diff --git a/container.yaml b/container.yaml
index 106b1bbb80c6a958346847554d84b5274a19b9ab..0502b778a5a7d2d3e3ae040175d3b149dba8629e 100755
--- a/container.yaml
+++ b/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: "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: ["cd /opt/biotools; rm -rf cross-species-scaffolding; git clone https://github.com/thackl/cross-species-scaffolding.git ; apt-get -y install samtools; cd cross-species-scaffolding; mkdir samples; make dependencies;"], env: "export PATH=/opt/biotools/cross-species-scaffolding/bin:$PATH" }
+,{ name: "cross-species-scaffolding", version: "0.1", description: "Generate in silico mate-pair reads from single-/paired-end reads of your organism of interest", documentation: "https://github.com/thackl/cross-species-scaffolding", install: ["cd /opt/biotools; rm -rf cross-species-scaffolding; git clone https://github.com/thackl/cross-species-scaffolding.git ; cd cross-species-scaffolding; mkdir samples; make util/bcftools; make util/samtools; make dependencies;"], env: "export PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$PATH" }
 ,{ 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: [] }