best installation of cross-species-scaffolding dependencies

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: ["git clone https://github.com/thackl/cross-species-scaffolding.git; apt-get -y install samtools; cd cross-species-scaffolding; make dependencies; echo export PATH=$PATH:$PWD/ >> /etc/profile.d/conda.sh"] }
+,{ 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: ["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;sed -i 's/make/make \&\& make install/g' Makefile; make dependencies; echo export PATH='$PATH':$PWD/ >> /.singularity.d/env/90-environment.sh"] }
 ,{ 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: [] }
@@ -62,7 +62,7 @@ containers: [
 ,{ name: "soapec", version: "2.03", description: "A correction tool for SOAPdenovo", documentation: "http://soap.genomics.org.cn/soapdenovo.html", install: ["conda install soapec=2.03"] }
 ,{ name: "spades", version: "3.11.1", description: "Tools (written in C using htslib) for manipulating next-generation sequencing data", documentation: "http://bioinf.spbau.ru/spades", install: ["conda install spades=3.11.1"] }
 ,{ name: "spectra-cluster-cli", version: "1.0.1", description: "PRIDE Cluster algorithm to cluster heterogeneous mass spectra", documentation: "https://github.com/spectra-cluster/spectra-cluster-cli", install: ["conda install spectra-cluster-cli=1.0.1"] }
-,{ name: "sra-tools", version: "latest", description: "", documentation: "", installation: ["cd /opt/biotools; wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz; tar -vxzf sratoolkit.tar.gz; chemin=`ls -1 -d sra*ubuntu*`; echo export PATH=$PATH:$PWD/$chemin/bin >> /etc/profile.d/conda.sh"] }
+,{ name: "sra-tools", version: "latest", description: "", documentation: "", installation: ["cd /opt/biotools; wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz; tar -vxzf sratoolkit.tar.gz; chemin=`ls -1 -d sra*ubuntu*`; echo export PATH='$PATH':$PWD/$chemin/bin >> /.singularity.d/env/90-environment.sh"] }
 ,{ name: "stacks", version: "1.44", description: "Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population", documentation: "http://catchenlab.life.illinois.edu/stacks/", install: ["conda install stacks=1.44"] }
 ,{ name: "stacks", version: "2.0", description: "Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population", documentation: "http://catchenlab.life.illinois.edu/stacks/", install: ["wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0.tar.gz \\",  "&& tar -zxvf stacks-2.0.tar.gz -C /opt/biotools/bin/ \\", "&& cd /opt/biotools/bin/stacks-2.0/ \\", "&& ./configure \\", "&& make \\", "&& make install"]}
 ,{ name: "tandem", version: "10-12-01-1", description: "software that can match tandem mass spectra with peptide sequences", documentation: "http://www.thegpm.org/tandem/", install: [] }