bowtie2 added

Program_Licenses.md

@@ -13,6 +13,7 @@ The licenses of the open-source software that is contained in these Docker image
 | BBTools | non-standard - see `licence.txt` and `legal.txt` that is included in docker image under `/bbmap/docs/`; Also on sourceforge repo for BBTools | https://jgi.doe.gov/disclaimer/ |
 | bcftools | MIT or **GNU GPLv3** (depends on how bcftools was compiled, I believe GNU GPLv3 applies here) | https://github.com/samtools/bcftools/blob/develop/LICENSE |
 | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE |
+| bowtie2 | GNU GPLv3 | https://github.com/BenLangmead/bowtie2/blob/master/LICENSE |
 | BWA | GNU GPLv3 | https://github.com/lh3/bwa/blob/master/COPYING |
 | Canu <br/> Racon <br/> Minimap2 | GNU GPLv3 (Canu), <br/> MIT (Racon), <br/> MIT (Minimap2) | https://github.com/marbl/canu/blob/master/README.license.GPL https://github.com/isovic/racon/blob/master/LICENSE https://github.com/lh3/minimap2/blob/master/LICENSE.txt |
 | centroid | GitHub No License | https://github.com/https://github.com/stjacqrm/centroid |

README.md

@@ -26,6 +26,7 @@ For many people Docker is not an option, but Singularity is. Most Docker contain
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/bbtools.svg?style=popout)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>38.76</li><li>38.86</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
 | [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/bcftools.svg?style=popout)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>1.10.2</li><li>1.11</li><li>1.12</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/bedtools.svg?style=popout)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
+| [bowtie2](https://hub.docker.com/r/staphb/bowtie2/) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/bowtie2.svg?style=popout)](https://hub.docker.com/r/staphb/bowtie2) | <ul><li>2.29.2</li><li>2.30.0</li></ul> | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2 |
 | [BWA](https://hub.docker.com/r/staphb/bwa) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/bwa.svg?style=popout)](https://hub.docker.com/r/staphb/bwa) | <ul><li>0.7.17</li></ul> | https://github.com/lh3/bwa |
 | [Canu](https://hub.docker.com/r/staphb/canu) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/canu.svg?style=popout)](https://hub.docker.com/r/staphb/canu)| <ul><li>2.0</li><li>2.1.1</ul> | https://canu.readthedocs.io/en/latest/ <BR/> https://github.com/marbl/canu |
 | [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/) <br/> [![docker pulls](https://img.shields.io/docker/pulls/staphb/canu-racon.svg?style=popout)](https://hub.docker.com/r/staphb/canu-racon) | <ul><li>1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)</li><li>1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li><li>1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)</li><li>2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li></ul> | https://canu.readthedocs.io/en/latest/ <br/> https://github.com/lbcb-sci/racon <br/> https://github.com/isovic/racon (ARCHIVED) <br/> https://lh3.github.io/minimap2/ |

bowtie2/2.4.4/Dockerfile

@@ -0,0 +1,62 @@
+# FROM defines the base docker image to start from. This command has to come first in the file
+FROM ubuntu:xenial
+
+ARG SAMTOOLSVER=1.11
+ARG BOWTIE2VER=2.4.4
+
+# metadata (there are a few other labels you can add, these are optional but preferred!)
+LABEL base.image="ubuntu:xenial"
+LABEL version="1"
+LABEL software="Bowtie2,\n Samtools"
+LABEL software.versions="2.4.4,\n 1.10"
+LABEL description="Bowtie2: Genome assembler using a reference and mapping\n Samtools: a set of tools for interacting with and reformatting sequence data"
+LABEL website="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml\n https://www.htslib.org/"
+LABEL maintainer="Holly Halstead"
+LABEL maintainer.email="holly.halstead@doh.wa.gov"
+
+ENV ZIP=bowtie2-${BOWTIE2VER}-linux-x86_64.zip
+ENV URL=https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE2VER}/
+ENV FOLDER=bowtie2-${BOWTIE2VER}
+ENV DST=/home/dock/bin
+ENV HOME /home/ubuntu
+
+# install dependencies, cleanup apt garbage.
+RUN mkdir -p $DST && \
+ apt-get update && apt-get install -y \
+ build-essential=12.1ubuntu2  \
+ autoconf=2.69-9 \
+ zlib1g-dev=1:1.2.8.dfsg-2ubuntu4.3  \
+ python3=3.5.1-3  \
+ wget=1.17.1-1ubuntu1.5 \
+ libbz2-dev=1.0.6-8ubuntu0.2 \
+ liblzma-dev=5.1.1alpha+20120614-2ubuntu2 \
+ libncurses5-dev=6.0+20160213-1ubuntu1 \
+ git=1:2.7.4-0ubuntu1.10 \
+ bedtools=2.25.0-1 \
+ python3-pip=8.1.1-2ubuntu0.6 \
+ vim=2:7.4.1689-3ubuntu1.5 \
+ unzip=6.0-20ubuntu1.1  \
+ nano=2.5.3-2ubuntu2 && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# download, unpack Bowtie2 and Samtools
+RUN wget -q -O bowtie2.zip http://sourceforge.net/projects/bowtie-bio/files/bowtie2/${BOWTIE2VER}/bowtie2-${BOWTIE2VER}-linux-x86_64.zip/download; \
+  unzip bowtie2.zip -d /opt/; \
+  ln -s /opt/bowtie2-${BOWTIE2VER}-linux-x86_64/ /opt/bowtie2; \
+  rm bowtie2.zip
+  ENV PATH $PATH:/opt/bowtie2
+
+
+#samtools# SAMtools
+RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \
+  tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \
+  rm samtools-${SAMTOOLSVER}.tar.bz2 && \
+  cd samtools-${SAMTOOLSVER} && \
+  ./configure && \
+  make && \
+  make install
+
+# set working directory
+  WORKDIR /data
+
+CMD ["bowtie2"]