diff --git a/README.md b/README.md index 316a18592..311b41a3c 100644 --- a/README.md +++ b/README.md @@ -204,7 +204,7 @@ To learn more about the docker pull rate limits and the open source software pro | [PopPUNK](https://hub.docker.com/r/staphb/poppunk/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/poppunk)](https://hub.docker.com/r/staphb/poppunk) | | https://github.com/bacpop/PopPUNK | | [Porechop](https://hub.docker.com/r/staphb/porechop/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | | https://github.com/rrwick/Porechop | | [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | | https://github.com/tseemann/prokka | -| [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | | https://github.com/moshi4/pyGenomeViz | +| [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | | https://github.com/moshi4/pyGenomeViz | | [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| | https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED) | diff --git a/pygenomeviz/0.4.3/Dockerfile b/pygenomeviz/0.4.3/Dockerfile new file mode 100644 index 000000000..65b7d411f --- /dev/null +++ b/pygenomeviz/0.4.3/Dockerfile @@ -0,0 +1,46 @@ +FROM python:3.9.17-slim as app + +ARG PYGENOMEVIZ_VER="0.4.3" + +LABEL base.image="python:3.9.17-slim" +LABEL dockerfile.version="1" +LABEL software="pyGenomeViz" +LABEL software.version=$PYGENOMEVIZ_VER +LABEL description="genome visualization python package for comparative genomics" +LABEL website="https://moshi4.github.io/pyGenomeViz/" +LABEL license="MIT License" +LABEL license.url="https://github.com/moshi4/pyGenomeViz/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +#mmseqs2=14-7e284+ds-1+b2 +#mummer=3.23+dfsg-8 +#progressivemauve=1.2.0+4713+dfsg-5+b1 +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + procps \ + mmseqs2 \ + mummer \ + progressivemauve && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN pip install --no-cache-dir pygenomeviz==$PYGENOMEVIZ_VER + +ENV LC_ALL=C.UTF-8 + +CMD pgv-simpleplot --help && pgv-mmseqs --help && pgv-mummer --help && pgv-pmauve --help + +WORKDIR /data + +FROM app as test + +WORKDIR /test + +RUN pgv-simpleplot --help && pgv-mmseqs --help && pgv-mummer --help && pgv-pmauve --help + +RUN pgv-download-dataset -n erwinia_phage && \ + pgv-mummer --gbk_resources MT939486.gbk MT939487.gbk MT939488.gbk LT960552.gbk -o mummer_test --tick_style axis --align_type left --feature_plotstyle arrow && \ + pgv-mmseqs --gbk_resources MT939486.gbk MT939487.gbk MT939488.gbk LT960552.gbk -o mmseqs_test --tick_style axis --align_type left --feature_plotstyle arrow && \ + pgv-download-dataset -n escherichia_coli && \ + pgv-pmauve --seq_files NC_000913.gbk NC_002695.gbk NC_011751.gbk NC_011750.gbk -o pmauve_test --tick_style bar && \ + ls mummer_test/result.png mmseqs_test/result.png pmauve_test/result.png diff --git a/pygenomeviz/0.4.3/README.md b/pygenomeviz/0.4.3/README.md new file mode 100644 index 000000000..1e48b6130 --- /dev/null +++ b/pygenomeviz/0.4.3/README.md @@ -0,0 +1,50 @@ +# pyGenomeViz container + +Main tool : [pyGenomeViz](https://moshi4.github.io/pyGenomeViz/) + +Additional tools: +- MMseqs2 v14-7e284+ds-1+b2 +- MUMmer v3.23+dfsg-8 +- progressiveMauve v1.2.0+4713+dfsg-5+b1 + +Full documentation: https://moshi4.github.io/pyGenomeViz/ + +> pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib. This package is developed for the purpose of easily and beautifully plotting genomic features and sequence similarity comparison links between multiple genomes. + +## Example Usage + +Using the CLI + +```bash +# Download four Erwinia phage genbank files +pgv-download-dataset -n erwinia_phage + +# run pyGenomeViz to visualize MUMmer alignment +pgv-mummer --gbk_resources MT939486.gbk MT939487.gbk MT939488.gbk LT960552.gbk -o mummer_example1 --tick_style axis --align_type left --feature_plotstyle arrow + +# run pyGenomeViz to visualize MMseqs2 alignment +pgv-mmseqs --gbk_resources MT939486.gbk:250000-358115 MT939487.gbk:250000-355376 MT939488.gbk:250000-356948 LT960552.gbk:270000-340000 -o mmseqs_example2 --tick_style bar --feature_plotstyle arrow + +# Download four E.coli genbank files +pgv-download-dataset -n escherichia_coli + +# run pyGenomeViz to visualize progressiveMauve alignment +pgv-pmauve --seq_files NC_000913.gbk NC_002695.gbk NC_011751.gbk NC_011750.gbk -o pmauve_example1 --tick_style bar +``` + +This container contains the pygenomeviz python package, so custom scripts can import pygenomeviz + +```python +from pygenomeviz import GenomeViz + +name, genome_size = "Tutorial 01", 5000 +cds_list = ((100, 900, -1), (1100, 1300, 1), (1350, 1500, 1), (1520, 1700, 1), (1900, 2200, -1), (2500, 2700, 1), (2700, 2800, -1), (2850, 3000, -1), (3100, 3500, 1), (3600, 3800, -1), (3900, 4200, -1), (4300, 4700, -1), (4800, 4850, 1)) + +gv = GenomeViz() +track = gv.add_feature_track(name, genome_size) +for idx, cds in enumerate(cds_list, 1): + start, end, strand = cds + track.add_feature(start, end, strand, label=f"CDS{idx:02d}") + +fig = gv.plotfig() +```