deploy_file_archive.sh

#!/bin/bash
# Create software file archive needed for shotgun pipeline deployment.
#
# For software downloaded as source, this script creates an executable
# and re-zips the results.
#
# This script does not download data files for deployment.  The
# deployment script expects the data files to be available from the
# same directory as the software files.
#
# Data files expected by the deployment script:
#  - hg38.zip (Human genome in FASTA format)
#  - phix.zip (Phi X 174 genome in FASTA format)
#  - kegg.zip (KEGG protein database in FASTA format)
set -x
set -e


## STEP 2: Quality control

# Trimmomatic
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip

# FastQC
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip

# seqtk
wget https://github.com/lh3/seqtk/archive/4feb6e8144.zip
mv 4feb6e8144.zip seqtk_4feb6e8144.zip


## STEP 3: Decontamination

# Bowtie2
wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/bowtie2-2.2.6-linux-x86_64.zip

# Bwa
wget http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.12.tar.bz2
tar xvjf bwa-0.7.12.tar.bz2
zip -r bwa-0.7.12.zip bwa-0.7.12
rm bwa-0.7.12.tar.bz2
rm -R bwa-0.7.12


## STEP 4: Taxonomic assignment

# MetaPhlan2
wget https://bitbucket.org/biobakery/metaphlan2/get/61ad257cc091.zip
mv 61ad257cc091.zip metaphlan2_61ad257cc091.zip


## STEP 5: Functional assignment

# RAPSearch2
wget http://sourceforge.net/projects/rapsearch2/files/RAPSearch2.23_64bits.tar.gz
tar xvzf RAPSearch2.23_64bits.tar.gz
zip -r RAPSearch2.23_64bits.zip RAPSearch2.23_64bits
rm RAPSearch2.23_64bits.tar.gz
rm -R RAPSearch2.23_64bits