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Commit c8fc63a7 authored by descoste's avatar descoste
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1 merge request!13fasterq hidden macs2 picard
BootStrap: docker
From: ubuntu:bionic
%help
This singularity installs picard tools v 2.22.1
%post
# ~~~~~~ General setup and folder creation ~~~~~~ #
apt-get update && apt-get install -y wget libreadline-dev
export LC_ALL=C
export LC_CTYPE=C
export LC_COLLATE=C
export LC_TIME=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_MEASUREMENT=C
# ~~~~~ MINICONDA ~~~~~ #
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
rm -f Miniconda3-latest-Linux-x86_64.sh
export PATH="/conda/bin:${PATH}"
# ~~~~ R v 4.1.2 ~~~~~~ #
conda install -c conda-forge r-base=4.1.2
# ~~~~~ PICARD TOOLS ~~~~~ #
conda install -y -c bioconda picard=2.22.1
%environment
export PATH="${PATH}:/conda/bin"
export LC_ALL=C
export LC_CTYPE=C
export LC_COLLATE=C
export LC_TIME=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_MEASUREMENT=C
%labels
Author Nicolas Descostes
Version v0.0.1
BootStrap: docker
From: ubuntu:bionic
%help
This singularity installs picard tools v 2.27.1
%post
# ~~~~~~ General setup and folder creation ~~~~~~ #
apt-get update && apt-get install -y wget libreadline-dev
export LC_ALL=C
export LC_CTYPE=C
export LC_COLLATE=C
export LC_TIME=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_MEASUREMENT=C
# ~~~~~ MINICONDA ~~~~~ #
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
rm -f Miniconda3-latest-Linux-x86_64.sh
export PATH="/conda/bin:${PATH}"
# ~~~~ R v 4.1.2 ~~~~~~ #
conda install -c conda-forge r-base=4.1.2
# ~~~~~ PICARD TOOLS ~~~~~ #
conda install -y -c bioconda picard=2.27.1
%environment
export PATH="${PATH}:/conda/bin"
export LC_ALL=C
export LC_CTYPE=C
export LC_COLLATE=C
export LC_TIME=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_MEASUREMENT=C
%labels
Author Nicolas Descostes
Version v0.0.1
BootStrap: docker
From: ubuntu:bionic
%help
This singularity install parallel-fastq-dump v0.6.3.
%post
# ~~~~~~ General setup and folder creation ~~~~~~ #
apt-get update && apt-get install -y wget bzip2
# ~~~~~ MINICONDA 3.4.0.5 ~~~~~ #
wget https://repo.anaconda.com/miniconda/Miniconda3-4.0.5-Linux-x86_64.sh && \
bash Miniconda3-4.0.5-Linux-x86_64.sh -b -p /conda && \
rm -f Miniconda3-4.0.5-Linux-x86_64.sh
export PATH="/conda/bin:${PATH}"
# ~~~~~ parallel-fastq-dump 0.6.3 ~~~~~ #
conda install -y -c bioconda parallel-fastq-dump=0.6.3
%environment
export PATH="${PATH}:/conda/bin"
%labels
Author Nicolas Descostes
Version v0.0.2
BootStrap: docker
From: ubuntu:xenial
%help
This singularity install hiddenDomains v3.1
%post
# ~~~~~~ General setup and folder creation ~~~~~~ #
apt-get update && apt-get install -y wget bzip2
export LC_ALL=en_US.UTF-8
export LC_COLLATE=C
export LC_CTYPE=C
export LC_MEASUREMENT=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_TIME=C
export LANG=C.UTF-8
# ~~~~~ MINICONDA 3.4.0.5 ~~~~~ #
wget https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh && \
bash Miniconda3-4.6.14-Linux-x86_64.sh -b -p /conda && \
rm -f Miniconda3-4.6.14-Linux-x86_64.sh
export PATH="/conda/bin:${PATH}"
# ~~~~~ perl 5.32.1 ~~~~~~~#
conda install -c conda-forge perl=5.32.1
# ~~~~ R v 4.1.2 ~~~~~~ #
conda install -c conda-forge r-base=4.1.2
# ~~~ r-depmixs4 v1.5_0 ~~~~#
conda install -c conda-forge r-depmixs4=1.5_0
#~~~~ r-hiddenmarkov v1.8_13 ~~~#
conda install -c conda-forge r-hiddenmarkov=1.8_13
# ~~~~~ hiddendomains v3.1 ~~~~~ #
conda install -y -c bioconda hiddendomains=3.1
%environment
export PATH="${PATH}:/conda/bin"
export LC_ALL=en_US.UTF-8
export LC_COLLATE=C
export LC_CTYPE=C
export LC_MEASUREMENT=C
export LC_MESSAGES=C
export LC_MONETARY=C
export LC_PAPER=C
export LC_TIME=C
export LANG=C.UTF-8
%labels
Author Nicolas Descostes
Version v0.0.5
Bootstrap: docker
From: biocontainers/macs2:2.2.7.1--py39hbf8eff0_4
%runscript
echo "Running container biocontainers/macs2:2.2.7.1--py39hbf8eff0_4, macs2 v2.2.7.1"
exec /bin/bash "$@"
%post
mkdir /cluster /work /tsd /projects
%labels
Author Nicolas Descostes
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