From 711d51013205718e02bffab4ea3db50906d11727 Mon Sep 17 00:00:00 2001
From: jlopez <jimmy.lopez0023@gmail.com>
Date: Wed, 11 Jul 2018 13:32:17 +0200
Subject: [PATCH] Add new tools & fix bugs
---
container.yaml | 9 ++++++++-
pages/pages_def_home.R | 4 +++-
server/opt_home.R | 9 +++++++--
3 files changed, 18 insertions(+), 4 deletions(-)
diff --git a/container.yaml b/container.yaml
index 690ea66..3c81739 100755
--- a/container.yaml
+++ b/container.yaml
@@ -4,7 +4,8 @@ containers: [
,{ name: "bamtools", version: "2.4.0", description: "C++ API & command-line toolkit for working with BAM data", documentation: "https://github.com/pezmaster31/bamtools/wiki", install: ["conda install bamtools=2.4.0"] }
,{ name: "bcftools", version: "1.5", description: "Bcftools is a program for variant calling and manipulating VCFs and BCFs", documentation: "https://samtools.github.io/bcftools/", install: ["conda install bcftools=1.5"] }
,{ name: "bedtools", version: "2.25.0", description: "a powerful toolset for genome arithmetic", documentation: "http://quinlanlab.org/tutorials/bedtools/bedtools.html", install: ["conda install bedtools=2.25.0"] }
-,{ name: "bior_annotate", version: "2.1.1", description: "", documentation: "", install: [] }
+,{ name: "bedtools", version: "2.27.1", description: "a powerful toolset for genome arithmetic", documentation: "http://quinlanlab.org/tutorials/bedtools/bedtools.html", install: ["conda install bedtools=2.27.1"] }
+#,{ name: "bior_annotate", version: "2.1.1", description: "", documentation: "", install: [] }
,{ name: "blast", version: "2.2.31", description: "basic local alignment search tool", documentation: "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome", install: ["conda install blast=2.2.31"] }
,{ name: "bowtie", version: "1.1.2", description: "an ultrafast memory-efficient short read aligner", documentation: "http://bowtie-bio.sourceforge.net/manual.shtml", install: ["conda install bowtie=1.1.2"] }
,{ name: "bowtie2", version: "2.2.8", description: "an ultrafast memory-efficient short read aligner", documentation: "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", install: ["conda install bowtie2=2.2.8"] }
@@ -15,6 +16,8 @@ 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: "CNVnator", version: "0.3.3", description: "an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.", documentation: "https://github.com/abyzovlab/CNVnator", install: ["cd /opt/biotools/ ; wget --quiet https://root.cern.ch/download/root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz ; tar zxf root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz", "export ROOTSYS=/opt/biotools/root", "export LD_LIBRARY_PATH=\"$ROOTSYS/lib:$LD_LIBRARY_PATH\"", "echo 'export ROOTSYS=/opt/biotools/root' >> $SINGULARITY_ENVIRONMENT", "echo 'export LD_LIBRARY_PATH=\"$ROOTSYS/lib:$LD_LIBRARY_PATH\"' >> $SINGULARITY_ENVIRONMENT", "cd /opt/biotools/ ; wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 -O bcftools.tar.bz2 ; tar -xjvf bcftools.tar.bz2 ; cd bcftools-1.3.1/ ; make ; make prefix=/usr/local/bin install", "ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools ", "cd /opt/biotools/ ; wget --quiet https://github.com/abyzovlab/CNVnator/releases/download/v0.3.3/CNVnator_v0.3.3.zip ; unzip CNVnator_v0.3.3.zip ; cd CNVnator_v0.3.3/src/samtools/htslib-1.3.1/ ; make ; make install ; cd ../ ; make ; make install ; cd ../ ; make", "ln -s /opt/biotools/CNVnator_v0.3.3/src/cnvnator /opt/biotools/bin/cnvnator"] }
+,{ name: "cnv-seq", version: "1.0", description: "CNV-seq, a new method to detect copy number variation using high-throughput sequencing", documentation: "http://tiger.dbs.nus.edu.sg/cnv-seq/", install: ["cd /opt/biotools/ ; wget http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz; tar -xvf cnv-seq.tar.gz; ln -s /opt/biotools/cnv-seq/cnv-seq.pl bin/cnv-seq"]}
,{ name: "cross-species-scaffolding", version: "0.1", description: "Generate in silico mate-pair reads from single-/paired-end reads of your organism of interest", documentation: "https://github.com/thackl/cross-species-scaffolding", install: ["cd /opt/biotools; rm -rf cross-species-scaffolding; git clone https://github.com/thackl/cross-species-scaffolding.git ; cd cross-species-scaffolding; mkdir samples; make util/bcftools; make util/samtools; make dependencies;"], env: "export PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$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: [] }
@@ -55,6 +58,8 @@ containers: [
,{ name: "proteinprophet", version: "201510131012", description: "Protein inference for MS/MS analysis", documentation: "http://proteinprophet.sourceforge.net/", install: [] }
,{ name: "proteowizard", version: "3_0_9992", description: "tools and software libraries that facilitate proteomics data analysis", documentation: "http://proteowizard.sourceforge.net/", install: ["conda install proteowizard=3_0_9992"] }
,{ name: "raremetalworker", version: "4.13.7", description: "single variant analysis, generating summary statistics for gene level meta analyses", documentation: " http://genome.sph.umich.edu/wiki/RAREMETALWORKER", install: [] }
+,{ name: "repeatmasker", version: "4.0.6", description: "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", documentation: "http://www.repeatmasker.org/", install: ["conda install -c bioconda repeatmasker=4.0.6; mkdir /share; ln -s /opt/conda/share/RepeatMasker /share/RepeatMasker"]}
+#,{ name: "root", version: "6.04", description: "", documentation: "", install: ["conda install -c nlesc root=6.04"]}
,{ 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: "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"] }
@@ -75,6 +80,8 @@ containers: [
,{ name: "toppas", version: "1.11.1-3", description: "a graphical workflow editor for the analysis of high-throughput proteomics data", documentation: "http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/", install: [] }
,{ name: "TPMCalculator", version: "0.0.1", description: "This program calculates the TPM (Transcript per Millions) values for the exons and introns from NGS RNA-Seq aligned reads (BAM files)", documentation: "https://github.com/r78v10a07/TPMCalculator", install: [] }
,{ name: "tpp", version: "5.0", description: "a collection of integrated tools for MS/MS proteomics", documentation: "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP", install: [] }
+,{ name: " trf", version: "4.09", description: "Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.", documentation: "https://tandem.bu.edu/trf/trf.html", install: ["conda install -c bioconda trf=4.09"]}
+,{ name: "trimmomatic", version: "0.36", description: "Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.", documentation: "http://www.usadellab.org/cms/?page=trimmomatic", install: ["conda install -c bioconda trimmomatic=0.36"] }
,{ name: "vcftools", version: "0.1.14", description: "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project", documentation: "https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html", install: ["conda install vcftools=0.1.14"] }
,{ name: "vcftools", version: "0.1.15", description: "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project", documentation: "https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html", install: ["conda install vcftools=0.1.15"] }
,{ name: "velvet", version: "1.2.10", description: "Short read de novo assembler using de Bruijn graphs", documentation: "https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf", install: ["conda install velvet=1.2.10" ] }
diff --git a/pages/pages_def_home.R b/pages/pages_def_home.R
index 8d6d2a9..f71c8de 100755
--- a/pages/pages_def_home.R
+++ b/pages/pages_def_home.R
@@ -33,7 +33,9 @@ tabHome = fluidPage(align="left",
textInput("imageName", "Image Name", ""),
br(),
- selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `r-base` = 'r-base'), selected = "r-base", multiple = FALSE),
+ #selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `r-base` = 'r-base'), selected = "r-base", multiple = FALSE),
+ selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04'), selected = "ubuntu:16.04", multiple = FALSE),
+
br(),
radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
br(),
diff --git a/server/opt_home.R b/server/opt_home.R
index b04da82..afcd5e2 100755
--- a/server/opt_home.R
+++ b/server/opt_home.R
@@ -79,6 +79,8 @@ createEnv <- function(result) {
if(!is.null(input$dtbiocontainer_rows_all)) {
result <- paste(result, "\texport PATH=/opt/conda/bin:$PATH", sep = "\n")
result <- paste(result, "\texport PATH=/opt/biotools/bin:$PATH", sep = "\n")
+ result <- paste(result, "\texport ROOTSYS=/opt/biotools/root", sep = "\n")
+ result <- paste(result, "\texport LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
result <- createPathBiocontainer(result)
}
@@ -103,6 +105,9 @@ createEnv <- function(result) {
if(!is.null(input$dtbiocontainer_rows_all)) {
result <- paste(result, "RUN export PATH=/opt/conda/bin:$PATH", sep = "\n")
result <- paste(result, "RUN export PATH=/opt/biotools/bin:$PATH", sep = "\n")
+ result <- paste(result, "RUN export ROOTSYS=/opt/biotools/root", sep = "\n")
+ result <- paste(result, "RUN export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
+
result <- createPathBiocontainer(result)
}
}
@@ -390,7 +395,7 @@ createBiocontainer <- function(result, haveR) {
result <- paste0(result, "\n")
- result <- paste(result, "\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev", sep = "\n")
+ result <- paste(result, "\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev", sep = "\n")
result <- paste(result, "\tapt-get update", sep = "\n")
result <- paste0(result, "\n")
@@ -439,7 +444,7 @@ createBiocontainer <- function(result, haveR) {
result <- paste0(result, "\n")
- result <- paste(result, "RUN apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev", sep = "\n")
+ result <- paste(result, "RUN apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev", sep = "\n")
result <- paste(result, "RUN apt-get update", sep = "\n")
result <- paste0(result, "\n")
--
GitLab