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# singularity_hub
[![https://www.singularity-hub.org/static/simg/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2878)
Singularity Container Registry made by [BEV](https://www.cefe.cnrs.fr/fr/recherche/bc/bev) team
\ No newline at end of file
# bioinfo_singularity_recipes
Singularity recipies for bioinformatic pipelines
GUERIN Pierre-Edouard, 2019-05-05
______
We provide ready to run versions of [Singularity containers](https://www.sylabs.io/)
# 1 Singularity containers
## 1.1 Install Singularity
See [https://www.sylabs.io/docs/](https://www.sylabs.io/docs/) for instructions to install Singularity.
## 1.2 Obitools
- The [OBITools package 1.0](http://metabarcoding.org/obitools) is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information.
- [ecoPrimers 1.0.1](https://git.metabarcoding.org/obitools/ecoprimers/) is a software that finds primers from a set of sequences.
- [ecoPCR 0.5](https://git.metabarcoding.org/obitools/ecopcr/) simulate _in silico_ PCR digestion.
### 1.2.1 Download the Obitools container
```
singularity pull --name obitools.simg shub://Grelot/bioinfo_singularity_recipes:obitools
```
Alternatively, if you're using the [Montpellier Bioinformatics Biodiversity platform](https://mbb.univ-montp2.fr/MBB/index.php), download this custom container :
```
singularity pull --name obitools.simg shub://Grelot/bioinfo_singularity_recipes:obitoolsmbb
```
### 1.2.2 Run the Obitools container
```
singularity run obitools.simg
```
it should output:
```
Opening container...ubuntu xenial: OBITOOLS,ecoPRIMERS,ecoPCR
```
### 1.2.3 Execute some programs from the container
```
## OBITOOLS: illuminapairedend
singularity exec obitools.simg illuminapairedend --help
## OBITOOLS: ngsfilter
singularity exec obitools.simg ngsfilter --help
## OBITOOLS: obigrep
singularity exec obitools.simg obigrep --help
## OBITOOLS: obiclean
singularity exec obitools.simg obiclean --help
## OBITOOLS: ecotag
singularity exec obitools.simg obiclean --help
## ecoPCR
singularity exec obitools.simg ecoPCR --help
## ecoPrimers
singularity exec obitools.simg ecoPrimers --help
```
## 1.3 Useful programs for eDNA analysis
- [vsearch 2.13.4](https://github.com/torognes/vsearch) supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
- [pear 0.9.11](https://cme.h-its.org/exelixis/web/software/pear/) is an ultrafast, memory-efficient and highly accurate pair-end read merger
- [fastq-join 1.3.1](https://github.com/brwnj/fastq-join) joins two paired-end reads on the overlapping ends.
- [pandaseq 2.11](https://github.com/neufeld/pandaseq) aligns Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
- [jellyfish 2.2.6](https://github.com/gmarcais/Jellyfish) reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts.
- [casper 0.8.2](http://best.snu.ac.kr/casper/) (Context-Aware Scheme for Paired-End Read) is state-of-the art paired-end reads merging tool.
- [FLASh 1.2.11](http://ccb.jhu.edu/software/FLASH/index.shtml) (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.
- [fastq-multx](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMultx.md) 1.3.1 demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields.
- [cutadapt 2.3](https://cutadapt.readthedocs.io/en/stable/guide.html) removes adapter sequences from high-throughput sequencing reads.
- [SWARM 2.2.2](https://github.com/torognes/swarm) performs clustering method for amplicon-based studies.
- [Reaper 13.274](https://www.ebi.ac.uk/research/enright/software/kraken) is a program for demultiplexing, trimming and filtering short read sequencing data. It can handle barcodes, trim adapter sequences, strip low quality bases and low complexity sequence, and has many more features.
- [TAGcleaner 0.16](http://tagcleaner.sourceforge.net/) detects and trims tag sequences from sequence data.
- [Flexbar 3.0.3](https://github.com/seqan/flexbar) preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included.
- [usearch 11.0.667](https://www.drive5.com/usearch/) offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
- [deML 1.0](https://grenaud.github.io/deML/) demultiplexes Illumina sequences.
### 1.3.1 Download the eDNA analysis container
```
singularity pull --name ednatools.simg shub://Grelot/bioinfo_singularity_recipes:ednatools
```
Alternatively, if you're using the [Montpellier Bioinformatics Biodiversity platform](https://mbb.univ-montp2.fr/MBB/index.php), download this custom container :
```
singularity pull --name ednatools.simg shub://Grelot/bioinfo_singularity_recipes:ednatoolsmbb
```
### 1.3.2 Run the eDNA analysis container
```
singularity run ednatools.simg
```
it should output:
```
Opening container...ubuntu beaver: vsearch, PEAR, fastq-join, pandaseq, jellyfish, casper, FLASH, fastq-multx, cutadapt, SWARM, REAPER, tally, minion, swan, tagCleaner, flexbar, usearch, deML
```
### 1.3.3 Execute some programs from the container
```
## vsearch
singularity exec ednatools.simg vsearch -h
## pear
singularity exec ednatools.simg pear -h
## pandaseq
singularity exec ednatools.simg pandaseq -h
## casper
singularity exec ednatools.simg casper -h
## FLASh
singularity exec ednatools.simg flash -h
## fastq-multx
singularity exec ednatools.simg fastq-multx -h
## fastq-join
singularity exec ednatools.simg fastq-join -h
## cutadapt
singularity exec ednatools.simg cutadapt -h
## SWARM
singularity exec ednatools.simg swarm -h
## Reaper
singularity exec ednatools.simg reaper -h
singularity exec ednatools.simg tally -h
singularity exec ednatools.simg minion -h
## TAGcleaner
singularity exec ednatools.simg tagcleaner -h
## Flexbar
singularity exec ednatools.simg flexbar -h
## usearch
singularity exec ednatools.simg usearch
## deML
singularity exec ednatools.simg deML -h
```
## 1.4 R for metabarcoding analysis
This recipe have been written thanks to [RPACIB](https://shiny.mbb.univ-montp2.fr/RPACIB/)
R with useful packages for metabarcoding analysis
- [R 3.6.0](https://cran.r-project.org/)
- `R-packages` tidyverse, rlang, dada2, seqRFLP, phyloseq
Download the container
```
singularity pull --name ednaR.simg shub://Grelot/bioinfo_singularity_recipes:ednar
```
Run R from the container
```
singularity shell ednaR.simg
R
```
or
```
singularity exec ednaR.simg R
```
## 1.5 Grinder
Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
- [Grinder 0.5.3](https://github.com/zyxue/biogrinder)
- [bioperl 5.22.1](https://bioperl.org/)
Download the container and run Grinder from the container
```
singularity pull --name grinder.simg shub://Grelot/bioinfo_singularity_recipes:grindermbb
singularity exec grinder.simg grinder -h
```
ednaR/Singularity.ednaR 0 → 100644
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Bootstrap: docker
From: ubuntu:16.04
IncludeCmd: yes
%environment
R_VERSION=3.6.0
export R_VERSION
R_CONFIG_DIR=/etc/R/
export R_CONFIG_DIR
export PATH=/opt/conda/bin:$PATH
export PATH=/opt/biotools/bin:$PATH
export ROOTSYS=/opt/biotools/root
export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
export PATH=/opt/workflows/bin:$PATH
%labels
MAINTAINER Pierre-Edouard_GUERIN
INSTITUTE CNRS
TEAM Biogeographie_Ecologie_Vertebres
BUILD 1.0
BUILD_DATE 2019 juin 19
SINGULARITY_VERSION 2.4.2-dist
R 3.6.0
R_PACKAGES tidyverse.rlang.dada2.seqRFLP.phyloseq.devtools
%post
apt-get update
apt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl
apt-get install -y gcc fort77 aptitude
aptitude install -y g++ xorg-dev libreadline-dev gfortran
apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev git
apt-get update
############### Install R From Source ##############
cd $HOME
wget https://cran.rstudio.com/src/base/R-3/R-3.6.0.tar.gz
tar xvf R-3.6.0.tar.gz
cd R-3.6.0
./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes
make
make install
############### Install CRAN Package ##############
R --slave -e "install.packages( c('tidyverse', 'rlang','devtools'), repos='https://cloud.r-project.org')"
############### Install Github Package ##############
R --slave -e "devtools::install_github(c('benjjneb/dada2','helixcn/seqRFLP','joey711/phyloseq'))"
apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev
apt-get update
echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ./miniconda.sh && \
/bin/bash ./miniconda.sh -b -p /opt/conda && \
rm ./miniconda.sh
TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
dpkg -i tini.deb && \
rm tini.deb && \
apt-get clean
if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
chmod 777 -R /opt/biotools/
export PATH=/opt/biotools/bin:$PATH
chmod 777 -R /opt/conda/
export PATH=/opt/conda/bin:$PATH
conda config --add channels bioconda
conda upgrade conda
if [ ! -d "/opt/workflows" ];then mkdir /opt/workflows; fi
if [ ! -d "/opt/workflows/bin" ];then mkdir /opt/workflows/bin; fi
chmod 777 -R /opt/workflows/
export PATH=/opt/workflows/bin:$PATH
%apprun run
exec /bin/bash "$@"
%runscript
exec /bin/bash "$@"
ednatools/Singularity.ednatools 0 → 100644
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BootStrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Include: bash vim less man-db apt-utils tzdata
%runscript
echo "Opening container...ubuntu beaver: vsearch, PEAR, fastq-join, pandaseq, jellyfish, casper, FLASH, fastq-multx, cutadapt, SWARM, REAPER, tally, minion, swan, tagCleaner, flexbar, usearch, deML, trimmomatic "
%environment
export LC_ALL=en_US.UTF-8
%labels
MAINTAINER Pierre-Edouard_GUERIN
INSTITUTE CNRS
TEAM Biogeographie_Ecologie_Vertebres
BUILD 1.1
SINGULARITY_VERSION 2.4.2-dist
PERL 5.26.1
PYTHON 3.6.8
VSEARCH 2.13.4
PEAR 0.9.11
FASTQ-JOIN 1.3.1
PANDASEQ 2.11
JELLYFISH 2.2.6
CASPER 0.8.2
FLASH 1.2.11
FASTQ-MULTX 1.3.1
CUTADAPT 2.3
SWARM 2.2.2
REAPER 13.274
TAGCLEANER 0.16
FLEXBAR 3.0.3
USEARCH 11.0.667
deML 1
JAVA 8.0
Trimmomatic 0.33
%post
mv /etc/apt/sources.list /etc/apt/sources.list.bak
echo "deb http://fr.archive.ubuntu.com/ubuntu/ bionic main restricted
deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates main restricted
deb http://fr.archive.ubuntu.com/ubuntu/ bionic universe
deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates universe
deb http://fr.archive.ubuntu.com/ubuntu/ bionic multiverse
deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates multiverse
deb http://fr.archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
deb http://security.ubuntu.com/ubuntu bionic-security main restricted
deb http://security.ubuntu.com/ubuntu bionic-security universe
deb http://security.ubuntu.com/ubuntu bionic-security multiverse" >> /etc/apt/sources.list
## git, make, wget
apt-get -y --force-yes update
yes | apt-get install build-essential
yes | apt-get install git
yes | apt install wget
yes | apt-get install autoconf autogen libtool
## zlib, boost, cmake
yes | apt install zlib1g-dev libbz2-dev pkg-config libboost-all-dev gettext cmake
## curl, lzma, unzip
yes | apt-get install curl liblzma-dev libncurses5-dev unzip
## python3
yes | apt install python3-pip
## JAVA
yes | apt-get install openjdk-8-jdk
## GNU parallel
yes | apt install parallel
## cutadapt
yes | python3 -m pip install cutadapt
## vsearch
wget https://github.com/torognes/vsearch/archive/v2.13.4.tar.gz
tar xzf v2.13.4.tar.gz
cd vsearch-2.13.4
./autogen.sh
./configure
make
make install
cd ..
## trimmomatic
curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
yes | unzip Trimmomatic-0.33.zip
cd Trimmomatic-0.33
cp -f ./adapters/* /usr/local/bin
cp -f trimmomatic-0.33.jar /usr/local/bin
cd ..
## PEAR
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/pear-0.9.11-linux-x86_64.tar.gz
tar xzf pear-0.9.11-linux-x86_64.tar.gz
cp pear-0.9.11-linux-x86_64/bin/pear /usr/local/bin/
## fastq-join
git clone https://github.com/brwnj/fastq-join
cd fastq-join
make
cp fastq-join /usr/local/bin/
cd ..
## pandaseq
git clone http://github.com/neufeld/pandaseq.git/
cd pandaseq
./autogen.sh
./configure
make
make install
cd ..
## yaggo
wget https://github.com/gmarcais/yaggo/releases/download/v1.5.10/yaggo
cp yaggo /usr/local/bin/
## jellyfish
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz
tar xzf jellyfish-2.2.6.tar.gz
cd jellyfish-2.2.6
autoreconf -i
./configure
make
make install
cd ..
## casper
wget http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz
tar xzf casper_v0.8.2.tar.gz
cd casper_v0.8.2
sed -i 's/fp==NULL/!fp/g' util.c
make
cp casper /usr/local/bin/
cd ..
## FLASH
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/FLASH-1.2.11.tar.gz
tar xzf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
make
cp flash /usr/local/bin/
cd ..
## fastq-multx
git clone https://github.com/brwnj/fastq-multx
cd fastq-multx
make
cp fastq-multx /usr/local/bin/
cd ..
## SWARM
git clone https://github.com/torognes/swarm.git
cd swarm/src/
make
cd ../../
cp swarm/bin/swarm /usr/local/bin/
## REAPER
#### tally
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/tally -O /usr/local/bin/tally
chmod 775 /usr/local/bin/tally
#### swan
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/swan -O /usr/local/bin/swan
chmod 775 /usr/local/bin/swan
#### reaper
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/reaper -O /usr/local/bin/reaper
chmod 775 /usr/local/bin/reaper
#### minion
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/minion -O /usr/local/bin/minion
chmod 775 /usr/local/bin/minion
## tagCleaner
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/tagcleaner-standalone-0.16.tar.gz
tar xzf tagcleaner-standalone-0.16.tar.gz
cp tagcleaner-standalone-0.16/tagcleaner.pl /usr/local/bin/tagcleaner
chmod 775 /usr/local/bin/tagcleaner
## flexbar
yes | apt install flexbar
## usearch
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/usearch11.0.667_i86linux32 -O /usr/local/bin/usearch
chmod 755 /usr/local/bin/usearch
## deML
git clone https://github.com/grenaud/deML.git
cd deML/
make
cp src/deML /usr/local/bin/deML
cd ..
ednatools/Singularity.ednatoolsMBB 0 → 100644
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BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
IncludeCmd: yes
Include: bash vim less man-db apt-utils tzdata
%runscript
echo "Opening container...ubuntu xenial: vsearch, PEAR, fastq-join, pandaseq, jellyfish, casper, FLASH, fastq-multx, cutadapt, SWARM, REAPER, tally, minion, swan, tagCleaner, flexbar, usearch, deML, trimmomatic "
%labels
MAINTAINER Pierre-Edouard_GUERIN
INSTITUTE CNRS
TEAM Biogeographie_Ecologie_Vertebres
BUILD 1.1
SINGULARITY_VERSION 2.4.2-dist
PERL 5.26.1
PYTHON 3.6.8
VSEARCH 2.13.4
PEAR 0.9.11
FASTQ-JOIN 1.3.1
PANDASEQ 2.11
JELLYFISH 2.2.6
CASPER 0.8.2
FLASH 1.2.11
FASTQ-MULTX 1.3.1
CUTADAPT 2.3
SWARM 2.2.2
REAPER 13.274
TAGCLEANER 0.16
FLEXBAR 3.0.3
USEARCH 11.0.667
deML 1.0
%environment
export LC_ALL=en_US.UTF-8
%post
mv /etc/apt/sources.list /etc/apt/sources.list.bak
echo "deb http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse" >> /etc/apt/sources.list
## MBB config
mkdir -p /share/apps/bin
mkdir /share/apps/lib
mkdir /share/apps/gridengine
mkdir /share/bio
mkdir -p /opt/gridengine
mkdir -p /export/scrach
mkdir -p /usr/lib64
/usr/sbin/groupadd --system --gid 400 sge
/usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
ln -s /bin/bash /bin/mbb_bash
ln -s /bin/bash /bin/isem_bash
## git, make, wget
apt-get -y --force-yes update
yes | apt-get install build-essential
yes | apt-get install git
yes | apt install wget
yes | apt-get install autoconf autogen libtool
## zlib, boost, cmake
yes | apt install zlib1g-dev libbz2-dev pkg-config libboost-all-dev gettext cmake
## python3
yes | apt install python3-pip
## GNU parallel
yes | apt install parallel
## cutadapt
yes | python3 -m pip install cutadapt
## vsearch
wget https://github.com/torognes/vsearch/archive/v2.13.4.tar.gz
tar xzf v2.13.4.tar.gz
cd vsearch-2.13.4
./autogen.sh
./configure
make
make install
cd ..
## PEAR
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/pear-0.9.11-linux-x86_64.tar.gz
tar xzf pear-0.9.11-linux-x86_64.tar.gz
cp pear-0.9.11-linux-x86_64/bin/pear /usr/local/bin/
## fastq-join
git clone https://github.com/brwnj/fastq-join
cd fastq-join
make
cp fastq-join /usr/local/bin/
cd ..
## pandaseq
git clone http://github.com/neufeld/pandaseq.git/
cd pandaseq
./autogen.sh
./configure
make
make install
cd ..
## yaggo
wget https://github.com/gmarcais/yaggo/releases/download/v1.5.10/yaggo
cp yaggo /usr/local/bin/
## jellyfish
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz
tar xzf jellyfish-2.2.6.tar.gz
cd jellyfish-2.2.6
autoreconf -i
./configure
make
make install
cd ..
## casper
wget http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz
tar xzf casper_v0.8.2.tar.gz
cd casper_v0.8.2
sed -i 's/fp==NULL/!fp/g' util.c
make
cp casper /usr/local/bin/
cd ..
## FLASH
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/FLASH-1.2.11.tar.gz
tar xzf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
make
cp flash /usr/local/bin/
cd ..
## fastq-multx
git clone https://github.com/brwnj/fastq-multx
cd fastq-multx
make
cp fastq-multx /usr/local/bin/
cd ..
## SWARM
git clone https://github.com/torognes/swarm.git
cd swarm/src/
make
cd ../../
cp swarm/bin/swarm /usr/local/bin/
## REAPER
#### tally
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/tally -O /usr/local/bin/tally
chmod 775 /usr/local/bin/tally
#### swan
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/swan -O /usr/local/bin/swan
chmod 775 /usr/local/bin/swan
#### reaper
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/reaper -O /usr/local/bin/reaper
chmod 775 /usr/local/bin/reaper
#### minion
wget http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/minion -O /usr/local/bin/minion
chmod 775 /usr/local/bin/minion
## tagCleaner
wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/tagcleaner-standalone-0.16.tar.gz
tar xzf tagcleaner-standalone-0.16.tar.gz