-
Notifications
You must be signed in to change notification settings - Fork 125
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* adding genovi version 0.4.3 * added labels
- Loading branch information
Showing
4 changed files
with
110 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| FROM python:3.7-slim as app | ||
|
|
||
| ARG GENOVI_VER="0.4.3" | ||
| ARG CIRCOS_VER="0.69-9" | ||
|
|
||
| LABEL base.image="python:3.7-slim" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="GenoVi" | ||
| LABEL software.version="${GENOVI_VER}" | ||
| LABEL description="Visualizing circos plots" | ||
| LABEL website="https://github.com/robotoD/GenoVi" | ||
| LABEL license="https://github.com/robotoD/GenoVi/blob/main/LICENSE.txt" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| # most of this is for circos. cairo is for genovi. | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| build-essential \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps \ | ||
| libgd-dev \ | ||
| perl \ | ||
| cpanminus \ | ||
| pkg-config \ | ||
| make \ | ||
| libgd-graph-perl \ | ||
| libcairo2-dev && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # these. are. all. for. circos | ||
| RUN cpanm Config::General \ | ||
| Number::Format \ | ||
| ExtUtils::Config \ | ||
| ExtUtils::InstallPaths \ | ||
| Clone \ | ||
| Font::TTF::Font \ | ||
| GD \ | ||
| GD::Polyline \ | ||
| Math::Bezier \ | ||
| Math::Round \ | ||
| Math::VecStat \ | ||
| Params::Validate \ | ||
| Readonly \ | ||
| Regexp::Common \ | ||
| List::MoreUtils \ | ||
| SVG \ | ||
| Set::IntSpan \ | ||
| Statistics::Basic \ | ||
| Text::Format | ||
|
|
||
| # there are often more up-to-date versions of genovi on pypi as opposed to github | ||
| # cariosvg is required for creating png, but not listed as a dependency | ||
| RUN pip3 install --no-cache genovi==${GENOVI_VER} cairosvg | ||
|
|
||
| # install circos (and a short test) | ||
| RUN wget -q http://circos.ca/distribution/circos-${CIRCOS_VER}.tgz && \ | ||
| tar -xvf circos-${CIRCOS_VER}.tgz && \ | ||
| rm circos-${CIRCOS_VER}.tgz && \ | ||
| cd /circos-${CIRCOS_VER}/bin && \ | ||
| ./list.modules && \ | ||
| ./test.modules | ||
|
|
||
| # adding circos to PATH | ||
| ENV PATH=/circos-${CIRCOS_VER}/bin:$PATH \ | ||
| LC_ALL=C.UTF-8 | ||
|
|
||
| CMD genovi --help | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| FROM app as test | ||
|
|
||
| WORKDIR /test | ||
|
|
||
| RUN genovi -h && genovi --version | ||
|
|
||
| # using the input files from a recent published version on github | ||
| RUN wget -q https://github.com/robotoD/GenoVi/archive/refs/tags/0.2.16.tar.gz && \ | ||
| tar -vxf 0.2.16.tar.gz && \ | ||
| genovi -i GenoVi-0.2.16/input_test/Corynebacterium_alimapuense_VA37.gbk -s draft -cs paradise --cogs_unclassified -bc white && \ | ||
| genovi -i GenoVi-0.2.16/input_test/Acinetobacter_radioresistens_DD78.gbff -cs strong -s complete --size |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| # genovi container | ||
|
|
||
| Main tool: [GenoVi](https://github.com/robotoD/GenoVi) | ||
|
|
||
| Code repository: https://github.com/robotoD/GenoVi | ||
|
|
||
| Additional tools: | ||
| - circos | ||
| - python: 3.7 | ||
|
|
||
| Basic information on how to use this tool: | ||
| - executable: genovi | ||
| - help: --help | ||
| - version: --version | ||
| - description: GenoVi generates circular genome representations. | ||
|
|
||
| > GenoVi generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes. GenoVi pipeline combines several python scripts to automatically generate all needed files for Circos to generate circular plots, including customisable options for colour palettes, fonts, font format, background colour and scaling options for genomes comprising more than 1 replicon. | ||
| Full documentation: https://github.com/robotoD/GenoVi | ||
|
|
||
| ## Example Usage | ||
|
|
||
| ```bash | ||
| genovi -i <input>.gbk -s complete -o out | ||
| ``` | ||
|
|