From a7a3d314d4bc04d68f5575b5529323e98deb29b7 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Mon, 9 Dec 2024 20:38:23 +0000 Subject: [PATCH] adding igv-reports version 1.12.0 --- Program_Licenses.md | 1 + README.md | 1 + igv-reports/1.12.0/Dockerfile | 56 +++++++++++++++++++++++++++++++++++ igv-reports/1.12.0/README.md | 30 +++++++++++++++++++ 4 files changed, 88 insertions(+) create mode 100644 igv-reports/1.12.0/Dockerfile create mode 100644 igv-reports/1.12.0/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index d57e19474..3da288bd4 100644 --- a/Program_Licenses.md +++ b/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 | diff --git a/README.md b/README.md index 363353eed..59e1f0ff6 100644 --- a/README.md +++ b/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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | | http://hmmer.org/ | | [homopolish](https://hub.docker.com/r/staphb/homopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | | https://github.com/ythuang0522/homopolish/ | | [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | +| [igv-reports](https://hub.docker.com/r/staphb/igv-reports)
[![docker pulls](https://badgen.net/docker/pulls/staphb/igv-reports)](https://hub.docker.com/r/staphb/igv-reports) | | https://github.com/igvteam/igv-reports | | [Integron Finder](https://hub.docker.com/r/staphb/integron_finder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/integron_finder)](https://hub.docker.com/r/staphb/integron_finder) | | https://github.com/gem-pasteur/Integron_Finder | | [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | | http://www.iqtree.org/ | | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | diff --git a/igv-reports/1.12.0/Dockerfile b/igv-reports/1.12.0/Dockerfile new file mode 100644 index 000000000..cdca831b0 --- /dev/null +++ b/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="${IGVREPORTS_VER}" +LABEL description="A Python application to generate self-contained HTML reports for variant review and other genomic applications." +LABEL website="https://github.com/igvteam/igv-reports" +LABEL license="https://github.com/igvteam/igv-reports/blob/master/LICENSE.md" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + python3-pip \ + libcurl4-gnutls-dev && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN pip install --no-cache-dir igv-reports==${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 + diff --git a/igv-reports/1.12.0/README.md b/igv-reports/1.12.0/README.md new file mode 100644 index 000000000..b1e4196be --- /dev/null +++ b/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 +```