BeeDeeM-Tools: making easy sequence-based data analysis pipelines

What for?

This project is a suite of command-line tools that can be used to setup a sequence annotation pipeline.

It provides:

• a tool to cut large sequence files into smaller ones (i.e. slice or page of sequences)
• a tool to index sequence (Fasta, Genbank, Genpept, ENA, EMBL, Uniprot and related)
• a tool to query index and get back only sequences of interest
• a tool to run PLAST high-performance sequence comparison tool
• a tool to export legacy NCBI BLAST XML results (BLAST or PLAST) as CSV files

All these tools are suited to handle the annotation data available from annotated databanks, among others: NCBI Taxonomy Gene Ontology, InterPro and Enzyme Commission classifications.

BeeDeeM-Tools is a suite of extensions to BeeDeeM.

Requirements

• Linux or macOS 64bits computer.
• Java Runtime 1.8+ from Oracle.

Use a Java Virtual Machine 1.8 (or above) from Oracle.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.

Installation

Check your JVM first

On a command-line simply type:

java -version

An Oracle JVM will display this line:

Java HotSpot(TM) 64-Bit Server VM

You do not see that line? Do not go further: we do not guarantee BeeDeeM-Tools be compatible with OpenJDK, gcj, etc.

Procedure

On a command-line simply type the following lines:

cd <where-you-want-to-install-the-software>
mkdir beedeem-tools-2.0.0
cd beedeem-tools-2.0.0
wget https://cloud.ifremer.fr/index.php/s/WQGxuP7bbbA5mFH/download -O beedeem-tools-2.0.0.tar.gz
gunzip beedeem-tools-2.0.0.tar.gz
tar -xf beedeem-tools-2.0.0.tar
rm beedeem-tools-2.0.0.tar
chmod +x *.sh

That's all folks!

Let's do a little check that software is working fine:

./test.sh -w /tmp/bdm-tools

This will run a complete test of all BeeDeeM-Tools.

When done (and test ok), have a look a the /tmp/bdm-tools directory. You can review what happened when using the BeeDeeM-Tools. That temporary directory can then be deleted.

User manual

Please refere to directory "documentation" of this project and read the tutorial.

License and dependencies

BeeDeeM-Tools itself is released under the GNU Affero General Public License, Version 3.0. AGPL

It depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.

-- (c) 2018-20 - Patrick G. Durand, Ifremer