adding igv-reports version 1.12.0

Program_Licenses.md

@@ -74,6 +74,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
 | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |
 | htslib | MIT | https://github.com/samtools/htslib/blob/develop/LICENSE |
+| IGV-Reports | MIT | https://github.com/igvteam/igv-reports/blob/master/LICENSE.md |
 | Integron Finder | GNU GPLv3 | https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING |
 | iqtree | GNU GPLv2 | https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE |
 | iqtree2 | GNU GPLv2 | https://github.com/iqtree/iqtree2/blob/master/LICENSE |

README.md

@@ -183,6 +183,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li><li>[1.20](./htslib/1.20/)</li><li>[1.20.c](./htslib/1.20.c/)</li><li>[1.21](./htslib/1.21/)</li></ul> | https://www.htslib.org/ |
+| [igv-reports](https://hub.docker.com/r/staphb/igv-reports) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/igv-reports)](https://hub.docker.com/r/staphb/igv-reports) | <ul><li>[1.12.0](./igv-reports/1.12.0/)</li></ul> | https://github.com/igvteam/igv-reports |
 | [Integron Finder](https://hub.docker.com/r/staphb/integron_finder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/integron_finder)](https://hub.docker.com/r/staphb/integron_finder) | <ul><li>[2.0.5](./integron_finder/2.0.5/)</li></ul> | https://github.com/gem-pasteur/Integron_Finder |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li><li>[2.2.2.7](iqtree2/2.2.2.7/)</li><li>[2.3.1](iqtree2/2.3.1/)</li><li>[2.3.4](iqtree2/2.3.4/)</li><li>[2.3.6](iqtree2/2.3.6/)</li></ul> | http://www.iqtree.org/ |

igv-reports/1.12.0/Dockerfile

@@ -0,0 +1,56 @@
+ARG IGVREPORTS_VER=1.12.0
+
+FROM ubuntu:jammy as app
+
+ARG IGVREPORTS_VER
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="IGV Reports"
+LABEL software.version="${IGVREPORTS_VER}"
+LABEL description="A Python application to generate self-contained HTML reports for variant review and other genomic applications."
+LABEL website="https://github.com/igvteam/igv-reports"
+LABEL license="https://github.com/igvteam/igv-reports/blob/master/LICENSE.md"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    python3-pip \
+    libcurl4-gnutls-dev && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN pip install --no-cache-dir igv-reports==${IGVREPORTS_VER}
+
+ENV PATH="$PATH" LC_ALL=C CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+
+CMD [ "create_report", "-h" ]
+
+WORKDIR /data
+
+FROM app as test
+
+ARG IGVREPORTS_VER
+
+WORKDIR /test
+
+RUN create_report -h
+
+RUN wget -q https://github.com/igvteam/igv-reports/archive/refs/tags/v${IGVREPORTS_VER}.tar.gz && \
+    tar -xvf v${IGVREPORTS_VER}.tar.gz && \
+    cd igv-reports-${IGVREPORTS_VER} && \
+    create_report test/data/variants/variants.vcf.gz \
+        --genome hg38 \
+        --ideogram test/data/hg38/cytoBandIdeo.txt \
+        --flanking 1000 \
+        --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
+        --samples reads_1_fastq \
+        --sample-columns DP GQ \
+        --tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam test/data/hg38/refGene.txt.gz \
+        --output example_vcf.html && \
+    wc -l example_vcf.html
+

igv-reports/1.12.0/README.md

@@ -0,0 +1,30 @@
+# igv-reports container
+
+Main tool: [igv-reports](https://github.com/igvteam/igv-reports)
+
+Code repository: https://github.com/igvteam/igv-reports
+
+Basic information on how to use this tool:
+- executable: create_report
+- help: -h
+- version: NA
+- description: Creates igv-style html report of variants
+
+Additional information: |
+> A Python application to generate self-contained HTML reports for variant review and other genomic applications. Reports consist of a table of genomic sites and an embedded IGV genome browser for viewing data for each site. The tool extracts slices of data for each site and embeds the data as blobs in the HTML report file. The report can be opened in a web browser as a static page, with no depenency on the original input files.
+
+
+Full documentation: https://github.com/igvteam/igv-reports
+
+## Example Usage
+
+```bash
+create_report input.vcf.gz \
+    --fasta reference.fa \
+    --flanking 1000 \
+    --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
+    --samples reads_1_fastq \
+    --sample-columns DP GQ \
+    --tracks input.vcf.gz recalibrated.bam \
+    --output output.html
+```