From 9d20c68e5298d380485586b40f28deb65d7d7bf9 Mon Sep 17 00:00:00 2001
From: Szilveszter Juhos <Szilveszter.Juhos@scilifelab.se>
Date: Wed, 15 Aug 2018 00:26:37 +0200
Subject: [PATCH] s/sarek-core/sarek/ also deleting build.sh

---
 containers/sarek/build.sh        | 103 -------------------------------
 containers/sarek/environment.yml |   2 +-
 2 files changed, 1 insertion(+), 104 deletions(-)
 delete mode 100755 containers/sarek/build.sh

diff --git a/containers/sarek/build.sh b/containers/sarek/build.sh
deleted file mode 100755
index fbe57b5aee..0000000000
--- a/containers/sarek/build.sh
+++ /dev/null
@@ -1,103 +0,0 @@
-#!/bin/sh
-set -eu pipefail
-
-# Local ENV variables
-BCFTOOLS_VERSION=1.5
-BWA_VERSION=0.7.16
-HTSLIB_VERSION=1.5
-MANTA_VERSION=1.1.1
-SAMTOOLS_VERSION=1.5
-STRELKA_VERSION=2.8.2
-
-# Install libraries
-apt-get update && apt-get install -y --no-install-recommends \
-  build-essential \
-  bzip2 \
-  ca-certificates \
-  g++ \
-  gcc \
-  git \
-  libbz2-dev \
-  liblzma-dev \
-  libncurses5-dev \
-  libncursesw5-dev \
-  make \
-  python \
-  python3 \
-  unzip \
-  wget \
-  zlib1g-dev
-
-# Install tools
-mkdir /build
-
-# Install BWA
-cd /build
-git clone http://github.com/lh3/bwa.git bwa \
-  --branch v${BWA_VERSION}
-cd bwa
-make
-cp bwa /usr/local/bin/bwa
-
-# Install HTSlib
-cd /build
-wget --quiet -O htslib-${HTSLIB_VERSION}.tar.bz2 \
-  https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
-tar xfj htslib-${HTSLIB_VERSION}.tar.bz2
-rm htslib-${HTSLIB_VERSION}.tar.bz2
-cd htslib-${HTSLIB_VERSION}
-./configure --prefix=/opt/htslib
-make && make install
-
-# Install BCFtools
-cd /build
-wget --quiet -O bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
-  https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
-tar xfj bcftools-${BCFTOOLS_VERSION}.tar.bz2
-rm bcftools-${BCFTOOLS_VERSION}.tar.bz2
-cd bcftools-${BCFTOOLS_VERSION}
-./configure --prefix=/opt/bcftools
-make && make install
-
-# Install Samtools
-cd /build
-wget --quiet -O samtools-${SAMTOOLS_VERSION}.tar.bz2 \
-  https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
-tar xfj samtools-${SAMTOOLS_VERSION}.tar.bz2
-rm samtools-${SAMTOOLS_VERSION}.tar.bz2
-cd samtools-${SAMTOOLS_VERSION}
-./configure --prefix=/opt/samtools
-make && make install
-
-# Install Manta
-cd /build
-wget --quiet -O manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2 \
-  https://github.com/Illumina/manta/releases/download/v${MANTA_VERSION}/manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-tar xvjf manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-mv manta-${MANTA_VERSION}.centos5_x86_64 $MANTA_INSTALL_PATH
-rm manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-
-# Install Strelka
-cd /build
-wget --quiet -O strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2 \
-  https://github.com/Illumina/strelka/releases/download/v${STRELKA_VERSION}/strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-tar xvjf strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-mv strelka-${STRELKA_VERSION}.centos5_x86_64 $STRELKA_INSTALL_PATH
-rm strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-
-# Clean up install
-cd /
-apt-get remove -y \
-  build-essential \
-  ca-certificates \
-  gcc \
-  git \
-  libbz2-dev \
-  liblzma-dev \
-  libncurses5-dev \
-  libncursesw5-dev \
-  unzip \
-  wget \
-  zlib1g-dev
-apt-get clean
-rm -rf /build /var/lib/apt/lists/* /opt/get-pip.py
diff --git a/containers/sarek/environment.yml b/containers/sarek/environment.yml
index 25f08613f0..af3ea825f4 100644
--- a/containers/sarek/environment.yml
+++ b/containers/sarek/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 # conda env create -f environment.yml
-name: sarek-core
+name: sarek
 channels:
   - bioconda
   - conda-forge