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singularity.def
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Bootstrap: docker
From: ubuntu:20.04
%help
Container for ChimeraTE v1.1.1
/~https://github.com/OliveiraDS-hub/ChimeraTE.git
#Includes
Bedtools 2.30.0
BLAST 2.13+
Bowtie 1.3.1
Bowtie 2.5.1
Cufflinks 2.2.1
express 1.5.1
RepeatMasker 4.1.2
Trinity 2.9.1
Seqtk 1.3
Samtools 1.7
STAR 2.7.10
Python 3.6
#Python libs
Termcolor 1.1.0
Pybedtools 0.9.0
Pandas 1.1.5
Dateutil 2.8.2
h5py 3.1.0
numpy 1.19.5
%labels
VERSION "ChimeraTE v1.1.1"
Maintainer Daniel S Oliveira <daniel.sdo2015@gmail.com>
Oct, 2023
%post
# faster apt downloads
export DEBIAN_FRONTEND=noninteractive
export LC_ALL=C
(
. /etc/os-release
cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse
_EOF_
mv /etc/apt/sources.list /etc/apt/sources.list.bak
cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
)
#apt installing
apt update
apt install -y ca-certificates
apt install -y \
apt-utils \
autoconf \
automake \
cmake \
gcc \
wget \
build-essential \
software-properties-common \
tar \
unzip \
zlib1g-dev \
sudo \
git-core \
locales \
python3-pip \
libbz2-dev \
liblzma-dev \
libncurses-dev \
libfile-which-perl \
libjson-perl \
liburi-perl \
liblwp-useragent-determined-perl \
libtext-soundex-perl \
perl \
default-jdk \
python-is-python3
python3 -m pip install biopython \
termcolor==1.1.0 \
pybedtools==0.9.0 \
pandas==1.1.5 \
python-dateutil==2.8.2 \
h5py==3.1.0 \
numpy==1.19.5
###STAR
cd /usr/bin
wget -q --show-progress /~https://github.com/alexdobin/STAR/releases/download/2.7.10b/STAR_2.7.10b.zip
unzip STAR_2.7.10b.zip
###Bowtie
wget -q --show-progress https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.1/bowtie2-2.5.1-linux-x86_64.zip
unzip bowtie2-2.5.1-linux-x86_64.zip
###Cufflinks
wget -q --show-progress http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -zxf cufflinks-2.2.1.Linux_x86_64.tar.gz
###express
wget -q --show-progress https://pachterlab.github.io/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz
tar -zxf express-1.5.1-linux_x86_64.tgz
###Bedtools
wget -q --show-progress /~https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz
tar -zxf bedtools-2.30.0.tar.gz
cd bedtools2
make && make install
###Seqtk
cd /usr/bin
wget -q --show-progress /~https://github.com/lh3/seqtk/archive/refs/tags/v1.3.zip
unzip v1.3.zip
cd seqtk-1.3/
make && make install
###Samtools
cd /usr/bin
wget -q --show-progress https://sourceforge.net/projects/samtools/files/samtools/1.7/samtools-1.7.tar.bz2
tar -xf samtools-1.7.tar.bz2
cd samtools-1.7
./configure && make && make install
###Jellyfish - Trinity dep
cd /usr/bin
wget -q --show-progress /~https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-linux
mv jellyfish-linux jellyfish
chmod +x jellyfish
###Salmon - Trinity dep
wget -q --show-progress /~https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz
tar -zxf salmon-1.10.0_linux_x86_64.tar.gz
chmod +x salmon-latest_linux_x86_64/bin/salmon
###Trinity
wget -q --show-progress /~https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.9.1/trinityrnaseq-v2.9.1.FULL.tar.gz
tar -zxf trinityrnaseq-v2.9.1.FULL.tar.gz
cd trinityrnaseq-v2.9.1
make
#BLAST
cd /usr/bin/
wget -q --show-progress https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.14.1/ncbi-blast-2.14.1+-x64-linux.tar.gz
tar -zxf ncbi-blast-2.14.1+-x64-linux.tar.gz
###RepeatMasker deps
#TRF
wget -q --show-progress /~https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64
mv trf*.linux64 trf && chmod +x trf
#hmmer
wget -q --show-progress http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz
tar -zxf hmmer-3.3.2.tar.gz
cd hmmer-3.3.2
./configure && make && make install
cd /usr/bin
#RMblast
wget -q --show-progress https://www.repeatmasker.org/rmblast/rmblast-2.13.0+-x64-linux.tar.gz
tar -zxf rmblast-2.13.0+-x64-linux.tar.gz
#RepeatMasker
wget -q --show-progress https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz
tar -zxf RepeatMasker-4.1.2-p1.tar.gz
cd RepeatMasker
perl configure \
-hmmer_dir=/usr/local/bin/ \
-rmblast_dir=/usr/bin/rmblast-2.13.0/bin \
-libdir=/usr/bin/RepeatMasker/Libraries \
-trf_prgm=/usr/bin \
-default_search_engine=rmblast
%environment
export LC_ALL=C
export PATH="$PATH:/usr/bin/ncbi-blast-2.14.1+/bin"
export PATH="$PATH:/usr/bin/bowtie2-2.5.1-linux-x86_64"
export PATH="$PATH:/usr/bin/cufflinks-2.2.1.Linux_x86_64"
export PATH="$PATH:/usr/bin/bowtie2-2.5.1-linux-x86_64"
export PATH="$PATH:/usr/bin/STAR_2.7.10b/Linux_x86_64"
export PATH="$PATH:/usr/bin/trinityrnaseq-v2.9.1"
export PATH="$PATH:/usr/bin/express-1.5.1-linux_x86_64"
export PATH="$PATH:/usr/bin/RepeatMasker"
export PATH="$PATH:/usr/bin/salmon-latest_linux_x86_64/bin"
#