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Makefile
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## Docker image makefile
# David Brawand <[email protected]>
VERSION=flatdog
login:
docker login
## PULL
pullall: pullprivate pullpublic
pullpublic: pull_base pull_ngstools pull_fastqc pull_kraken pull_platypus pull_trimmomatic pull_align pull_alpaca pull_bamutil pull_crossmap pull_delly pull_freebayes pull_lumpy pull_picard pull_reporting pull_samblaster pull_vardict pull_varscan pull_lofreq pull_exomedepth pull_gviz pull_manta pull_pindel
pullprivate: login pull_protected
pull_protected:
docker pull dbrawand/snappy_protected:$(VERSION)
pull_base:
docker pull viapath/snappy_base:$(VERSION)
# base deps
pull_ngstools:
docker pull viapath/snappy_ngstools:$(VERSION)
pull_fastqc:
docker pull viapath/snappy_fastqc:$(VERSION)
pull_kraken:
docker pull viapath/snappy_kraken:$(VERSION)
pull_platypus:
docker pull viapath/snappy_platypus:$(VERSION)
pull_trimmomatic:
docker pull viapath/snappy_trimmomatic:$(VERSION)
# ngstools deps
pull_align:
docker pull viapath/snappy_align:$(VERSION)
pull_alpaca:
docker pull viapath/snappy_alpaca:$(VERSION)
pull_bamutil:
docker pull viapath/snappy_bamutil:$(VERSION)
pull_crossmap:
docker pull viapath/snappy_crossmap:$(VERSION)
pull_delly:
docker pull viapath/snappy_delly:$(VERSION)
pull_freebayes:
docker pull viapath/snappy_freebayes:$(VERSION)
pull_lumpy:
docker pull viapath/snappy_lumpy:$(VERSION)
pull_manta:
docker pull viapath/snappy_manta:$(VERSION)
pull_pindel:
docker pull viapath/snappy_pindel:$(VERSION)
pull_picard:
docker pull viapath/snappy_picard:$(VERSION)
pull_reporting:
docker pull viapath/snappy_reporting:$(VERSION)
pull_samblaster:
docker pull viapath/snappy_samblaster:$(VERSION)
pull_vardict:
docker pull viapath/snappy_vardict:$(VERSION)
pull_varscan:
docker pull viapath/snappy_varscan:$(VERSION)
# picard deps
pull_lofreq:
docker pull viapath/snappy_lofreq:$(VERSION)
# reporting deps
pull_exomedepth:
docker pull viapath/snappy_exomedepth:$(VERSION)
pull_gviz:
docker pull viapath/snappy_gviz:$(VERSION)
pull_bcl2fastq:
docker pull viapath/snappy_bcl2fastq:$(VERSION)
pull_vep:
docker pull viapath/snappy_vep:$(VERSION)
## BUILD
buildall: buildpublic buildprivate
buildpublic: baseimage ngstools bcl2fastq align bamutil crossmap delly exomedepth fastqc freebayes gviz kraken lumpy lofreq manta pindel picard platypus reporting samblaster trimmomatic vardict varscan
buildprivate: protected
baseimage:
docker build -t viapath/snappy_base:$(VERSION) snappy_base
ngstools: baseimage
docker build -t viapath/snappy_ngstools:$(VERSION) snappy_ngstools
align: ngstools
docker build -t viapath/snappy_align:$(VERSION) snappy_align
alpaca: ngstools
docker build -t viapath/snappy_alpaca:$(VERSION) snappy_alpaca
bamutil: ngstools
docker build -t viapath/snappy_bamutil:$(VERSION) snappy_bamutil
bcl2fastq: ngstools
docker build -t viapath/snappy_bcl2fastq:$(VERSION) snappy_bcl2fastq
crossmap: ngstools
docker build -t viapath/snappy_crossmap:$(VERSION) snappy_crossmap
delly: ngstools
docker build -t viapath/snappy_delly:$(VERSION) snappy_delly
exomedepth: reporting
docker build -t viapath/snappy_exomedepth:$(VERSION) snappy_exomedepth
fastqc: baseimage
docker build -t viapath/snappy_fastqc:$(VERSION) snappy_fastqc
freebayes: ngstools
docker build -t viapath/snappy_freebayes:$(VERSION) snappy_freebayes
gviz: reporting
docker build -t viapath/snappy_gviz:$(VERSION) snappy_gviz
kraken: baseimage
docker build -t viapath/snappy_kraken:$(VERSION) snappy_kraken
lumpy: ngstools
docker build -t viapath/snappy_lumpy:$(VERSION) snappy_lumpy
lofreq: ngstools
docker build -t viapath/snappy_lofreq:$(VERSION) snappy_lofreq
manta: ngstools
docker build -t viapath/snappy_manta:$(VERSION) snappy_manta
pindel: ngstools
docker build -t viapath/snappy_pindel:$(VERSION) snappy_pindel
picard: ngstools
docker build -t viapath/snappy_picard:$(VERSION) snappy_picard
platypus: ngstools
docker build -t viapath/snappy_platypus:$(VERSION) snappy_platypus
protected: ngstools
docker build -t dbrawand/snappy_protected:$(VERSION) snappy_protected
reporting: ngstools
docker build -t viapath/snappy_reporting:$(VERSION) snappy_reporting
samblaster: ngstools
docker build -t viapath/snappy_samblaster:$(VERSION) snappy_samblaster
trimmomatic: ngstools
docker build -t viapath/snappy_trimmomatic:$(VERSION) snappy_trimmomatic
vardict: ngstools
docker build -t viapath/snappy_vardict:$(VERSION) snappy_vardict
varscan: ngstools
docker build -t viapath/snappy_varscan:$(VERSION) snappy_varscan
vep: ngstools
docker build -t viapath/snappy_vep:$(VERSION) snappy_vep