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Remove Sniffles

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MillironX 2021-08-10 18:22:58 -05:00
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sniffles/README.md
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# Sniffles
[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/master/sniffles)
[![Sniffles source](https://img.shields.io/static/v1?label=Sniffles%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/fritzsedlazeck/Sniffles)
[![Version 1.0.12b](https://img.shields.io/static/v1?label=Latest%20version&message=v1.0.12b&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/sniffles)
[![Docs](https://img.shields.io/static/v1?label=Docs&message=wiki&color=blue&style=flat-square)](https://github.com/fritzsedlazeck/Sniffles/wiki)
[![Debian base](https://img.shields.io/static/v1?label=Base%20image&message=Debian&color=a80030&logo=debian&style=flat-square)](https://www.debian.org/)
Sniffles is a structural variation caller using third generation sequencing
(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
evidence from split-read alignments, high-mismatch regions, and coverage
analysis.
## Tools installed
### Sniffles
- `sniffles`
- `sniffles-debug`

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sniffles/sniffles.def
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Bootstrap: library
From: default/debian:buster
%post
# Declare version variable
export SNIFFLES_VERSION='1.0.12'
export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
# Install dependencies
apt-get update
apt-get install -y --no-install-recommends \
git cmake make gcc g++ libghc-zlib-dev bash procps build-essential
# Get Sniffles
cd /opt || exit 1
git config --global http.sslverify false
git clone https://github.com/fritzsedlazeck/Sniffles.git
cd Sniffles || exit 1
git checkout $SNIFFLES_TAG
# Build Sniffles
mkdir build && cd build || exit 1
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
make
# Install Sniffles
cd ../bin/sniffles-core-$SNIFFLES_VERSION || exit 1
install -D -m 0755 sniffles -t /usr/local/bin
install -D -m 0755 sniffles-debug -t /usr/local/bin
# Cleanup repo
cd ../.. || exit 1
rm -rf Sniffles
# Cleanup packages
rm -rf /var/lib/apt/lists/*
%test
command -v bash
command -v ps
command -v sniffles
command -v sniffles-debug
%runscript
sniffles "$@"
%labels
Author 25492070+MillironX@users.noreply.github.com
SoftwareVersion v1.0.12b
SingularityDefinitionVersion 3
%help
Sniffles
========
Sniffles is a structural variation caller using third generation sequencing
(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
evidence from split-read alignments, high-mismatch regions, and coverage
analysis.
For more help, see
- <https://github.com/fritzsedlazeck/Sniffles>
- <https://github.com/MillironX/singularity-builds>