adding lima version 2.12.0 (#1147)

erinyoung · web-flow · commit 998186347f4f · 2025-01-02T08:12:20.000-05:00
* adding lima version 2.12.0

* Update README.md

* Rename lima/2.12.0-Rscripts/Dockerfile to build-files/lima/2.12.0-Rscripts/Dockerfile

* Rename lima/2.12.0-Rscripts/README.md to build-files/lima/2.12.0-Rscripts/README.md

* Rename lima/2.12.0/Dockerfile to build-files/lima/2.12.0/Dockerfile

* Rename lima/2.12.0/README.md to build-files/lima/2.12.0/README.md
diff --git a/README.md b/README.md
@@ -210,7 +210,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [label](https://hub.docker.com/r/staphb/label/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/label)](https://hub.docker.com/r/staphb/label)| <ul><li>[0.6.4](./label/0.6.4/)</li></ul> | https://wonder.cdc.gov/amd/flu/label |
 | [legsta](https://hub.docker.com/r/staphb/legsta/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/legsta)](https://hub.docker.com/r/staphb/legsta)| <ul><li>0.3.7</li><li>0.5.1</li></ul> | https://github.com/tseemann/legsta |
 | [liftoff](https://hub.docker.com/r/staphb/liftoff/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/liftoff)](https://hub.docker.com/r/staphb/liftoff)| <ul><li>1.6.3</li></ul> | https://github.com/agshumate/Liftoff |
-| [lima](https://hub.docker.com/r/staphb/lima/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/lima)](https://hub.docker.com/r/staphb/lima)| <ul><li>[2.9.0](./lima/2.9.0/)</li><li>[2.9.0+Rscripts](./lima/2.9.0+Rscripts/)</li></ul> | https://github.com/PacificBiosciences/barcoding |
+| [lima](https://hub.docker.com/r/staphb/lima/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/lima)](https://hub.docker.com/r/staphb/lima)| <ul><li>[2.9.0](./build-files/lima/2.9.0/)</li><li>[2.9.0-Rscripts](./build-files/lima/2.9.0-Rscripts/)</li><li>[2.12.0](./build-files/lima/2.12.0/)</li><li>[2.12.0-Rscripts](./build-files/lima/2.12.0-Rscripts/)</li></ul> | https://github.com/PacificBiosciences/barcoding |
 | [longshot](https://hub.docker.com/r/staphb/longshot/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/longshot)](https://hub.docker.com/r/staphb/longshot)| <ul><li>[0.4.5](longshot/0.4.5)</li><li>[1.0.0](longshot/1.0.0/)</li></ul> | https://github.com/pjedge/longshot |
 | [lrge](https://hub.docker.com/r/staphb/lrge/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/lrge)](https://hub.docker.com/r/staphb/lrge)| <ul><li>[0.1.3](./lrge/0.1.3/)</li></ul> | https://github.com/mbhall88/lrge |
 | [Lyve-SET (includes CG-Pipeline scripts and raxml)](https://hub.docker.com/r/staphb/lyveset/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/lyveset)](https://hub.docker.com/r/staphb/lyveset) | <ul><li>1.1.4f</li><li>2.0.1</li></ul> | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |
diff --git a/build-files/lima/2.12.0-Rscripts/Dockerfile b/build-files/lima/2.12.0-Rscripts/Dockerfile
@@ -0,0 +1,74 @@
+ARG LIMA_VER="2.12.0"
+
+## Builder ##
+FROM ubuntu:jammy AS builder
+
+ARG LIMA_VER
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y \
+    wget \
+    build-essential \
+    gfortran \
+    r-base
+
+# build required R packages
+RUN R -e "install.packages(c('ggplot2', 'dplyr', 'tidyr' ,'viridis', 'scales', 'data.table', 'hexbin'), quietly = TRUE, warn.conflicts = FALSE, repos = 'http://cran.us.r-project.org')"
+
+# Rscripts
+RUN wget -P /usr/local/bin/ https://github.com/PacificBiosciences/barcoding/raw/master/scripts/r/report_summary.R \
+    https://github.com/PacificBiosciences/barcoding/raw/master/scripts/r/report_detail.R &&\
+    chmod +x /usr/local/bin/report_summary.R /usr/local/bin/report_detail.R
+
+## App ##
+FROM ubuntu:jammy AS app
+
+ARG LIMA_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Lima"
+LABEL software.version="${LIMA_VER}"
+LABEL description="The PacBio Barcode Demultiplixer & Primer Remover"
+LABEL website="https://github.com/PacificBiosciences/barcoding"
+LABEL license="https://github.com/PacificBiosciences/barcoding/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    r-base &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/
+COPY --from=builder /usr/local/bin/ /usr/local/bin/
+
+RUN wget https://github.com/PacificBiosciences/barcoding/releases/download/v${LIMA_VER}/lima.tar.gz &&\
+    tar -C /usr/local/bin -xvf lima.tar.gz &&\
+    rm lima.tar.gz
+
+ENV LC_ALL=C
+
+CMD lima -h && lima-undo -h
+
+WORKDIR /data
+
+FROM app AS test
+
+RUN lima -h && lima-undo -h
+
+# download test files
+RUN wget -q https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/HiFiViral_Barcoded_M13_Primer_Plate.fasta \
+    https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/InqabaOmicronSamples_Barcoded_Sample.csv \
+    https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/m64187e_211217_130958.hifi_reads.bam
+# run test
+RUN lima m64187e_211217_130958.hifi_reads.bam HiFiViral_Barcoded_M13_Primer_Plate.fasta demux.hifi.bam --biosample-csv InqabaOmicronSamples_Barcoded_Sample.csv --hifi-preset ASYMMETRIC &&\
+    cat demux.hifi.lima.summary
+    
+RUN report_summary.R demux.hifi.lima.report &&\
+    ls | grep png
+
+
+
+
+
diff --git a/build-files/lima/2.12.0-Rscripts/README.md b/build-files/lima/2.12.0-Rscripts/README.md
@@ -0,0 +1,31 @@
+# Lima container with Rscripts
+
+Main tool: [lima](https://lima.how/)
+  
+Code repository: https://github.com/PacificBiosciences/barcoding
+
+Additional tools:
+- report_detail.R
+- report_summary.R
+
+Basic information on how to use this tool:
+- executables: lima, lima-undo
+- help: -h
+- version: --version
+- description: lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
+
+Additional information:
+
+This container includes two Rscripts that can visualize various metrics from the lima report.
+  
+Full documentation: https://lima.how/
+
+## Example Usage
+```bash
+lima [options] <INPUT.bam|xml|fa|fq|gz> <BARCODES.fa> <OUTPUT.bam|xml|fa|fq|gz>
+
+report_summry.R lima.report
+
+report_detail.R lima.report [pdf|png] [barcode_pair_names]
+```
+
diff --git a/build-files/lima/2.12.0/Dockerfile b/build-files/lima/2.12.0/Dockerfile
@@ -0,0 +1,45 @@
+FROM ubuntu:jammy AS app
+
+ARG LIMA_VER="2.12.0"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Lima"
+LABEL software.version="${LIMA_VER}"
+LABEL description="The PacBio Barcode Demultiplixer & Primer Remover"
+LABEL website="https://github.com/PacificBiosciences/barcoding"
+LABEL license="https://github.com/PacificBiosciences/barcoding/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/PacificBiosciences/barcoding/releases/download/v${LIMA_VER}/lima.tar.gz &&\
+    tar -C /usr/local/bin -xvf lima.tar.gz &&\
+    rm lima.tar.gz
+
+ENV LC_ALL=C
+
+CMD lima -h && lima-undo -h
+
+WORKDIR /data
+
+FROM app AS test
+
+RUN lima -h && lima-undo -h
+
+# download test files
+RUN wget -q --no-check-certificate https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/HiFiViral_Barcoded_M13_Primer_Plate.fasta \
+    https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/InqabaOmicronSamples_Barcoded_Sample.csv \
+    https://downloads.pacbcloud.com/public/dataset/HiFiViral/Jan_2022/m64187e_211217_130958.hifi_reads.bam
+
+# run test
+RUN lima m64187e_211217_130958.hifi_reads.bam HiFiViral_Barcoded_M13_Primer_Plate.fasta demux.hifi.bam --biosample-csv InqabaOmicronSamples_Barcoded_Sample.csv --hifi-preset ASYMMETRIC &&\
+    cat demux.hifi.lima.summary
+
+
+
+
+
diff --git a/build-files/lima/2.12.0/README.md b/build-files/lima/2.12.0/README.md
@@ -0,0 +1,18 @@
+# Lima container
+
+Main tool: [lima](https://lima.how/)
+  
+Code repository: https://github.com/PacificBiosciences/barcoding
+
+Basic information on how to use this tool:
+- executables: lima, lima-undo
+- help: -h
+- version: --version
+- description: lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
+
+Full documentation: https://lima.how/
+
+## Example Usage
+```bash
+lima [options] <INPUT.bam|xml|fa|fq|gz> <BARCODES.fa> <OUTPUT.bam|xml|fa|fq|gz>
+```
