Merge pull request #1146 from taylorpaisie/tkp-bindashtree

Add bindashtree v0.1.0

Author: erinyoung

Program_Licenses.md

@@ -21,6 +21,7 @@ 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 & **GNU GPLv3** | https://github.com/samtools/bcftools/blob/develop/LICENSE |
 | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE |
+| bindashtree | MIT | https://github.com/jianshu93/bindashtree?tab=MIT-1-ov-file#readme |
 | blast+ | Public Domain | https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE |
 | bowtie2 | GNU GPLv3 | https://github.com/BenLangmead/bowtie2/blob/master/LICENSE |
 | Bracken | GNU GPLv3 | https://github.com/jenniferlu717/Bracken/blob/master/LICENSE |

README.md

@@ -129,6 +129,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li><li>[1.21](./bcftools/1.21/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
 | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |
+| [bindashtree](https://hub.docker.com/r/staphb/bindashtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bindashtree)](https://hub.docker.com/r/staphb/bindashtree) | <ul><li>[0.1.0](./build-files/bindashtree/0.1.0/)</li></ul> | https://github.com/jianshu93/bindashtree |
 | [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>[2.13.0](blast/2.13.0/)</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li><li>[2.15.0](blast/2.15.0/)</li><li>[2.16.0](./blast/2.16.0/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
 | [bowtie2](https://hub.docker.com/r/staphb/bowtie2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | <ul><li>[2.4.4](./bowtie2/2.4.4/)</li><li>[2.4.5](./bowtie2/2.4.5/)</li><li>[2.5.1](./bowtie2/2.5.1/)</li><li>[2.5.3](./bowtie2/2.5.3/)</li><li>[2.5.4](./bowtie2/2.5.4/)</li></ul> | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2 |
 | [Bracken](https://hub.docker.com/r/staphb/bracken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | <ul><li>[2.9](./bracken/2.9)</li></ul> | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken |

build-files/bindashtree/0.1.0/Dockerfile

@@ -0,0 +1,81 @@
+# Stage 1: Build stage
+FROM ubuntu:focal AS builder
+
+# Set global variables
+ARG BINDASHTREE_VER="0.1.0"
+
+# Update package manager and install necessary tools
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    curl \
+    build-essential \
+    gcc \
+    pkg-config \
+    libssl-dev \
+    ca-certificates \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install Rust and Cargo using rustup
+RUN curl https://sh.rustup.rs -sSf | sh -s -- -y && \
+    export PATH="$HOME/.cargo/bin:$PATH" && \
+    rustup default stable
+
+# Ensure Rust and Cargo are available
+ENV PATH="/root/.cargo/bin:$PATH"
+
+# Download, extract, and build bindashtree
+RUN wget https://github.com/jianshu93/bindashtree/archive/refs/tags/v${BINDASHTREE_VER}.tar.gz && \
+    tar -xzvf v${BINDASHTREE_VER}.tar.gz && \
+    cd bindashtree-${BINDASHTREE_VER} && \
+    /root/.cargo/bin/cargo build --release
+
+# Stage 2: Final image
+FROM ubuntu:focal AS app
+ARG BINDASHTREE_VER="0.1.0"
+
+# Install wget for test stage compatibility
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Labels for metadata
+LABEL base.image="ubuntu:focal" \
+      dockerfile.version="1" \
+      software="bindashtree" \
+      software.version="${BINDASHTREE_VER}" \
+      description="Binwise Densified MinHash and Rapid Neighbor-joining Tree Construction for microbial genomes." \
+      website="https://github.com/jianshu93/bindashtree" \
+      license.url="https://github.com/jianshu93/bindashtree?tab=MIT-1-ov-file#readme" \
+      maintainer="Taylor K. Paisie" \
+      maintainer.email="ltj8@cdc.gov"
+
+# Copy built binaries from the builder stage
+COPY --from=builder /bindashtree-${BINDASHTREE_VER}/target/release/bindashtree /usr/local/bin/
+
+CMD ["bindashtree", "--help"]
+
+WORKDIR /data
+
+# Stage 3: Test stage
+FROM app AS test
+
+# Set working directory
+WORKDIR /data/test
+
+# Install wget if not installed (redundancy for safety)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Download test files
+RUN wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/587/385/GCA_002587385.1_ASM258738v1/GCA_002587385.1_ASM258738v1_genomic.fna.gz && \
+    wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/596/765/GCA_002596765.1_ASM259676v1/GCA_002596765.1_ASM259676v1_genomic.fna.gz && \
+    wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/598/005/GCA_002598005.1_ASM259800v1/GCA_002598005.1_ASM259800v1_genomic.fna.gz
+
+RUN ls /data/test/*.fna.gz > name.txt
+
+#### for highly similar genomes, e.g., > 99.9% ANI, a large sketch size should be used. -s 10204 works well for ANI below 99%.
+RUN bindashtree -i name.txt -k 16 -s 10240 -d 1 -t 8 --output_tree try.nwk
+
+FROM app

build-files/bindashtree/0.1.0/README.md

@@ -0,0 +1,59 @@
+# bindashtree container
+
+Main tool: [bindashtree](https://github.com/jianshu93/bindashtree)
+  
+Code repository: https://github.com/jianshu93/bindashtree
+
+Basic information on how to use this tool:
+- executable: |
+
+```
+Binwise Densified MinHash and Rapid Neighbor-joining Tree Construction
+
+Usage: bindashtree [OPTIONS] --input <INPUT_LIST_FILE> --output_tree <OUTPUT_TREE_FILE>
+
+Options:
+  -i, --input <INPUT_LIST_FILE>
+          Genome list file (one FASTA/FNA file per line), gz supported
+  -k, --kmer_size <KMER_SIZE>
+          K-mer size [default: 16]
+  -s, --sketch_size <SKETCH_SIZE>
+          MinHash sketch size [default: 10240]
+  -d, --densification <DENS_OPT>
+          Densification strategy: 0=Optimal Densification, 1=Reverse Optimal Densification/faster Densification [default: 0]
+  -t, --threads <THREADS>
+          Number of threads to use in parallel [default: 1]
+      --tree <TREE_METHOD>
+          Tree construction method: naive, rapidnj, hybrid [default: rapidnj]
+      --chunk_size <chunk_size>
+          Chunk size for RapidNJ/Hybrid methods [default: 30]
+      --naive_percentage <naive_percentage>
+          Percentage of steps naive for hybrid method [default: 90]
+      --output_matrix <OUTPUT_MATRIX_FILE>
+          Output the phylip distance matrix to a file
+      --output_tree <OUTPUT_TREE_FILE>
+          Output the resulting tree in Newick format to a file
+  -h, --help
+          Print help
+  -V, --version
+          Print version
+```
+
+Additional information:
+One Permutation Hashing with Optimal Densification can be use for genomic distance estimation (1-ANI) and then we can perform rapid neighbor-joining based on the genomic distance. We also provided a new densification strategy called faster densification (or reverse optimal densification), which is more accurate and faster for large sketch size.
+
+  
+Full documentation: https://github.com/jianshu93/bindashtree
+
+## Testing for bindashtree
+
+```
+# Download test files
+wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/587/385/GCA_002587385.1_ASM258738v1/GCA_002587385.1_ASM258738v1_genomic.fna.gz && \
+wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/596/765/GCA_002596765.1_ASM259676v1/GCA_002596765.1_ASM259676v1_genomic.fna.gz && \
+wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/598/005/GCA_002598005.1_ASM259800v1/GCA_002598005.1_ASM259800v1_genomic.fna.gz
+
+ls /data/test/*.fna.gz > name.txt
+
+bindashtree -i name.txt -k 16 -s 10240 -d 1 -t 8 --output_tree try.nwk
+```