Commit 6faff451 authored by khalid's avatar khalid
Browse files

Add recipe for minimap2 and nanopolish

parent e67ec0ef
......@@ -38,6 +38,8 @@ containers: [
,{ name: "magicblast", version: "1.3.0", description: "Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome", documentation: "https://ncbi.github.io/magicblast/", install: ["wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-x64-linux.tar.gz -O /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz \\", "&& tar xzfv /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz -C /opt/biotools/bin/ \\", "&& cd /opt/biotools/bin/ncbi-magicblast-1.3.0/ \\", "&& chmod -R 755 /opt/biotools/bin/ncbi-magicblast-1.3.0 \\", "&& ln -s /opt/biotools/bin/ncbi-magicblast-1.3.0/bin/magicblast /opt/biotools/bin/magicblast_1.3.0 \\", "&& ln -s /opt/biotools/bin/ncbi-magicblast-1.3.0/bin/makeblastdb /opt/biotools/bin/makeblastdb_1.3.0 \\", "&& rm -rf /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz"] }
,{ name: "msamanda", version: "1.0.0.5242", description: "scoring system to identify peptides out of tandem mass spectrometry", documentation: "http://ms.imp.ac.at/?goto=msamanda", install: [] }
,{ name: "msgfp", version: "9949", description: "MS/MS database search tool", documentation: "http://proteomics.ucsd.edu/Software/MSGFPlus/", install: [] }
,{ name: "minimap2", version: "2.1.0",description: "a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database", documentation: "https://github.com/lh3/minimap2", install: ["cd /opt/biotools/bin/;curl -L https://github.com/lh3/minimap2/releases/download/v2.10/minimap2-2.10_x64-linux.tar.bz2 | tar -jxvf - "], env: "export PATH:'$PATH':/opt/biotools/bin/minimap2-2.10_x64-linux/"}
,{name: "nanopolish", version: "latest", description: "signal-level analysis of Oxford Nanopore sequencing data.", documentation: "https://github.com/jts/nanopolish", install: ["cd /opt/biotools/bin;git clone --recursive https://github.com/jts/nanopolish.git;cd nanopolish;make;"], env: "export PATH='$PATH':/opt/biotools/bin/nanopolish"}
,{ name: "novor", version: "1b", description: "real-time peptide de novo sequencing", documentation: "http://www.rapidnovor.com/", install: ["wget https://github.com/BioDocker/software-archive/releases/download/NovoR/novor_academic_latest.zip -O /tmp/novor_academic_latest.zip \\", "&& unzip /tmp/novor_academic_latest.zip -d /opt/biotools/bin/ \\", "&& bash -c 'echo -e \"#!/bin/bash\\njava -jar /opt/biotools/bin/novor_v1b/lib/novor.jar $@\" > /opt/biotools/bin/novor_1b' && \\", "&& chmod +x /opt/biotools/bin/novor_1b \\", "&& rm -rf /tmp/novor_academic_latest.zip "] }
,{ name: "openms", version: "2.2.0", description: "C++ libraries ans tools for MS/MS data analysis", documentation: "http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.2.0-documentation/html/index.html", install: [] }
,{ name: "pepnovo", version: "20101117", description: "de novo sequencing of low precision MS/MS data", documentation: "http://proteomics.ucsd.edu/Software/PepNovo/", install: ["conda install pepnovo=20101117"] }
......@@ -63,7 +65,7 @@ containers: [
,{ name: "soapec", version: "2.03", description: "A correction tool for SOAPdenovo", documentation: "http://soap.genomics.org.cn/soapdenovo.html", install: ["conda install soapec=2.03"] }
,{ name: "spades", version: "3.11.1", description: "Tools (written in C using htslib) for manipulating next-generation sequencing data", documentation: "http://bioinf.spbau.ru/spades", install: ["conda install spades=3.11.1"] }
,{ name: "spectra-cluster-cli", version: "1.0.1", description: "PRIDE Cluster algorithm to cluster heterogeneous mass spectra", documentation: "https://github.com/spectra-cluster/spectra-cluster-cli", install: ["conda install spectra-cluster-cli=1.0.1"] }
,{ name: "sra-tools", version: "latest", description: "", documentation: "", installation: ["cd /opt/biotools; wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz; tar -vxzf sratoolkit.tar.gz; rm sratoolkit.tar.gz; mv sratoolkit.*-ubuntu64 sratoolkit"], env: "export PATH=$PATH:$PWD/sratoolkit/bin" }
,{ name: "sra-tools", version: "latest", description: "", documentation: "", installation: ["cd /opt/biotools; wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz; tar -vxzf sratoolkit.tar.gz; rm sratoolkit.tar.gz; mv sratoolkit.*-ubuntu64 sratoolkit"], env: "export PATH=$PATH:/opt/biotools/sratoolkit/bin" }
,{ 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: [] }
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