From 4026ce02349b0b090d7f514a75365530ad7fb9b5 Mon Sep 17 00:00:00 2001
From: mmassaviol <mathieu.massaviol@hotmail.fr>
Date: Tue, 27 Nov 2018 11:31:50 +0100
Subject: [PATCH] Add kallisto & salmon tools

---
 container.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/container.yaml b/container.yaml
index 124af24..58d39be 100755
--- a/container.yaml
+++ b/container.yaml
@@ -41,6 +41,7 @@ containers: [
 ,{ name: "htslib", version: "1.8", description: "", documentation: "", install: ["conda install htslib=1.8"] }
 ,{ name: "jbrowse", version: "1.12.1", description: "", documentation: "", install: ["conda install jbrowse=1.12.1"] }
 ,{ name: "jellyfish", version: "2.2.6", description: "", documentation: "", install: ["conda install jellyfish=2.2.6"] }
+,{ name: "kallisto", version: "0.44.0", description: "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads", documentation: "https://pachterlab.github.io/kallisto/manual", install: ["conda install -c bioconda -c conda-forge kallisto=0.44.0"] }
 ,{ 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: [] }
@@ -66,6 +67,7 @@ containers: [
 #,{ name: "root", version: "6.04", description: "", documentation: "", install: ["conda install -c nlesc root=6.04"]}
 ,{ name: "sambamba", version: "0.6.6", description: "Tools for working with SAM/BAM data", documentation: "http://lomereiter.github.io/sambamba/", install: [" conda install -c bioconda sambamba=0.6.6"]}
 ,{ name: "saintq", version: "0.0.2", description: "assigning confidence scores to protein-protein interactions based on quantitative proteomics", documentation: "http://saint-apms.sourceforge.net/Main.html", install: [] }
+,{ name: "salmon", version: "0.11.3", description: "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data", documentation: "https://salmon.readthedocs.io/en/latest/", install: "conda install -c bioconda -c conda-forge salmon=0.11.3"}
 ,{ name: "samtools", version: "1.2", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.2"] }
 ,{ name: "samtools", version: "1.3", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.3"] }
 ,{ name: "samtools", version: "1.3.1", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.3.1"] }
-- 
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