New package ...

container.yaml

@@ -15,6 +15,7 @@ containers: [
 ,{ name: "cava", version: "1.1.1", description: "lightweight, fast and flexible NGS variant annotation tool", documentation: "http://www.well.ox.ac.uk/cava", install: [] }
 ,{ name: "clustal-omega", version: "1.2.1-1", description: "general purpose multiple sequence alignment program for proteins", documentation: "http://www.clustal.org/omega/#Documentation", install: ["apt-get install  clustalo"] }
 ,{ name: "comet", version: "1.1.0", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_2016010/", install: ["conda install -c auto comet=1.1.0"] }
+,{ name: "cross-species scaffolding", version: "", description: "Generate in silico mate-pair reads from single-/paired-end reads of your organism of interest", documentation: "https://github.com/thackl/cross-species-scaffolding", install: ["git clone https://github.com/thackl/cross-species-scaffolding.git; cd cross-species-scaffolding; make dependencies"] }
 ,{ name: "crux", version: "2.1", description: "a software toolkit for tandem mass spectrometry analysis", documentation: "http://cruxtoolkit.sourceforge.net/", install: [] }
 ,{ name: "denovogui", version: "1.10.4", description: "graphical user interface for de novo sequencing of tandem mass spectra", documentation: "https://github.com/compomics/denovogui", install: [] }
 ,{ name: "denovogui", version: "1.5.2", description: "graphical user interface for de novo sequencing of tandem mass spectra", documentation: "https://github.com/compomics/denovogui", install: [] }

pages/pages_def_home.R

@@ -20,8 +20,11 @@ tabHome = fluidPage(align="left",
                              p("Add your tools by clicking on the corresponding field in the table. They appear in the field so below."),
                              br(),
                              p("Use 'Generate' button to generate your recipe in the preview area then copy/paste the text or use dowload button to get your file."),
-                             br()
-                             
+                             p("# To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"),
+                             p("sudo singularity build ubuntu6.10_stacks2.0.simg ubuntu6.10_stacks2.0.recipes"),
+                             p("# to run a program inside the image container :"),
+                             p(" singularity exec ubuntu6.10_stacks2.0.simg python --version "),
+                             p("singularity exec ubuntu6.10_stacks2.0.simg python -c 'import pysam; print 2*2'")
                            )),
   
                     column(width = 2,