Merge pull request #780 from Kincekara/pavian

adds Pavian

Program_Licenses.md

@@ -91,6 +91,7 @@ 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 |

README.md

@@ -195,6 +195,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Pangolin](https://hub.docker.com/r/staphb/pangolin) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) | <details><summary> Click to see Pangolin v4.2 and older versions! </summary> **Pangolin version & pangoLEARN data release date** <ul><li>1.1.14</li><li>2.0.4 & 2020-07-20</li><li>2.0.5 & 2020-07-20</li><li>2.1.1 & 2020-12-17</li><li>2.1.3 & 2020-12-17</li><li>2.1.6 & 2021-01-06</li><li>2.1.7 & 2021-01-11</li><li>2.1.7 & 2021-01-20</li><li>2.1.8 & 2021-01-22</li><li>2.1.10 & 2021-02-01</li><li>2.1.11 & 2021-02-01</li><li>2.1.11 & 2021-02-05</li><li>2.2.1 & 2021-02-06</li><li>2.2.2 & 2021-02-06</li><li>2.2.2 & 2021-02-11</li><li>2.2.2 & 2021-02-12</li><li>2.3.0 & 2021-02-12</li><li>2.3.0 & 2021-02-18</li><li>2.3.0 & 2021-02-21</li><li>2.3.2 & 2021-02-21</li><li>2.3.3 & 2021-03-16</li><li>2.3.4 & 2021-03-16</li><li>2.3.5 & 2021-03-16</li><li>2.3.6 & 2021-03-16</li><li>2.3.6 & 2021-03-29</li><li>2.3.8 & 2021-04-01</li><li>2.3.8 & 2021-04-14</li><li>2.3.8 & 2021-04-21</li><li>2.3.8 & 2021-04-23</li><li>2.4 & 2021-04-28</li><li>2.4.1 & 2021-04-28</li><li>2.4.2 & 2021-04-28</li><li>2.4.2 & 2021-05-10</li><li>2.4.2 & 2021-05-11</li><li>2.4.2 & 2021-05-19</li><li>3.0.5 & 2021-06-05</li><li>3.1.3 & 2021-06-15</li><li>3.1.5 & 2021-06-15</li><li>3.1.5 & 2021-07-07-2</li><li>3.1.7 & 2021-07-09</li><li>3.1.8 & 2021-07-28</li><li>3.1.10 & 2021-07-28</li><li>3.1.11 & 2021-08-09</li><li>3.1.11 & 2021-08-24</li><li>3.1.11 & 2021-09-17</li><li>3.1.14 & 2021-09-28</li><li>3.1.14 & 2021-10-13</li><li>3.1.16 & 2021-10-18</li><li>3.1.16 & 2021-11-04</li><li>3.1.16 & 2021-11-09</li><li>3.1.16 & 2021-11-18</li><li>3.1.16 & 2021-11-25</li><li>3.1.17 & 2021-11-25</li><li>3.1.17 & 2021-12-06</li><li>3.1.17 & 2022-01-05</li><li>3.1.18 & 2022-01-20</li><li>3.1.19 & 2022-01-20</li><li>3.1.20 & 2022-02-02</li><li>3.1.20 & 2022-02-28</li></ul> **Pangolin version & pangolin-data version** <ul><li>4.0 & 1.2.133</li><li>4.0.1 & 1.2.133</li><li>4.0.2 & 1.2.133</li><li>4.0.3 & 1.2.133</li><li>4.0.4 & 1.2.133</li><li>4.0.5 & 1.3</li><li>4.0.6 & 1.6</li><li>4.0.6 & 1.8</li><li>4.0.6 & 1.9</li><li>4.1.1 & 1.11</li><li>4.1.2 & 1.12</li><li>4.1.2 & 1.13</li><li>4.1.2 & 1.14</li><li>4.1.3 & 1.15.1</li><li>4.1.3 & 1.16</li><li>4.1.3 & 1.17</li><li>4.2 & 1.18</li><li>4.2 & 1.18.1</li><li>4.2 & 1.18.1.1</li><li>4.2 & 1.19</li></ul> </details> **Pangolin version & pangolin-data version** <ul><li>[4.3 & 1.20](pangolin/4.3-pdata-1.20/)</li><li>[4.3 & 1.21](pangolin/4.3-pdata-1.21/)</li><li>[4.3.1 & 1.22](pangolin/4.3.1-pdata-1.22/)</li><li>[4.3.1 & 1.23](pangolin/4.3.1-pdata-1.23/)</li><li>[4.3.1 & 1.23.1](pangolin/4.3.1-pdata-1.23.1/)</li></ul> |  https://github.com/cov-lineages/pangolin<br/>https://github.com/cov-lineages/pangoLEARN<br/>https://github.com/cov-lineages/pango-designation<br/>https://github.com/cov-lineages/scorpio<br/>https://github.com/cov-lineages/constellations<br/>https://github.com/cov-lineages/lineages (archived)<br/>https://github.com/hCoV-2019/pangolin (archived) |
 | [parallel-perl](https://hub.docker.com/r/staphb/parallel-perl) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/parallel-perl)](https://hub.docker.com/r/staphb/parallel-perl) | <ul><li>20200722</li></ul> | https://www.gnu.org/software/parallel |
 | [pasty](https://hub.docker.com/r/staphb/pasty) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | <ul><li>1.0.2</li></ul> | https://github.com/rpetit3/pasty |
+| [Pavian](https://hub.docker.com/r/staphb/pavian) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | <ul><li>[1.2.1](pavian/1.2.1/)</li></ul> | https://github.com/fbreitwieser/pavian |
 | [pbptyper](https://hub.docker.com/r/staphb/pbptyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | <ul><li>1.0.0</li><li>1.0.1</li><li>1.0.4</li></ul> | https://github.com/rpetit3/pbptyper |
 | [Phyml](https://hub.docker.com/r/staphb/phyml) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/phyml)](https://hub.docker.com/r/staphb/phyml) | <ul><li>3.3.20220408</li></ul> | https://github.com/stephaneguindon/phyml |
 | [Piggy](https://hub.docker.com/r/staphb/piggy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/piggy)](https://hub.docker.com/r/staphb/piggy) | <ul><li>1.5</li></ul> | https://github.com/harry-thorpe/piggy |

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="[email protected]"
+
+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

pavian/1.2.1/README.md

@@ -0,0 +1,27 @@
+
+# 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
+# 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