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Change sniffles base image

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MillironX 2021-08-10 17:35:08 -05:00
parent aa9cef8d49
commit 96f1410056
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 17 additions and 17 deletions
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2
sniffles/README.md
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@ -4,7 +4,7 @@
[![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)
[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
[![Debian base](https://img.shields.io/static/v1?label=Base%20image&message=Debian&color=a80030&logo=debian&style=flat-square)](https://www.alpinelinux.org/)
Sniffles is a structural variation caller using third generation sequencing
(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using

32
sniffles/sniffles.def
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@ -1,20 +1,19 @@
Bootstrap: library
From: default/alpine:3.14.0
From: default/debian:buster
%post
# Declare version variable
export SNIFFLES_VERSION='1.0.12'
export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
# Install build dependencies
apk add --no-cache --virtual .build-deps \
git cmake make gcc g++ zlib-dev
# Install real dependencies
apk add --no-cache bash
# 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 $SNIFFLES_TAG
@ -24,16 +23,17 @@ From: default/alpine:3.14.0
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
make
# Add Sniffles to PATH
export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH
# Install Sniffles
cd ../bin/sniffles-core-$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
apk del --no-cache .build-deps
%environment
export SNIFFLES_VERSION='1.0.12'
export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH
rm -rf /var/lib/apt/lists/*
%test
command -v bash
@ -47,7 +47,7 @@ From: default/alpine:3.14.0
%labels
Author 25492070+MillironX@users.noreply.github.com
SoftwareVersion v1.0.12b
SingularityDefinitionVersion 2
SingularityDefinitionVersion 3
%help
Sniffles