sra-toolkit

container.yaml

@@ -15,7 +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; apt-get -y install samtools; cd cross-species-scaffolding; make dependencies; export PATH=\$PATH:\$PWD/"] }
+,{ name: "cross-species-scaffolding", version: "0.1", 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; apt-get -y install samtools; cd cross-species-scaffolding; make dependencies; export PATH=\$PATH:\$PWD/"] }
 ,{ 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: [] }

server/opt_home.R

@@ -147,7 +147,7 @@ createLibPrePost <- function(result) {
       result <- paste(result, "\tapt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl", sep = "\n")
       result <- paste(result, "\tapt-get install -y gcc fort77 aptitude", sep = "\n")
       result <- paste(result, "\taptitude install -y g++ xorg-dev libreadline-dev  gfortran", sep = "\n")
-      result <- paste(result, "\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev", sep = "\n")
+      result <- paste(result, "\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev git", sep = "\n")
       result <- paste(result, "\tapt-get update", sep = "\n")
   } else {
       result <- paste(result, "RUN apt-get update", sep = "\n")