Merge pull request #1691 from RaheelSyedAhmed/bedder-rs-0.1.14

Adding new tool, bedder-rs 0.1.14

Author: erinyoung

Program_Licenses.md

@@ -26,6 +26,7 @@ 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://github.com/bbushnell/BBTools/blob/master/license.txt |
 | bcftools | MIT & **GNU GPLv3** | https://github.com/samtools/bcftools/blob/develop/LICENSE |
 | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE |
+| bedder-rs| MIT | https://github.com/quinlan-lab/bedder-rs/blob/main/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 |

README.md

@@ -131,6 +131,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <details><summary>Click to see all versions</summary> <ul><li>[38.76](./build-files/bbtools/38.76/)</li><li>[38.86](./build-files/bbtools/38.86/)</li><li>[38.95](./build-files/bbtools/38.95/)</li><li>[38.96](./build-files/bbtools/38.96/)</li><li>[38.97](./build-files/bbtools/38.97/)</li><li>[38.98](./build-files/bbtools/38.98/)</li><li>[38.99](./build-files/bbtools/38.99/)</li><li>[39.00](./build-files/bbtools/39.00/)</li><li>[39.01](./build-files/bbtools/39.01/)</li><li>[39.06](./build-files/bbtools/39.06/)</li><li>[39.10](./build-files/bbtools/39.10/)</li><li>[39.13](./build-files/bbtools/39.13/)</li><li>[39.16](./build-files/bbtools/39.16/)</li><li>[39.23](./build-files/bbtools/39.23/)</li><li>[39.25](./build-files/bbtools/39.25/)</li><li>[39.33](./build-files/bbtools/39.33/)</li><li>[39.34](./build-files/bbtools/39.34/)</li><li>[39.38](./build-files/bbtools/39.38/)</li><li>[39.49](./build-files/bbtools/39.49/)</li><li>[39.60](./build-files/bbtools/39.60/)</li><li>[39.68](./build-files/bbtools/39.68/)</li><li>[39.75](./build-files/bbtools/39.75/)</li><li>[39.77](./build-files/bbtools/39.77/)</li><li>[39.81](./build-files/bbtools/39.81/)</li><li>[39.84](./build-files/bbtools/39.84/)</li></ul></details> | https://bbmap.org/ |
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.10.2](./build-files/bcftools/1.10.2/)</li><li>[1.11](./build-files/bcftools/1.11/)</li><li>[1.12](./build-files/bcftools/1.12/)</li><li>[1.13](./build-files/bcftools/1.13/)</li><li>[1.14](./build-files/bcftools/1.14/)</li><li>[1.15](./build-files/bcftools/1.15/)</li><li>[1.16](./build-files/bcftools/1.16/)</li><li>[1.17](./build-files/bcftools/1.17/)</li><li>[1.18](./build-files/bcftools/1.18/)</li><li>[1.19](./build-files/bcftools/1.19/)</li><li>[1.20](./build-files/bcftools/1.20/)</li><li>[1.20.c](./build-files/bcftools/1.20.c/)</li><li>[1.21](./build-files/bcftools/1.21/)</li><li>[1.22](./build-files/bcftools/1.22/)</li><li>[1.23](./build-files/bcftools/1.23/)</li><li>[1.23.1](./build-files/bcftools/1.23.1/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[2.29.2](./build-files/bedtools/2.29.2/)</li><li>[2.30.0](./build-files/bedtools/2.30.0/)</li><li>[2.31.0](./build-files/bedtools/2.31.0/)</li><li>[2.31.1](./build-files/bedtools/2.31.1/)</li></ul> </details> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
+| [bedder-rs](https://hub.docker.com/r/staphb/bedder-rs/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedder-rs)](https://hub.docker.com/r/staphb/bedder-rs) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.14](./build-files/bedder-rs/0.1.14/)</li></ul> </details> | https://brentp.github.io/bedder-docs/latest/ <br/>https://github.com/quinlan-lab/bedder-rs |
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0](./build-files/berrywood-report-env/1.0/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.0](./build-files/bindashtree/0.1.0/)</li><li>[0.1.1](./build-files/bindashtree/0.1.1/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[2.13.0](./build-files/blast/2.13.0/)</li><li>[2.14.0](./build-files/blast/2.14.0/)</li><li>[2.14.1](./build-files/blast/2.14.1/)</li><li>[2.15.0](./build-files/blast/2.15.0/)</li><li>[2.16.0](./build-files/blast/2.16.0/)</li><li>[2.17.0](./build-files/blast/2.17.0/)</li></ul> </details> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |

build-files/bedder-rs/0.1.14/Dockerfile

@@ -0,0 +1,56 @@
+ARG BEDDER_RS_VER="0.1.14"
+
+FROM python:3.13-slim AS app
+ARG BEDDER_RS_VER
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="bedder-rs"
+LABEL software.version="${BEDDER_RS_VER}"
+LABEL description="A rust-based command-line tool for genomic analysis serving as a successor to bedtools."
+LABEL website="https://github.com/quinlan-lab/bedder-rs"
+LABEL license="https://github.com/quinlan-lab/bedder-rs/blob/main/LICENSE"
+LABEL maintainer="Raheel Ahmed"
+LABEL maintainer.email="raheelsyedahmed@gmail.com"
+
+WORKDIR /opt
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/quinlan-lab/bedder-rs/releases/download/v${BEDDER_RS_VER}/bedder-static-linux-x86_64 && \
+    ls -lah && \
+    mv bedder-static-linux-x86_64 /usr/local/bin/bedder && \
+    chmod +x /usr/local/bin/bedder
+
+ENV PYTHONHOME=/usr/local \
+    PYTHONPATH=/usr/local/lib/python3.13 \
+    LC_ALL=C
+
+CMD [ "bedder", "--help" ]
+
+WORKDIR /data
+
+
+FROM app AS test
+ARG BEDDER_RS_VER
+
+WORKDIR /test
+
+RUN bedder --help && \
+    bedder --version
+
+RUN wget -q https://github.com/quinlan-lab/bedder-rs/archive/refs/tags/v${BEDDER_RS_VER}.tar.gz && \
+    tar -xzf v${BEDDER_RS_VER}.tar.gz && \
+    rm v${BEDDER_RS_VER}.tar.gz
+    
+
+RUN cd bedder-rs-${BEDDER_RS_VER} && \
+    echo "intersect test" && \
+    bedder intersect -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-piece whole-wide --b-piece none && \
+    echo "map test" && \
+    bedder map -a tests/map_a.bed -b tests/map_b.bed -g tests/examples/fake.fai

build-files/bedder-rs/0.1.14/README.md

@@ -0,0 +1,32 @@
+# bedder-rs container
+Main tool: [bedder-rs](https://github.com/quinlan-lab/bedder-rs)
+  
+Code repository: https://github.com/quinlan-lab/bedder-rs
+
+Basic information on how to use this tool:
+- executable: bedder
+- help: `-h`, `--help`
+- version: `-V`, `--version`
+- description: A rust-based command-line tool for genomic analysis serving as a successor to bedtools.
+
+Additional information:
+
+This program is a successor to BEDTools using rust as its primary backend language. The tool offers flexibility for use cases supported by BEDTools, speed, and extensibility with support for python functions to allow for more information in columns as output. 
+  
+Full documentation: https://brentp.github.io/bedder-docs/latest/
+
+Python API: https://quinlan-lab.github.io/bedder-rs/main/bedder.html
+
+## Example Usage
+#### Reporting a single line for the a interval if it overlaps using whole-wide and none of the b interval
+```bash
+bedder intersect -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-piece whole-wide --b-piece none
+```
+#### Find the closest intervals in target.bed for each interval in query.bed:
+```bash
+bedder closest -a query.bed -b target.bed -g genome.fai -n 1 -c distance
+```
+#### Default behavior maps BED score (-c 5) with sum:
+```bash
+bedder map -a tests/examples/map_a.bed -b tests/examples/map_b.bed -g tests/examples/fake.fai
+```