From 6fa9010716039a9dffcb6094b76969c429c076ad Mon Sep 17 00:00:00 2001
From: johnMcGonigle <john@repositive.io>
Date: Tue, 7 Aug 2018 15:54:08 +0100
Subject: [PATCH] Updated options for HTSlib dockerfiles

---
 bcftools/1.9/Dockerfile | 29 +++++++++++++++++++++++++++++
 htslib/1.9/Dockerfile   | 29 +++++++++++++++++++++++++++++
 samtools/1.9/Dockerfile | 26 ++++++++++++++++++++++++++
 3 files changed, 84 insertions(+)
 create mode 100644 bcftools/1.9/Dockerfile
 create mode 100644 htslib/1.9/Dockerfile
 create mode 100644 samtools/1.9/Dockerfile

diff --git a/bcftools/1.9/Dockerfile b/bcftools/1.9/Dockerfile
new file mode 100644
index 000000000..d4cddf480
--- /dev/null
+++ b/bcftools/1.9/Dockerfile
@@ -0,0 +1,29 @@
+################## BASE IMAGE ######################
+
+FROM biocontainers/biocontainers:latest
+
+################## METADATA ######################
+
+LABEL base_image="biocontainers:latest"
+LABEL version="1"
+LABEL software="bcftools"
+LABEL software.version="1.9"
+LABEL about.summary="Bcftools is a program for variant calling and manipulating VCFs and BCFs"
+LABEL about.home="https://samtools.github.io/bcftools/"
+LABEL about.documentation="https://samtools.github.io/bcftools/"
+LABEL about.license_file="https://github.com/samtools/bcftools/blob/develop/LICENSE"
+LABEL about.license="SPDX:MIT"
+LABEL extra.identifiers.biotools="bcftools"
+LABEL about.tags="Genomics"
+
+################## MAINTAINER ######################
+
+MAINTAINER John McGonigle <j.e.mcgonigle@gmail.com>
+
+################## INSTALLATION ######################
+
+RUN conda install bcftools=1.9
+
+WORKDIR /data/
+
+CMD ["bcftools"]
diff --git a/htslib/1.9/Dockerfile b/htslib/1.9/Dockerfile
new file mode 100644
index 000000000..7044a8ddf
--- /dev/null
+++ b/htslib/1.9/Dockerfile
@@ -0,0 +1,29 @@
+############################### Dockerfile ##################################
+
+FROM biocontainers/biocontainers:latest
+
+################################# METADATA ###################################
+
+LABEL base_image="biocontainers:latest"
+LABEL version="1"
+LABEL software="htslib"
+LABEL software.version="1.9"
+LABEL about.summary="C library for high-throughput sequencing data formats"
+LABEL about.home="https://github.com/samtools/htslib"
+LABEL about.provides="htslib 1.9"
+LABEL about.license_file="https://github.com/samtools/htslib/blob/develop/LICENSE"
+LABEL about.license="SPDX:MIT"
+LABEL about.tags="Genomics"
+LABEL extra.identifiers.biotools="HTSlib"
+
+################## MAINTAINER ######################
+
+MAINTAINER John McGonigle <j.e.mcgonigle@gmail.com>
+
+################## INSTALLATION ######################
+
+RUN conda install htslib=1.9
+
+WORKDIR /data/
+
+CMD ["bcftools"]
\ No newline at end of file
diff --git a/samtools/1.9/Dockerfile b/samtools/1.9/Dockerfile
new file mode 100644
index 000000000..fad73f490
--- /dev/null
+++ b/samtools/1.9/Dockerfile
@@ -0,0 +1,26 @@
+################## BASE IMAGE ######################
+
+FROM biocontainers/biocontainers:latest
+
+################## METADATA ######################
+LABEL base_image="biocontainers:latest"
+LABEL version="2"
+LABEL software="Samtools"
+LABEL software.version="1.9"
+LABEL about.summary="Tools for manipulating next-generation sequencing data"
+LABEL about.home="https://github.com/samtools/samtools"
+LABEL about.documentation="https://github.com/samtools/samtools"
+LABEL about.license_file="https://github.com/samtools/samtools"
+LABEL about.license_file="https://github.com/samtools/samtools/blob/develop/LICENSE"
+LABEL about.license="SPDX:MIT"
+LABEL about.tags="Genomics"
+LABEL extra.identifiers.biotools="SAM"
+
+################## MAINTAINER ######################
+MAINTAINER John McGonigle <j.e.mcgonigle@gmail.com>
+RUN conda install samtools=1.9
+RUN conda install -c conda-forge ncurses # Fix to deal with the issue with libtinfow.so.5
+
+WORKDIR /data/
+
+CMD ["samtools"]