thakk/biobase:latest
$ singularity pull shub://thakk/biobase: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
- Subread
- 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
# ############################ Subread package ###################
%apprun featureCounts
exec featureCounts
%appinstall featureCounts
wget -O subread.tar.gz https://sourceforge.net/projects/subread/files/subread-2.0.1/subread-2.0.1-source.tar.gz/download
tar zxvf subread.tar.gz
cd subread-2.0.1-source/src
make -f Makefile.Linux
cd ../bin
cp -R * /usr/local/bin/
cd ../..
rm subread.tar.gz
%apphelp featureCounts
Subread 2.0.1 featureCounts http://bioinf.wehi.edu.au/subread-package/
# ############################ 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/biobase
- License: None
View on Datalad
Metrics
| key | value |
|---|---|
| id | /containers/thakk-biobase-latest |
| collection name | thakk/biobase |
| branch | master |
| tag | latest |
| commit | d76758db6efc723d136494cc0e0027bc680e808e |
| version (container hash) | 10d20187508010e1ed85d13f0af77253 |
| build date | 2021-02-27T20:46:58.765Z |
| size (MB) | 6474.0 |
| size (bytes) | 2668269599 |
| SIF | Download URL (please use pull with shub://) |
| Datalad URL | View on Datalad |
| Singularity Recipe | Singularity Recipe on Datalad |
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