqGrapheR can be found in vignette (obsolete).

Installation

SeqGrapheR requires program ggobi (http://www.ggobi.org/docs/) installed.

For full functionality, SeqGrapheR needs also the following programs installed:

• Staden (http://staden.sourceforge.net/)
• Dotter (https://www.sanger.ac.uk/science/tools/seqtools)
• legacy NCBI blast (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/)

In Debian/Ubuntu based linux distributions, the above programs can be installed using:

sudo apt-get -y install ncbi-blast+-legacy acedb-other-dotter staden ggobi

R programming environment and some dependencies can be installed using:

sudo apt-get -y install r-base libcurl4-openssl-dev libxml2-dev libgtk2.0-dev libssl-dev build-essential gfortran libblas-dev liblapack-dev

Installation requires R package devtools and Bioconductor package Biostrings. Start R session in terminal and install R packages:

# install devtools:
install.packages("devtools")
# install biostrings:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")
library(devtools)
install_github("kavonrtep/SeqGrapheR")

Note the installation of SeqGrapheR fails because packages gWidgets, gWidgetsRGtk2 and rggobi are not supported by your R version, you can try to install these packages manually from archived packages:

install_version("gWidgets", version = "0.0-54.1", repos = "http://cran.us.r-project.org")
install_version("gWidgetsRGtk2", version = "0.0-86", repos = "http://cran.us.r-project.org")
install_version("rggobi", version = "2.1.22", repos = "http://cran.us.r-project.org")

Alternative installation using Singularity container

This is the simplest way how to run SeqGrapheR. Singularity can be installed either from source (see installation guide https://sylabs.io/guides/latest/user-guide/) or it can be installed using conda:

conda install -c conda-forge singularity=3.6.3

Then, run SeqGrapheR use command:

singularity run shub://kavonrtep/SeqGrapheR

With the above command you can automatically access data in you home directory. If you need to work with data which are not located in your home directory use the command:

singularity run -B /path_to_you_data_directory:/data shub://kavonrtep/SeqGrapheR

this way the local directory /path_to_you_data_directory will be bind to directory /data in singularity container.

Alternative installation using conda

R packages and dependencies can be installed using conda.

conda create -n seqgrapher -c petrnovak -c iuc -c conda-forge -c bioconda -c pkgw-forge r-seqgrapher

activate seqgrapher environment using:

conda activate seqgrapher

programs Staden and dotter are not available in Anaconda repository and must be installed from linux distrubution repository. In Debian/Ubuntu based linux distributions, you can use command

sudo apt-get -y install acedb-other-dotter staden 

Alternative installation using Windows Subsystem for Linux (WSL)

Because SeqGrapheR has a graphical user interface you will probably need to set up xrdp to Remote Desktop onto the linux virtual machine. There is a guide here to do that: https://dev.to/darksmile92/linux-on-windows-wsl-with-desktop-environment-via-rdp-522g

One of the comments from the link above suggests these steps. Open WSL and run:

sudo apt-get install xrdp
sudo apt-get install xfce4
sudo apt-get install xfce4-goodies
sudo cp /etc/xrdp/xrdp.ini /etc/xrdp/xrdp.ini.bak
sudo sed -i 's/3389/3390/g' /etc/xrdp/xrdp.ini
sudo sed -i 's/max_bpp=32/#max_bpp=32\nmax_bpp=128/g' /etc/xrdp/xrdp.ini
sudo sed -i 's/xserverbpp=24/#xserverbpp=24\nxserverbpp=128/g' /etc/xrdp/xrdp.ini
echo xfce4-session > ~/.xsession

You’ll then need to edit the /// file. You can use any command-line editor to do this, e.g. nano.

sudo nano /etc/xrdp/startwm.sh

Comment out these lines:

#test -x /etc/X11/Xsession && exec /etc/X11/Xsession
#exec /bin/sh /etc/X11/Xsession

And add these lines to the bottom of the file:

# xfce
startxfce4

Once that’s set up you should be able to run the command below and use Remote Desktop to connect to your virtual machine.

sudo /etc/init.d/xrdp start

Remote Desktop to th virtual machine (localhost:3390) and open a terminal. Before you can continue with the install you’ll need to check if the PKG_CONFIG_PATH environment variable is set. If not, set it to “usr/lib/pkgconfig”.

echo $PKG_CONFIG_PATH
export PKG_CONFIG_PATH=/usr/lib/pkgconfig

When you launch R you can check if this environment variable is set correctly with the following line:

Sys.getenv("PKG_CONFIG_PATH")

NOTE: If running R with the sudo command you’ll want to use the -E option to preserve environment variables.

The following commands will get SeqGrapheR up and running:

sudo apt-get -y install r-base ncbi-blast+-legacy acedb-other-dotter staden ggobi libcurl4-openssl-dev libxml2-dev libgtk2.0-dev libssl-dev build-essential gfortran libblas-dev liblapack-dev

sudo -E R
Sys.getenv("PKG_CONFIG_PATH")
install.packages("devtools")
install.packages("BiocManager")
BiocManager::install("Biostrings")
library(devtools)
install_version("gWidgets", version = "0.0-54.1", repos = "http://cran.us.r-project.org")
install_version("gWidgetsRGtk2", version = "0.0-86", repos = "http://cran.us.r-project.org")
install_version("rggobi", version = "2.1.22", repos = "http://cran.us.r-project.org")
install_github("kavonrtep/SeqGrapheR")
SeqGrapheR()

How to run SeqGrapheR

In terminal window start R environment. In R session run:

library(SeqGrapheR)
# start GUI:
SeqGrapheR()