Package Information

Development year: 2013

Authors:

Tatyana Goldberg goldberg@rostlab.org
Maximilian Hecht hecht@rostlab.org
Tobias Hamp hampt@rostlab.org
Burkhard Rost rost@rostlab.org

Programming language: Perl

Methodology used:

The method predicts three localization classes in Archaea, six in Bacteria, and 18 in Eukaryota.
Incorporation of annotation by sequence homology (PSI-BLAST searches)
Printable SVM probability scores along the prediction path of a LocTree2 tree

On Elixir Registry: Loctree3 (this tool) and Loctree2 (the older previous method; note, these versions do not match with the repository ones).

Installation

Required environment: you need a Debian repository (tested on Wheezy (7)) or Ubuntu repository (tested on 14). You can also run the prepared Docker image.

To install this package, execute the following commands:

git clone git@github.com:Rostlab/LocTree3.git
cd LocTree3
aclocal && autoconf && autoheader; automake --add-missing
./configure --prefix=$(pwd)/install
make && make install

loctree3 executable will be in LocTree3/install/bin

Note: make sure to have the following packages installed:

Dependencies

Debian packages

Install: automake make libconfig-inifiles-perl pp-popularity-contest

blastpgp

To use loctree3 it is necessary to have blastpgp, which can be obtained by downloading the package blast-2.2.26 for the corresponding platform from the following FTP: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/

For example for a Linux x64 architecture it can be installed with the following commands:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/blast-2.2.26-x64-linux.tar.gz
tar xf blast-2.2.26-x64-linux.tar.gz
echo -e "[NCBI]\nData=$(pwd)/blast-2.2.26/data/" > ~/.ncbirc

The location of the blastpgp binaries must also be added tho the PATH environment variable:

export PATH=$PATH:$(pwd)/blast-2.2.26/bin

Usage

For example:

cd LocTree3/install/bin
./loctree3 -i ../share/doc/loctree3/examples/arch/ --resfile ./arch_output.lc3 --domain arch

will generate the output file arch_output.lc3 with the predicted sub-cellular localization

Reading the man page of loctree3, which offers additional information, can be done the following way:

MANPATH=LocTree3/install/share/man/ man loctree3

Docker

Alternatively, the following docker recipe will create a working machine:

FROM ubuntu:14.04
RUN apt-get -y update && apt-get install -y wget unzip automake make libconfig-inifiles-perl pp-popularity-contest
RUN wget -q https://github.com/Rostlab/LocTree3/archive/develop.zip && unzip -q develop.zip
RUN cd LocTree3-develop && aclocal && autoconf && autoheader; automake --add-missing && ./configure && make && make install
RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/blast-2.2.26-x64-linux.tar.gz && tar xf blast-2.2.26-x64-linux.tar.gz
RUN /bin/echo -e "[NCBI]\nData=/blast-2.2.26/data/" > ~/.ncbirc && /bin/echo -e "export PATH=$PATH:/blast-2.2.26/bin" >> ~/.bashrc

To build the docker image put these previous lines in a file called Dockerfile and then run

docker build -t loctree-docker .

After the building is done you can open a bash shell in the docker image by executing:

docker run -ti loctree-docker /bin/bash

On this virtual image loctree can be used immediately by running for example:

loctree3 -i /usr/local/share/doc/loctree3/examples/arch/ --resfile ./arch_output.lc3 --domain arch