thakk/bioinformatics:latest

$ singularity pull shub://thakk/bioinformatics:latest

Singularity Recipe

Bootstrap: docker
From: centos:8
Stage: build

%setup

%files

%help

   Bionformatics tools.

   Complete list of installed tools:
      - Samtools
      - BEDTools
      - FastQC
      - Bowtie2
      - MultiQC
      - Cutadapt
      - STAR
      - Hisat2
      - Picard
      - Trimmomatic
      - Samblaster
      - VarScan
      - Vcfanno
      - Plink
      - MACS2
      - Homer
      - NextFlow
      - nf-core
      - MAGeCK
      - TrimGalore
      - Bismark
      - UCSC tools:
         - addCols
         - ameme
         - autoDtd
         - autoSql
         - autoXml
         - ave
         - aveCols
         - axtChain
         - axtSort
         - axtSwap
         - axtToMaf
         - axtToPsl
         - bamToPsl
         - bedClip
         - bedCommonRegions
         - bedCoverage
         - bedExtendRanges
         - bedGeneParts
         - bedGraphPack
         - bedGraphToBigWig
         - bedIntersect
         - bedItemOverlapCount
         - bedJoinTabOffset
         - bedJoinTabOffset.py
         - bedMergeAdjacent
         - bedPartition
         - bedPileUps
         - bedRemoveOverlap
         - bedRestrictToPositions
         - bedSort
         - bedToBigBed
         - bedToExons
         - bedToGenePred
         - bedToPsl
         - bedWeedOverlapping
         - bigBedInfo
         - bigBedNamedItems
         - bigBedSummary
         - bigBedToBed
         - bigMafToMaf
         - bigPslToPsl
         - bigWigAverageOverBed
         - bigWigCat
         - bigWigCluster
         - bigWigCorrelate
         - bigWigInfo
         - bigWigMerge
         - bigWigSummary
         - bigWigToBedGraph
         - bigWigToWig
         - binFromRange
         - blastToPsl
         - blastXmlToPsl
         - blat
         - calc
         - catDir
         - catUncomment
         - chainAntiRepeat
         - chainBridge
         - chainFilter
         - chainMergeSort
         - chainNet
         - chainPreNet
         - chainSort
         - chainSplit
         - chainStitchId
         - chainSwap
         - chainToAxt
         - chainToPsl
         - chainToPslBasic
         - checkAgpAndFa
         - checkCoverageGaps
         - checkHgFindSpec
         - checkTableCoords
         - chopFaLines
         - chromGraphFromBin
         - chromGraphToBin
         - clusterGenes
         - colTransform
         - countChars
         - cpg_lh
         - crTreeIndexBed
         - crTreeSearchBed
         - dbSnoop
         - dbTrash
         - endsInLf
         - estOrient
         - expMatrixToBarchartBed
         - faAlign
         - faCmp
         - faCount
         - faFilter
         - faFilterN
         - faFrag
         - faNoise
         - faOneRecord
         - faPolyASizes
         - faRandomize
         - faRc
         - faSize
         - faSomeRecords
         - faSplit
         - faToFastq
         - faToTab
         - faToTwoBit
         - faTrans
         - fastqStatsAndSubsample
         - fastqToFa
         - featureBits
         - fetchChromSizes
         - findMotif
         - fixStepToBedGraph.pl
         - gapToLift
         - genePredCheck
         - genePredFilter
         - genePredHisto
         - genePredSingleCover
         - genePredToBed
         - genePredToBigGenePred
         - genePredToFakePsl
         - genePredToGtf
         - genePredToMafFrames
         - genePredToProt
         - gensub2
         - getRna
         - getRnaPred
         - gfClient
         - gfServer
         - gff3ToGenePred
         - gff3ToPsl
         - gmtime
         - gtfToGenePred
         - headRest
         - hgBbiDbLink
         - hgFakeAgp
         - hgFindSpec
         - hgGcPercent
         - hgGoldGapGl
         - hgLoadBed
         - hgLoadChain
         - hgLoadGap
         - hgLoadMaf
         - hgLoadMafSummary
         - hgLoadNet
         - hgLoadOut
         - hgLoadOutJoined
         - hgLoadSqlTab
         - hgLoadWiggle
         - hgSpeciesRna
         - hgTrackDb
         - hgWiggle
         - hgsqldump
         - hgvsToVcf
         - hicInfo
         - htmlCheck
         - hubCheck
         - hubClone
         - hubPublicCheck
         - ixIxx
         - lavToAxt
         - lavToPsl
         - ldHgGene
         - liftOver
         - liftOverMerge
         - liftUp
         - linesToRa
         - localtime
         - mafAddIRows
         - mafAddQRows
         - mafCoverage
         - mafFetch
         - mafFilter
         - mafFrag
         - mafFrags
         - mafGene
         - mafMeFirst
         - mafNoAlign
         - mafOrder
         - mafRanges
         - mafSpeciesList
         - mafSpeciesSubset
         - mafSplit
         - mafSplitPos
         - mafToAxt
         - mafToBigMaf
         - mafToPsl
         - mafToSnpBed
         - mafsInRegion
         - makeTableList
         - maskOutFa
         - mktime
         - mrnaToGene
         - netChainSubset
         - netClass
         - netFilter
         - netSplit
         - netSyntenic
         - netToAxt
         - netToBed
         - newProg
         - newPythonProg
         - nibFrag
         - nibSize
         - oligoMatch
         - overlapSelect
         - para
         - paraFetch
         - paraHub
         - paraHubStop
         - paraNode
         - paraNodeStart
         - paraNodeStatus
         - paraNodeStop
         - paraSync
         - paraTestJob
         - parasol
         - positionalTblCheck
         - pslCDnaFilter
         - pslCat
         - pslCheck
         - pslDropOverlap
         - pslFilter
         - pslHisto
         - pslLiftSubrangeBlat
         - pslMap
         - pslMapPostChain
         - pslMrnaCover
         - pslPairs
         - pslPartition
         - pslPosTarget
         - pslPretty
         - pslRc
         - pslRecalcMatch
         - pslReps
         - pslScore
         - pslSelect
         - pslSomeRecords
         - pslSort
         - pslStats
         - pslSwap
         - pslToBed
         - pslToBigPsl
         - pslToChain
         - pslToPslx
         - pslxToFa
         - qaToQac
         - qacAgpLift
         - qacToQa
         - qacToWig
         - raSqlQuery
         - raToLines
         - raToTab
         - randomLines
         - rmFaDups
         - rowsToCols
         - sizeof
         - spacedToTab
         - splitFile
         - splitFileByColumn
         - sqlToXml
         - strexCalc
         - stringify
         - subChar
         - subColumn
         - tailLines
         - tdbQuery
         - tdbRename
         - tdbSort
         - textHistogram
         - tickToDate
         - toLower
         - toUpper
         - transMapPslToGenePred
         - trfBig
         - twoBitDup
         - twoBitInfo
         - twoBitMask
         - twoBitToFa
         - ucscApiClient
         - vai.pl
         - validateFiles
         - validateManifest
         - varStepToBedGraph.pl
         - webSync
         - wigCorrelate
         - wigEncode
         - wigToBigWig
         - wordLine
         - xmlCat
         - xmlToSql


## END HELP



%post

   NOW=`date`
   echo "export NOW=\"${NOW}\"" >> $SINGULARITY_ENVIRONMENT
   set -e

   dnf -y makecache
   dnf -y group install "Development Tools"
   dnf -y install --allowerasing  hostname which dnf-utils \
     python3-pip git zlib zlib-devel bzip2 bzip2-devel \
     xz xz-devel libcurl libcurl-devel ncurses ncurses-devel \
     unzip wget gnuplot rsync java-1.8.0-openjdk java-1.8.0-openjdk-devel \
     openssl-devel libffi-devel python36-devel

   ln -s /usr/bin/python3 /usr/bin/python
   ln -s /usr/bin/pip3 /usr/bin/pip

   pip install numpy pandas matplotlib scikit-learn scipy opencv-contrib-python

   # Intel Threading Building Blocks 2019 U8
   echo "/usr/local/lib" >> /etc/ld.so.conf.d/usr_local_lib.conf
   rm -rf tbb
   git clone https://github.com/intel/tbb
   cd tbb
   make -j 8
   find . -name '*so' | grep release | xargs -I{} cp {} /usr/local/lib/  # Copy release libs to sys dir
   find . -name '*so.2' | grep release | xargs -I{} cp {} /usr/local/lib/
   cp -R include/* /usr/local/include/
   cd ..
   ldconfig
   mkdir -p /usr/local/lib64/python3.6/site-packages


%runscript

    echo "Container was created $NOW"
    echo "Arguments received: $*"
    exec echo "$@"


%labels
   Author "tomi.hakkinen@tuni.fi and francesco.tabaro@tuni.fi"
   Version 0.29

%environment
#    GLOBAL=variables
#    AVAILABLE="to all apps"
   export PATH=$PATH:/usr/bin:/usr/local/bin/homer/bin:/opt/ucsc_tools:/opt/Bismark-0.22.3
   LANG="en_US.UTF-8"
   export LANG
   PYTHONWARNINGS=ignore::yaml.YAMLLoadWarning

# ################### Samtools #################################

%apprun samtools
   exec samtools

%appinstall samtools
   rm -rf htslib
   git clone https://github.com/samtools/htslib
   cd htslib
   autoheader
   autoconf
   ./configure
   make -j 8
   make install
   cd ..
   rm -rf samtools
   git clone https://github.com/samtools/samtools
   cd samtools
   autoheader
   autoconf -Wno-syntax
   ./configure
   make -j 8
   make install
   cd ..

%apphelp samtools
   Samtools 1.9. https://github.com/samtools/samtools

# ######################## Bedtools ###################################

%apprun bedtools
    exec bedtools

%appinstall bedtools
   rm -rf bedtools2
   git clone https://github.com/arq5x/bedtools2/
   #wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/
   #bedtools-2.28.0.tar.gz
   #tar -zxf bedtools-2.28.0.tar.gz
   cd bedtools2
   make -j 8
   cp bin/* /usr/local/bin/

%apphelp bedtools
    Bedtools 2.28.0. https://github.com/arq5x/bedtools2/


# ######################## FastQC ###################################

%apprun fastqc
   exec fastqc

%appinstall fastqc
   #git clone https://github.com/s-andrews/FastQC
   cd /usr/local/bin
   wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
   unzip -o fastqc_v0.11.8.zip
   chmod +x FastQC/fastqc
   ln -sf FastQC/fastqc .
   rm fastqc_v0.11.8.zip

%apphelp fastqc
   FastQC v0.11.8. https://github.com/s-andrews/FastQC


# ######################## Bowtie2 ################################

%apprun bowtie2
   exec bowtie2

%appinstall bowtie2
   wget -O bowtie.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5.1/bowtie2-2.3.5.1-source.zip/download
   unzip -o bowtie.zip
   cd bowtie2-2.3.5.1
   make -j 8
   cp bowtie2* /usr/local/bin/
   cd ..


%apphelp bowtie2
   Bowtie 2 v. 2.3.5.1 . http://bowtie-bio.sourceforge.net/bowtie2/index.shtml


# ######################## MultiQC ##################################

%apprun multiqc
   exec multiqc

%appinstall multiqc
   pip install  git+https://github.com/ewels/MultiQC.git

%apphelp multiqc
   MultiQC v1.8dev. https://multiqc.info/

# ######################## Cutadapt ################################

%apprun cutadapt
   exec cutadapt

%appinstall cutadapt
   pip install cutadapt

%apphelp cutadapt
   Cutadapt 2.4.. https://cutadapt.readthedocs.io/en/stable/guide.html

# ######################### STAR ###################################

%apprun star
   exec star

%appinstall star
   rm -rf STAR
   git clone https://github.com/alexdobin/STAR.git
   cd STAR/source
   make -j 8 STAR
   cp STAR /usr/local/bin/
   ln -sf /usr/local/bin/STAR /usr/local/bin/star
   cd ..
   cd ..

%apphelp star
   STAR 2.7.1a. https://github.com/alexdobin/STAR

# ######################## HISAT2 #################################

%apprun hisat2
   exec hisat2

%appinstall hisat2
   rm -rf hisat2-2.1.0
   wget http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-source.zip
   unzip hisat2-2.1.0-source.zip
   cd hisat2-2.1.0
   make -j 8
   #find . -name '*py' | xargs -I{} cp {} /usr/local/bin/
   find . -executable -type f | grep -v tinythread | xargs -I{} cp {} /usr/local/bin/
   cd ..

%apphelp hisat2
   HISAT2 2.1.0. https://ccb.jhu.edu/software/hisat2/index.shtml


# ######################## Picard #########################

%apprun picard
   exec picard

%appinstall picard
   wget https://github.com/broadinstitute/picard/releases/download/2.20.5/picard.jar
   mv picard.jar /usr/local/bin
   echo "#"'!'"/usr/bin/bash" > /usr/local/bin/picard
   echo "java -jar /usr/local/bin/picard.jar \"\$@\"" >> /usr/local/bin/picard
   chmod +x /usr/local/bin/picard

%apphelp picard
   Picard 2.20.5. http://broadinstitute.github.io/picard/


# ######################### Trimmomatic #######################

%apprun trimmomatic
   exec trimmomatic

%appinstall trimmomatic
   wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
   unzip -o Trimmomatic-0.39.zip -d /usr/local/bin
   echo "#"'!'"/usr/bin/bash" > /usr/local/bin/trimmomatic
   echo "java -jar /usr/local/bin/Trimmomatic-0.39/trimmomatic-0.39.jar \"\$@\"" >> /usr/local/bin/trimmomatic
   chmod +x /usr/local/bin/trimmomatic
   rm Trimmomatic-0.39.zip

%apphelp trimmomatic
   Trimmomatic 0.39. http://www.usadellab.org/cms/?page=trimmomatic


# ######################### Samblaster ############################

%apprun samblaster
   exec samblaster

%appinstall samblaster
   git clone git://github.com/GregoryFaust/samblaster.git
   cd samblaster
   make -j 8
   cp samblaster /usr/local/bin/
   cd ..
   rm -r samblaster

%apphelp samblaster
   Samblaster 0.1.24 . https://github.com/GregoryFaust/samblaster


# ########################## VarScan #################################

%apprun varscan
   exec varscan

%appinstall varscan
   wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar
   mv VarScan.v2.4.4.jar /usr/local/bin/
   echo "#"'!'"/usr/bin/bash" > /usr/local/bin/varscan
   echo "java -jar /usr/local/bin/VarScan.v2.4.4.jar \"\$@\"" >> /usr/local/bin/varscan
   chmod +x /usr/local/bin/varscan

%apphelp varscan
   VarScan 2.4.4 . https://github.com/dkoboldt/varscan


# ########################### VcfAnno ###############################

%apprun vcfanno
   exec vcfanno

%appinstall vcfanno
   wget https://github.com/brentp/vcfanno/releases/download/v0.3.2/vcfanno_linux64 -O /usr/local/bin/vcfanno
   chmod +x /usr/local/bin/vcfanno

%apphelp vcfanno
   VcfAnno 0.3.2 . https://github.com/brentp/vcfanno/releases/


# ############################ Plink ##################################

%apprun plink
   exec plink

%appinstall plink
   wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip
   unzip plink_linux_x86_64_20190617.zip
   mv plink /usr/local/bin/
   mv prettify /usr/local/bin/


%apphelp plink
   PLINK v1.90b6.10 64-bit (17 Jun 2019) . https://www.cog-genomics.org/plink2


# ############################ MACS2 ######################################

%apprun macs2
   exec macs2

%appinstall macs2
   export PYTHONPATH=$PYTHONPATH:/usr/local/lib64/python3.6/site-packages/
   git clone https://github.com/taoliu/MACS.git
   cd MACS/
   python setup.py install --prefix /usr/local
   cd ..
   rm -r MACS

%apphelp macs2
   MACS2 2.2.4 ( Oct 7 2019) . https://github.com/taoliu/MACS

# ############################ Homer ########################

%apprun homer
   exec homer

%appinstall homer
   mkdir -p /usr/local/bin/homer
   cd /usr/local/bin/homer
   wget http://homer.ucsd.edu/homer/configureHomer.pl
   perl configureHomer.pl -install

%apphelp homer
   Homer 4.10 ( Oct 7 2019 ) . http://homer.ucsd.edu/homer/

# ############################ Nextflow #######################

%apprun nextflow
   exec nextflow

%appinstall nextflow
   cd /usr/local/bin
   curl -s https://get.nextflow.io | bash
   chmod 777 /usr/local/bin/nextflow

%apphelp nextflow
   Nextflow 19.09 ( Oct 7 2019 ) . https://www.nextflow.io/index.html

# ############################ nf-core ########################

%apprun nfcore
   exec nf-core

%appinstall nfcore
   LANG="en_US.UTF-8"
   export LANG
   pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git

%apphelp nfcore
   Nf-Core . https://nf-co.re/ . A community effort to collect a curated set of analysis pipelines built using Nextflow.

# ############################ MAGeCK ########################

%apprun mageck
   exec mageck

%appinstall mageck
   wget "https://downloads.sourceforge.net/project/mageck/0.5/liulab-mageck-0.5.9.2.tar.gz"
   tar zxvf liulab-mageck-0.5.9.2.tar.gz
   cd liulab-mageck-ef7c39474ed0
   python setup.py install
   cd ..
   rm -r liulab-mageck-ef7c39474ed0

%apphelp mageck
   MAGeCK (0.5.9.2) enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

# ############################ TrimGalore ########################

%apprun trim_galore
   exec trim_galore

%appinstall trim_galore
   curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.5.tar.gz -o trim_galore.tar.gz
    tar xzf trim_galore.tar.gz
    cp TrimGalore-0.6.5/trim_galore /usr/local/bin
    rm -r TrimGalore-0.6.5


%apphelp trim_galore
    TrimGalore (0.6.5) . https://github.com/FelixKrueger/TrimGalore


# ############################ Bismark ########################

%apprun bismark
   exec bismark

%appinstall bismark
    curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.22.3.tar.gz -o Bismark_0.22.3.tar.gz
    tar xzf Bismark_0.22.3.tar.gz -C /opt/

%apphelp bismark
    Bismark (0.22.3) . https://github.com/FelixKrueger/Bismark


# ############################ UCSC tools ########################

%appinstall ucsc_tools
    mkdir -p /opt/ucsc_tools
    cd /opt/ucsc_tools
    rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./


%apphelp ucsc_tools
    UCSC tools (v390) . http://hgdownload.soe.ucsc.edu/admin/exe/ DOC: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt

Collection

• Name: thakk/bioinformatics
• License: None

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