From 7d3d3165f5393e8fea6d95bbe03451d4e10eb321 Mon Sep 17 00:00:00 2001 From: Kincekara Date: Thu, 2 Nov 2023 19:47:41 +0000 Subject: [PATCH 1/2] add pavian --- Program_Licenses.md | 1 + README.md | 1 + pavian/1.2.1/Dockerfile | 40 ++++++++++++++++++++++++++++++++++++++++ pavian/1.2.1/README.md | 25 +++++++++++++++++++++++++ 4 files changed, 67 insertions(+) create mode 100644 pavian/1.2.1/Dockerfile create mode 100644 pavian/1.2.1/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index f35c5bc2e..d1306e403 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -90,6 +90,7 @@ The licenses of the open-source software that is contained in these Docker image | Panaroo | MIT | https://github.com/gtonkinhill/panaroo/blob/master/LICENSE | | Pangolin | GNU GPLv3 | https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt | | pasty | Apache 2.0 | https://github.com/rpetit3/pasty/blob/main/LICENSE | +| Pavian | GNU GPLv3 | https://github.com/fbreitwieser/pavian/blob/master/DESCRIPTION | | pbptyper | MIT | https://github.com/rpetit3/pbptyper/blob/main/LICENSE | | Phyml | GNU GPLv3 | https://github.com/stephaneguindon/phyml/blob/master/COPYING | | Piggy | GNU GPLv3 | https://github.com/harry-thorpe/piggy/blob/master/LICENSE | diff --git a/README.md b/README.md index 8985a627f..3960fe262 100644 --- a/README.md +++ b/README.md @@ -194,6 +194,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) |
Click to see Pangolin v4.2 and older versions! **Pangolin version & pangoLEARN data release date** **Pangolin version & pangolin-data version**
**Pangolin version & pangolin-data version** | https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) | | [parallel-perl](https://hub.docker.com/r/staphb/parallel-perl)
[![docker pulls](https://badgen.net/docker/pulls/staphb/parallel-perl)](https://hub.docker.com/r/staphb/parallel-perl) | | https://www.gnu.org/software/parallel | | [pasty](https://hub.docker.com/r/staphb/pasty)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | | https://github.com/rpetit3/pasty | +| [Pavian](https://hub.docker.com/r/staphb/pavian)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | | https://github.com/fbreitwieser/pavian | | [pbptyper](https://hub.docker.com/r/staphb/pbptyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | | https://github.com/rpetit3/pbptyper | | [Phyml](https://hub.docker.com/r/staphb/phyml)
[![docker pulls](https://badgen.net/docker/pulls/staphb/phyml)](https://hub.docker.com/r/staphb/phyml) | | https://github.com/stephaneguindon/phyml | | [Piggy](https://hub.docker.com/r/staphb/piggy)
[![docker pulls](https://badgen.net/docker/pulls/staphb/piggy)](https://hub.docker.com/r/staphb/piggy) | | https://github.com/harry-thorpe/piggy | diff --git a/pavian/1.2.1/Dockerfile b/pavian/1.2.1/Dockerfile new file mode 100644 index 000000000..25b2471c8 --- /dev/null +++ b/pavian/1.2.1/Dockerfile @@ -0,0 +1,40 @@ +FROM rocker/shiny:4.1.0 as app + +ARG SOFTWARENAME_VER="1.2.1" + +LABEL base.image="rocker/shiny:4.1.0" +LABEL dockerfile.version="1" +LABEL software="Pavian" +LABEL software.version="${SOFTWARENAME_VER}" +LABEL description="Interactive analysis of metagenomics data for microbiome studies and pathogen identification." +LABEL website="https://github.com/fbreitwieser/pavian" +LABEL license="https://github.com/fbreitwieser/pavian/blob/master/DESCRIPTION" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + liblzma-dev \ + libbz2-dev &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# based on https://github.com/fbreitwieser/pavian/blob/master/inst/docker/Dockerfile by Florian Breitwieser +RUN R -e "install.packages('BiocManager', version = 3.13 , clean = TRUE); BiocManager::install('Rsamtools', ask=FALSE)" &&\ + R -e "install.packages('remotes', clean = TRUE);remotes::install_github('fbreitwieser/pavian@750a18073bae3c443d8b9465d8d6e997595788be', clean = TRUE)" &&\ + rm -rf /srv/shiny-server/* &&\ + R -e "sapply(list.files(system.file('shinyapp',package='pavian'),full.names=TRUE),file.copy,to='/srv/shiny-server/',recursive=TRUE)" + +EXPOSE 3838 + +CMD ["/usr/bin/shiny-server"] + +ENV LC_ALL=C + +WORKDIR /data + +## Test ## +FROM app as test + +CMD ["/bin/bash"] + +RUN R -e "installed.packages()" > test.log &&\ + cat test.log diff --git a/pavian/1.2.1/README.md b/pavian/1.2.1/README.md new file mode 100644 index 000000000..381638f36 --- /dev/null +++ b/pavian/1.2.1/README.md @@ -0,0 +1,25 @@ + +# Pavian container + +Main tool: [Pavian](https://github.com/fbreitwieser/pavian) + +Code repository: https://github.com/fbreitwieser/pavian + +Additional tools: +- R: 4.1.0 + +Basic information on how to use this tool: + +Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. It also provides an alignment viewer for validation of matches to a particular genome. + +![image](https://cloud.githubusercontent.com/assets/516060/20188595/5c8b9808-a747-11e6-9235-296a2314659a.png) + +Full documentation: https://github.com/fbreitwieser/pavian + +## Example Usage +You should publish a container's port(s) to the host while running pavian. +```bash +docker run --rm -p 3838:3838 staphb/pavian:1.2.1 +``` +Pavian will then be available at http://127.0.0.1:3838 in your web browser + From 89eaa30d11e7bd466f9b84d78a6a9bd98b5b02ce Mon Sep 17 00:00:00 2001 From: Kincekara Date: Fri, 3 Nov 2023 13:34:28 +0000 Subject: [PATCH 2/2] update readme --- pavian/1.2.1/README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pavian/1.2.1/README.md b/pavian/1.2.1/README.md index 381638f36..f1c334f93 100644 --- a/pavian/1.2.1/README.md +++ b/pavian/1.2.1/README.md @@ -19,7 +19,9 @@ Full documentation: https://github.com/fbreitwieser/pavian ## Example Usage You should publish a container's port(s) to the host while running pavian. ```bash +# run as root docker run --rm -p 3838:3838 staphb/pavian:1.2.1 +# non-root +docker run --rm --user shiny -p 3838:3838 staphb/pavian:1.2.1 ``` Pavian will then be available at http://127.0.0.1:3838 in your web browser -