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Add samtools to VarScan image

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This commit is contained in:
MillironX 2021-08-09 11:09:11 -05:00
parent 1181f417e0
commit 48683f6b80
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 36 additions and 3 deletions
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39
varscan/varscan.def
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@ -2,8 +2,37 @@ Bootstrap: library
From: default/alpine:3.14.0
%post
# Install java and bash (for Nextflow)
apk add --no-cache openjdk8 bash
# Part 1: Install Samtools
# ========================
# Get the actual dependencies
apk add --no-cache ncurses libbz2 xz zlib
# Get the build dependencies
apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
# Make versioning easier
SAMTOOLS_VERSION='1.13'
# Download the source tarball and build
cd /tmp || exit 1
wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
cd samtools-$SAMTOOLS_VERSION || exit 1
./configure
make && make install
cd .. || exit 1
rm -rf samtools-$SAMTOOLS_VERSION*
cd || exit 1
# Cleanup build packages
apk del --no-cache .build-deps
# Part 2: Install VarScan
# ========================
# Install java
apk add --no-cache openjdk8
# Make versioning easier
VARSCAN_VERSION='v2.4.4'
@ -16,10 +45,14 @@ From: default/alpine:3.14.0
echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan
chmod +x /usr/local/bin/varscan
# Part 3: Install Nextflow dependencies
# =====================================
apk add --no-cache bash
%test
cat << "EOF" > /tmp/singularity-test.sh
#!/bin/bash
CMDS=('bash' 'ps' 'java' 'varscan')
CMDS=('bash' 'ps' 'java' 'varscan' 'samtools')
for CMD in "${CMDS[@]}"; do
if ! command -v "$CMD"; then
echo "command $CMD not found!"