From ac28a6ef13cf97f4dd58e6f221e5ec5e8df3a92d Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@univ-montp2.fr>
Date: Wed, 13 Jun 2018 14:21:42 +0200
Subject: [PATCH] Add a new env field to change envirenment variables needed by
tools
---
container.yaml | 5 +++--
pages/pages_def_home.R | 2 +-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/container.yaml b/container.yaml
index 3566a5d..c5aa786 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; echo export PATH='$PATH':$PWD/bin >> /.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: ["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: "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: [] }
@@ -30,6 +30,7 @@ containers: [
,{ name: "frc_align", version: "20150723", description: "Computes FRC from SAM/BAM file and not from afg files", documentation: "https://github.com/jts/frc_courve", install: [] }
,{ name: "gapcloser", version: "1.12", description: "A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes", documentation: "http://soap.genomics.org.cn/gapcloser.html", install: ["conda install soapdenovo2-gapcloser=1.12"] }
,{ name: "gatk", version: "3.8", description: "The full Genome Analysis Toolkit (GATK) framework, license restricted.", documentation: "", install: ["conda install gatk=3.8"] }
+,{ name: "gatk4", version: "4.0", description: "The full Genome Analysis Toolkit (GATK) framework, license restricted.", documentation: "", install: ["conda install gatk=3.8"] }
,{ name: "gcta", version: "1.24.7", description: "", documentation: "", install: ["conda install -c biobuilds gcta=1.26.0"] }
,{ 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"] }
@@ -62,7 +63,7 @@ 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 >> /.singularity.d/env/90-environment.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; rm sratoolkit.tar.gz; mv sratoolkit.*-ubuntu64 sratoolkit"], env: "export PATH='$PATH':$PWD/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: [] }
diff --git a/pages/pages_def_home.R b/pages/pages_def_home.R
index 4e1f26c..8d6d2a9 100755
--- a/pages/pages_def_home.R
+++ b/pages/pages_def_home.R
@@ -16,7 +16,7 @@ tabHome = fluidPage(align="left",
tags$b("Github R Packages: "),
p("Select each tool by clicking on the corresponding field in the table. They appear in the field below."),
p("Use 'Generate' button to generate your recipe in the preview area then copy/paste the text or use dowload button to get your file."),
- tags$b("To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"),
+ tags$b("For Singularity containers: To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"),
p("sudo singularity build ubuntu6.10_stacks2.0.simg ubuntu6.10_stacks2.0.recipes"),
tags$b("To run a program inside the image container :"),
p(" singularity exec ubuntu6.10_stacks2.0.simg python --version "),
--
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