update about

Cristianetaniguti · Jan 7, 2024 · a8d00f2 · a8d00f2
1 parent 45fe044
commit a8d00f2
Show file tree

Hide file tree

Showing 2 changed files with 60 additions and 39 deletions.
diff --git a/README.md b/README.md
@@ -17,11 +17,11 @@ By now, only one chromosome is evaluated in both workflows. However, the Empiric
 
 ### How to use 
 
-**warning**: The App current version is 0.0.1, it is compatible with Reads2Map workflows:
+**warning**: The App current version is 0.0.2, it is compatible with Reads2Map workflows:
 
 * SimulatedReads2Map_v1.0.2 or above
-* EmpiricalReads2Map_v1.5.0 or above
-* EmpiricalMap_v1.3.0 or above
+* EmpiricalReads2Map_v1.5.1 or above
+* EmpiricalMap_v1.3.1 or above
 
 
 ```{r, eval=FALSE}

diff --git a/inst/ext/about.Rmd b/inst/ext/about.Rmd
@@ -1,36 +1,57 @@
----
-title: "About"
-output: html_document
----
-
-<p align="center">
-<br>
-<img src="www/logo.svg" width="450"/>
-<br>
-<p/>
-
-## Reads2Map App
-
-This shiny app plots graphics for descriptive analyses of the datasets generated by the [Reads2Map workflow](https://github.com/Cristianetaniguti/Reads2Map) workflows. Upload your results in the `Upload data` session. 
-
-Each icon at the left corner of this page points to a different dataset and produces interactive plots.
-
-By now, only one chromosome is evaluated in both workflows. However, the EmpiricalReads2Map workflow also provide the complete VCF file to users reproduce only the chosen pipeline in the other chromosomes. Therefore, users can select the best pipeline using one chromosome and apply it to the others without spent all the time and computer resources needed to compare all the methods for all chromosomes. We showed an example of Reads2Map workflows usage in [Quickstart](https://cristianetaniguti.github.io/Tutorials/Reads2Map/Setup_and_run_Reads2Map_workflows.html)
-
-### How to use 
-
-**warning**: The App current version is 0.0.1, it is compatible with Reads2Map workflows:
-
-* SimulatedReads2Map_v1.0.2 or above
-* EmpiricalReads2Map_v1.5.0 or above
-* EmpiricalMap_v1.3.0 or above
-
-```{r, eval=FALSE}
-devtools::install_github('Cristianetaniguti/Reads2MapApp')
-Reads2MapApp::run_app()
-```
-
-## How to cite
-
-* [Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;  Byrne, D.;  Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092](https://doi.org/10.1093/gigascience/giad092)
-
+---
+title: "About"
+output: html_document
+---
+
+<p align="center">
+<br>
+<img src="www/logo.svg" width="450"/>
+<br>
+<p/>
+
+## Reads2Map App
+
+This shiny app plots graphics for descriptive analyses of the datasets generated by the [Reads2Map ](https://github.com/Cristianetaniguti/Reads2Map) workflows. Upload your results in the `Upload data` session. 
+
+Each icon at the left corner of this page points to a different dataset and produces interactive plots.
+
+By now, only one chromosome is evaluated in both workflows. However, the EmpiricalReads2Map workflow also provide the complete VCF file to users reproduce only the chosen pipeline in the other chromosomes. Therefore, users can select the best pipeline using one chromosome and apply it to the others without spent all the time and computer resources needed to compare all the methods for all chromosomes. We showed an example of Reads2Map workflows usage in [Quickstart](https://cristianetaniguti.github.io/Tutorials/Reads2Map/Setup_and_run_Reads2Map_workflows.html)
+
+### How to use 
+
+**warning**: The App current version is 0.0.2, it is compatible with Reads2Map workflows:
+
+* SimulatedReads2Map_v1.0.2 or above
+* EmpiricalReads2Map_v1.5.1 or above
+* EmpiricalMap_v1.3.1 or above
+
+
+```{r, eval=FALSE}
+devtools::install_github('Cristianetaniguti/Reads2MapApp')
+Reads2MapApp::run_app()
+```
+
+### Reads2MapApp versions
+
+We adapt the Reads2MapApp according to Reads2Map updates, if you have datasets from older versions of Reads2Map, use the compatible docker images Reads2MapApp version:
+
+Reads2Map workflow | workflow version | Reads2MapApp version
+--- | --- | --- 
+SimulatedReads2Map | 1.0.2 | 0.0.1 
+EmpiricalReads2Map | 1.5.0 | 0.0.1
+EmpiricalMap | 1.3.0 | 0.0.1
+EmpiricalReads2Map | 1.5.1 | 0.0.2
+EmpiricalMap | 1.3.1 | 0.0.2
+
+To download and deploy the image use:
+
+```{bash, eval=FALSE}
+docker pull cristaniguti/reads2mapapp:0.0.2  
+docker run --rm -e USERID=$(id -u) -e GROUPID=$(id -g) -p 8085:80 -e DISABLE_AUTH=true cristaniguti/reads2mapapp:0.0.2
+```
+
+This will make the container available in port 8085 (choose other if you prefer). After, you just need to go to your favorite browser and search for <your_localhost>:8085 (example: 127.0.0.1:8085). That is it! Everything you need is there.
+
+## How to cite
+
+* [Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;  Byrne, D.;  Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092](https://doi.org/10.1093/gigascience/giad092)