Computational-Plant-Science/DIRT:latest
$ singularity pull shub://Computational-Plant-Science/DIRT:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%help
Container for running DIRT 1.1 - An automatic highthroughput root phenotyping platform
(c) 2014 Alexander Bucksch - bucksch@uga.edu
Web application by Abhiram Das - abhiram.das@gmail.com
Singularity container by Chris Cotter - cotter@uga.edu
http://dirt.iplantcollaborative.org
University of Georgia
------------------------------------------------------------
Program usage: python main.py (please configure the program with the options.csv file)
<run file path> full path to file with the root image
<unique id> ID which will be a folder name in the working directory. Integer value needed
<mask threshold> multiplier for the automatically determined mask threshold. 1.0 works fine and is default. If flashlight is used, the 0.6 is a good choice.
<excised root> 1 - excised root analysis is on, 0 - excised root analysis is off
<crown root> 1 - crown root analysis is on, 0 - crown root analysis is off
<segmentation> 1 - is on, 0 - is off
<marker diameter> a simple decimal e.g. 25.4. If 0.0 is used, then the output will have pixels as unit.
<stem reconstruction> 1 - reconstruction is turned on, 0 - reconstruction is turned off
<plots> 1 - plotting data is stored, 0 - plotting data is not stored
<output format> 1 - the full trait set is put into one excel file containing empty cells for traits that were not computed, 0 - only computed files are written to the output file
<working directory> full path to folder were the result is stored
<trait file path> full path to .csv file containing the traits to be computed
Example:
singularity run DIRT.simg /Documents/image_name.jpg 8 25.0 1 1 1 25.1 0 0 0 /Documents/image_folder/ /Documents/traits.csv
%labels
Maintainer Chris Cotter
Version v1.0
%post
# Required for graph-tools
apt-key adv --keyserver pgp.skewed.de --recv-key 612DEFB798507F25
echo 'deb http://downloads.skewed.de/apt/xenial xenial universe' | tee -a /etc/apt/sources.list
echo 'deb-src http://downloads.skewed.de/apt/xenial xenial universe' | tee -a /etc/apt/sources.list
apt-get update
apt-get -y install git python2.7 python-pip python-graph-tool
cd /opt
git clone git://github.com/Computational-Plant-Science/DIRT.git
cd /opt/DIRT
sed -i 's#/usr/local/bin/zbarimg#/usr/bin/zbarimg#' /opt/DIRT/DirtOcr/__init__.py
pip install -r /opt/DIRT/requirements.txt
#cleanup
apt-get clean
apt-get purge
%environment
export LC_ALL=C #Required for pip to run correctly
export DISPLAY=:0 #Addresses "Failed to connect to Mir:" error
%runscript
python /opt/DIRT/main.py "$@"
Collection
- Name: Computational-Plant-Science/DIRT
- License: Other
View on Datalad
Metrics
key | value |
---|---|
id | /containers/Computational-Plant-Science-DIRT-latest |
collection name | Computational-Plant-Science/DIRT |
branch | master |
tag | latest |
commit | 52c477b4cc9a99cdda01d1b84a90eb616b734224 |
version (container hash) | 42e4a2b1dbf881441a90a72c39a166bc |
build date | 2020-12-22T03:59:28.608Z |
size (MB) | 1288 |
size (bytes) | 477188127 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.