Commit 463741dc authored by khalid's avatar khalid
Browse files

best installation of cross-species-scaffolding dependencies

parent 9a05c39c
......@@ -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: ["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: "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; make dependencies; echo export PATH='$PATH':$PWD/bin >> /.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: [] }
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