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Makefile
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#
# Makefile for jvarkit
#
SHELL=/bin/bash
this.makefile=$(lastword $(MAKEFILE_LIST))
this.dir=$(dir $(realpath ${this.makefile}))
#need local settings ? create a file 'local.mk' in this directory
ifneq ($(realpath local.mk),)
include $(realpath local.mk)
endif
# proxy for curl, etc...
curl.proxy=$(if ${http.proxy.host}${http.proxy.port},-x "${http.proxy.host}:${http.proxy.port}",)
xjc.proxy=$(if ${http.proxy.host}${http.proxy.port}, -httpproxy "${http.proxy.host}:${http.proxy.port}" ,)
ANT?=ant
JAVAC?=javac
JAVA?=java
JAVACC?=javacc
JAR?=jar
XJC?=xjc
#
# include java libraries from Maven
#
include maven.mk
src.dir=${this.dir}src/main/java
generated.dir=${this.dir}src/main/generated-sources
tmp.dir=${this.dir}_tmp-${htsjdk.version}
tmp.mft=${tmp.dir}/META-INF/MANIFEST.MF
export dist.dir?=${this.dir}dist
wiki.dir?=${this.dir}doc/wiki
galaxy.dir?=galaxy
mysql.version?=5.1.34
mysql.jar?=lib/mysql-connector-java-${mysql.version}-bin.jar
berkeleydb.version?=6.2.31
berkeleydb.jar?=lib/je-${berkeleydb.version}.jar
bigwig.version=20150429
bigwig.jar?=lib/BigWig.jar
bigwig.log4j.jar=$(dir ${bigwig.jar})/log4j-1.2.15.jar
bigwig.jars=${bigwig.jar} ${bigwig.log4j.jar}
common.math.version?=3.4.1
common.math.jar?=lib/commons-math3-${common.math.version}.jar
jvarkit.package=com.github.lindenb.jvarkit
## http://stackoverflow.com/questions/9551416
EMPTY :=
SPACE := $(EMPTY) $(EMPTY)
define compile-htsjdk-cmd
## 1 : target name
## 2 : qualified main class name
## 3 : other deps
$(1) : ${htsjdk.jars} \
${generated.dir}/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java \
$(addsuffix .java,$(addprefix ${src.dir}/,$(subst .,/,$(2)))) \
$(filter-out wiki_flag,$(filter-out galaxy_flag,$(3))) ${apache.commons.cli.jars} ${slf4j.jars}
echo "### COMPILING $(1) ######"
mkdir -p ${tmp.dir}/META-INF ${dist.dir}
#generate java code if needed = a file with .xml exists, requires xsltproc, preprocessing file twice
if [ -e "$(addsuffix .xml,$(addprefix ${src.dir}/,$(subst .,/,$(2))))" ] ; then mkdir -p ${generated.dir}/java/$(dir $(subst .,/,$(2))) && \
xsltproc \
--xinclude \
--stringparam jarname '$(1)' \
--stringparam githash $$(if $$(realpath ${this.dir}.git/refs/heads/master), `cat $$(realpath ${this.dir}.git/refs/heads/master) `, "undefined") \
-o "$(addsuffix .proc.xml,${generated.dir}/$(2))" \
${this.dir}src/main/resources/xsl/commandpreproc.xsl \
"$(addsuffix .xml,$(addprefix ${src.dir}/,$(subst .,/,$(2))))" && \
xsltproc \
--xinclude \
--path "${this.dir}src/main/resources/xml" \
-o ${generated.dir}/java/$(dir $(subst .,/,$(2)))Abstract$(notdir $(subst .,/,$(2))).java \
${this.dir}src/main/resources/xsl/command2java.xsl \
"$(addsuffix .proc.xml,${generated.dir}/$(2))" && \
xsltproc \
-o "$(addsuffix .elixir.jsonx,${generated.dir}/$(2))" \
${this.dir}src/main/resources/xsl/jsonxelixir.xsl \
"$(addsuffix .proc.xml,${generated.dir}/$(2))" && \
xsltproc \
-o "$(addsuffix .elixir.json,${generated.dir}/$(2))" \
${this.dir}src/main/resources/xsl/jsonx2json.xsl \
"$(addsuffix .elixir.jsonx,${generated.dir}/$(2))" \
$(if $(filter galaxy_flag,$(3)), && mkdir -p ${galaxy.dir} && xsltproc ${this.dir}src/main/resources/xsl/tools2galaxy.xsl "$(addsuffix .proc.xml,${generated.dir}/$(2))" | sed 's/__DOLLAR__//g' > ${galaxy.dir}/$(1).xml ) \
$(if $(filter wiki_flag,$(3)), && mkdir -p ${wiki.dir} && xsltproc -o "${wiki.dir}/$(notdir $(subst .,/,$(2))).md" ${this.dir}src/main/resources/xsl/command2md.xsl "$(addsuffix .proc.xml,${generated.dir}/$(2))" ) \
; fi
#copy resource
cp ${this.dir}src/main/resources/messages/messages.properties ${tmp.dir}
echo '### Printing javac version : it should be 1.8. if Not, check your $$$${PATH}.'
${JAVAC} -version
#compile
${JAVAC} -d ${tmp.dir} -g -classpath "$$(subst $$(SPACE),:,$$(filter %.jar,$$^))" -sourcepath ${src.dir}:${generated.dir}/java $$(filter %.java,$$^)
ifeq (${standalone},yes)
$$(foreach J,$$(filter %.jar,$$^),unzip -o $${J} -d ${tmp.dir};)
endif
#create META-INF/MANIFEST.MF
echo "Manifest-Version: 1.0" > ${tmp.mft}
echo "Main-Class: $(2)" >> ${tmp.mft}
ifneq (${standalone},yes)
echo "Class-Path: $$(realpath $$(filter %.jar,$$^)) ${dist.dir}/$(1).jar" | fold -w 71 | awk '{printf("%s%s\n",(NR==1?"": " "),$$$$0);}' >> ${tmp.mft}
endif
echo -n "Git-Hash: " >> ${tmp.mft}
$$(if $$(realpath .git/refs/heads/master),cat $$(realpath .git/refs/heads/master), echo "undefined") >> ${tmp.mft}
echo -n "Compile-Date: " >> ${tmp.mft}
date +%Y-%m-%d:%H-%m-%S >> ${tmp.mft}
#create jar
${JAR} cfm ${dist.dir}/$(1).jar ${tmp.mft} -C ${tmp.dir} .
#create bash executable
echo '#!/bin/bash' > ${dist.dir}/$(1)
echo -n '${JAVA} -Djvarkit.log.name=$(1) -Dfile.encoding=UTF8 -Xmx500m $(if ${http.proxy.host},-Dhtt.proxyHost=${http.proxy.host}) $(if ${http.proxy.port},-Dhtt.proxyPort=${http.proxy.port}) ' >> ${dist.dir}/$(1)
ifeq (${standalone},yes)
echo -n ' -jar "${dist.dir}/$(1).jar" ' >> ${dist.dir}/$(1)
else
echo -n ' -cp "$$(subst $$(SPACE),:,$$(realpath $$(filter %.jar,$$^))):${dist.dir}/$(1).jar" $(2) ' >> ${dist.dir}/$(1)
endif
echo '$$$$*' >> ${dist.dir}/$(1)
chmod ugo+rx ${dist.dir}/$(1)
#cleanup
rm -rf ${tmp.dir}
endef
##
## Creates a CGI script for java app
##
define compile-cgi-cmd
${dist.dir}/$(1).cgi : $(1)
echo "#!/bin/bash" > $$@
echo "PREFIX=$$(dirname $$0)" >> $$@
echo "${JAVA} -Dfile.encoding=UTF8 -Xmx500m -Dprefs.file.xml=/var/www/cgi-bin/prefs.xml -jar $PREFIX/$(1).jar $$*" >> $$@
endef
#
# $1 :biostar post-id
# $2: other deps
#
define compile_biostar_cmd
$(call compile-htsjdk-cmd,biostar$(1),${jvarkit.package}.tools.biostar.Biostar$(1),$(2))
endef
#
# All executables
#
GALAXY_APPS=vcffixindels vcftail vcfhead vcfburdenfisherh vcfburdenfisherv vcfburdenmaf vcfburdenexac vcfmulti2oneallele vcfin vcffilterso vcffilterjs vcfburdensplitter vcfpredictions \
vcfpolyx vcfburdenfiltergenes vcfbed vcfbedsetfilter
APPS= ${GALAXY_APPS} vcftrio groupbygene \
addlinearindextobed allelefreqcalc almostsortedvcf backlocate bam2fastq bam2raster bam2svg \
bam2xml bam2wig bamcmpcoverage bamgenscan bamindexreadnames bamliftover bamqueryreadnames \
bamrenamechr bamsnvwig bamstats04 bamstats05 bamtreepack bamviewgui batchigvpictures bedliftover \
bedrenamechr biostar103303 biostar106668 biostar130456 biostar59647 biostar76892 biostar77288 \
biostar77828 biostar78285 biostar78400 biostar81455 biostar84452 biostar84786 biostar86363 \
biostar86480 biostar90204 msa2vcf biostar95652 biostar139647 biostar145820 blast2sam reduceblast blastmapannots \
blastn2snp buildwpontology bwamemdigest bwamemnop cmpbams cmpbamsandbuild coveragenormalizer \
deseqcount downsamplevcf evs2bed evs2vcf evs2xml extendbed fastq2fasta kg2bed \
fastqentropy fastqgrep fastqjs fastqphred64to33 fastqrecordtreepack fastqrevcomp fastqshuffle \
fastqsplitinterleaved findallcoverageatposition findavariation findcorruptedfiles findmyvirus findnewsplicesites fixvarscanmissingheader \
fixvcf fixvcfformat fixvcfmissinggenotypes gcanddepth genomicjaspar genscan \
howmanybamdict illuminadir ilmnfastqstats impactofduplicates jeter \
liftover2svg mapuniprot mergesplittedblast ncbitaxonomy2xml metrics2xml ngsfilessummary noemptyvcf \
nozerovariationvcf pademptyfastq paintcontext pubmeddump pubmedorcidgraph pubmedfilterjs referencetovcf sam2json \
sam2psl sam2tsv sam4weblogo samclipindelfraction samextractclip samfindclippedregions samfixcigar \
samgrep samjs samshortinvert samstats01 sigframe sortvcfoninfo \
sortvcfonref2 splitbam3 splitbytile splitread tview tview.cgi \
vcf2hilbert vcf2ps vcf2rdf vcf2sql vcf2xml vcfannobam \
vcfbedjs vcfbiomart vcfcadd vcfcmppred vcfcomm vcfcompare vcfcomparegt \
vcfconcat vcfcutsamples vcffilterdoid vcfgo \
vcfjaspar vcfliftover vcfmapuniprot vcfmerge vcfmulti2one \
vcfrebase vcfregistry.cgi vcfregulomedb vcfrenamechr vcfrenamesamples \
vcfresetvcf vcfsetdict vcfshuffle vcfsimulator vcfstats vcfcombinetwosnvs vcfstripannot \
vcftabixml vcftreepack vcfvcf vcfviewgui worldmapgenome \
uniprotfilterjs skipxmlelements vcfensemblvep vcfgroupbypop bamtile xcontaminations \
biostar3654 vcfjoinvcfjs bioalcidae vcfburden vcfreplacetag vcfindextabix \
vcfpeekvcf vcfgetvariantbyindex vcfmulti2oneinfo bedindextabix vcf2bam vcffilterxpath \
biostar140111 pcrclipreads extendrefwithreads pcrslicereads samjmx vcfjmx gtf2xml sortsamrefname biostar154220 \
biostar160470 biostar165777 blastfilterjs vcfcomparecallers bamclip2insertion localrealignreads biostar170742 biostar172515 \
biostar173114 samslop biostar175929 vcfcalledwithanothermethod biostar178713 \
vcfremovegenotypejs vcfgenesplitter bamstats02 bamstats02view sammaskalignedbases biostar105754 gff2kg \
bam2sql vcfinjectpedigree vcfburdenrscriptv vcffilternotinpedigree vcfderby01 vcf2zip pubmedgender pubmedmap vcfdoest splitvcf \
forkvcf gbrowserhtml bim2vcf queue2make concatsam samreadlengthdistribution biostar214299
.PHONY: all tests $(APPS) clean download_all_maven library top galaxy burden
top:
@echo "This is the top target. Run 'make name-of-target' to build the desired target. Run 'make all' if you're Pierre Lindenbaum"
all: $(APPS)
galaxy: ${GALAXY_APPS}
mkdir -p '${galaxy.dir}'
cp ${this.dir}src/main/resources/xml/tool_dependencies.xml ${galaxy.dir}/tool_dependencies.xml
echo "$^" | tr " " "\n" | awk 'BEGIN {printf("<section id=\"jvk\" name=\"JVARKIT\">\n");} {printf(" <tool file=\"jvarkit/%s\"/>\n",$$1);} END { printf("</section>\n");}' > ${galaxy.dir}/tool_conf.fragment
-planemo lint --skip "tests" ${galaxy.dir}/*.xml
burden: vcfburden vcfburdensplitter vcfburdenfisherh vcfburdenfisherv vcfburdenmaf vcfburdenexac vcfburdenfiltergenes vcfinjectpedigree vcfburdenrscriptv vcffilternotinpedigree vcfderby01
tests:
(cd ${this.dir}tests && $(MAKE))
#bigwig
$(eval $(call compile-htsjdk-cmd,vcfbigwig, ${jvarkit.package}.tools.vcfbigwig.VCFBigWig,${bigwig.jars}))
$(eval $(call compile-htsjdk-cmd,vcfensemblreg, ${jvarkit.package}.tools.ensemblreg.VcfEnsemblReg,${bigwig.jars}))
$(eval $(call compile_biostar_cmd,105754,${bigwig.jar} wiki_flag))
# common math
$(eval $(call compile-htsjdk-cmd,cnv01,${jvarkit.package}.tools.redon.CopyNumber01,${common.math.jar}))
#berkeley
$(eval $(call compile-htsjdk-cmd,vcfphylotree,${jvarkit.package}.tools.phylo.VcfPhyloTree,${berkeleydb.jar}))
$(eval $(call compile-htsjdk-cmd,ngsfilesscanner,${jvarkit.package}.tools.ngsfiles.NgsFilesScanner,${berkeleydb.jar}))
$(eval $(call compile_biostar_cmd,92368,${berkeleydb.jar}))
#mysql
$(eval $(call compile-htsjdk-cmd,vcfucsc,${jvarkit.package}.tools.vcfucsc.VcfUcsc,${mysql.jar}))
$(eval $(call compile-htsjdk-cmd,addlinearindextobed,${jvarkit.package}.tools.misc.AddLinearIndexToBed))
$(eval $(call compile-htsjdk-cmd,allelefreqcalc,${jvarkit.package}.tools.misc.AlleleFrequencyCalculator))
$(eval $(call compile-htsjdk-cmd,bam2xml,${jvarkit.package}.tools.bam2xml.Bam2Xml))
$(eval $(call compile-htsjdk-cmd,almostsortedvcf,${jvarkit.package}.tools.sortvcfonref.AlmostSortedVcf))
$(eval $(call compile-htsjdk-cmd,backlocate,${jvarkit.package}.tools.backlocate.BackLocate,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bam2fastq,${jvarkit.package}.tools.fastq.BamToFastq))
$(eval $(call compile-htsjdk-cmd,bam2raster,${jvarkit.package}.tools.bam2graphics.Bam2Raster,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bam2svg,${jvarkit.package}.tools.bam2svg.BamToSVG))
$(eval $(call compile-htsjdk-cmd,bam2wig,${jvarkit.package}.tools.bam2wig.Bam2Wig))
$(eval $(call compile-htsjdk-cmd,bamcmpcoverage,${jvarkit.package}.tools.misc.BamCmpCoverage))
$(eval $(call compile-htsjdk-cmd,bamgenscan,${jvarkit.package}.tools.genscan.BamGenScan))
$(eval $(call compile-htsjdk-cmd,bamindexreadnames,${jvarkit.package}.tools.bamindexnames.BamIndexReadNames))
$(eval $(call compile-htsjdk-cmd,bamliftover,${jvarkit.package}.tools.liftover.BamLiftOver,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamqueryreadnames,${jvarkit.package}.tools.bamindexnames.BamQueryReadNames))
$(eval $(call compile-htsjdk-cmd,bamrenamechr,${jvarkit.package}.tools.misc.ConvertBamChromosomes))
$(eval $(call compile-htsjdk-cmd,bamstats02,${jvarkit.package}.tools.bamstats01.BamStats02,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamstats02view,${jvarkit.package}.tools.bamstats01.BamStats02View,bamstats02 wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamstats04,${jvarkit.package}.tools.bamstats04.BamStats04,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamstats05,${jvarkit.package}.tools.bamstats04.BamStats05,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamtreepack,${jvarkit.package}.tools.treepack.BamTreePack,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bamviewgui,${jvarkit.package}.tools.bamviewgui.BamViewGui))
$(eval $(call compile-htsjdk-cmd,batchigvpictures,${jvarkit.package}.tools.batchpicts.BatchIGVPictures,copy.opendoc.odp.resources))
$(eval $(call compile-htsjdk-cmd,bedliftover,${jvarkit.package}.tools.liftover.BedLiftOver))
$(eval $(call compile-htsjdk-cmd,bedrenamechr,${jvarkit.package}.tools.misc.ConvertBedChromosomes))
$(eval $(call compile_biostar_cmd,103303))
$(eval $(call compile_biostar_cmd,106668))
$(eval $(call compile_biostar_cmd,130456,wiki_flag))
$(eval $(call compile_biostar_cmd,145820))
$(eval $(call compile_biostar_cmd,59647))
$(eval $(call compile_biostar_cmd,76892))
$(eval $(call compile_biostar_cmd,77288))
$(eval $(call compile_biostar_cmd,77828))
$(eval $(call compile_biostar_cmd,78285))
$(eval $(call compile_biostar_cmd,78400,wiki_flag))
$(eval $(call compile_biostar_cmd,81455))
$(eval $(call compile_biostar_cmd,84452))
$(eval $(call compile_biostar_cmd,84786))
$(eval $(call compile_biostar_cmd,86363))
$(eval $(call compile_biostar_cmd,86480))
$(eval $(call compile_biostar_cmd,90204))
$(eval $(call compile_biostar_cmd,95652,api.ncbi.gb))
$(eval $(call compile_biostar_cmd,3654,api.ncbi.insdseq api.ncbi.blast))
$(eval $(call compile_biostar_cmd,154220))
$(eval $(call compile_biostar_cmd,140111,api.ncbi.dbsnp.gt ${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/gt/package-info.java))
$(eval $(call compile_biostar_cmd,160470,api.ncbi.blast wiki_flag))
$(eval $(call compile_biostar_cmd,165777))
$(eval $(call compile_biostar_cmd,170742))
$(eval $(call compile_biostar_cmd,172515))
$(eval $(call compile_biostar_cmd,173114))
$(eval $(call compile_biostar_cmd,175929,wiki_flag))
$(eval $(call compile_biostar_cmd,178713))
$(eval $(call compile_biostar_cmd,214299,wiki_flag))
$(eval $(call compile-htsjdk-cmd,blast2sam,${jvarkit.package}.tools.blast2sam.BlastToSam,api.ncbi.blast wiki_flag))
$(eval $(call compile-htsjdk-cmd,blastfastq,${jvarkit.package}.tools.bwamempcr.BlastFastQ))
$(eval $(call compile-htsjdk-cmd,blastmapannots, ${jvarkit.package}.tools.blastmapannots.BlastMapAnnotations, api.ncbi.blast api.ncbi.gb ${generated.dir}/java/org/uniprot/package-info.java))
$(eval $(call compile-htsjdk-cmd,blastn2snp,${jvarkit.package}.tools.blast.BlastNToSnp,api.ncbi.blast wiki_flag))
$(eval $(call compile-htsjdk-cmd,reduceblast,${jvarkit.package}.tools.blast.ReduceBlast,api.ncbi.blast wiki_flag))
$(eval $(call compile-htsjdk-cmd,buildwpontology,${jvarkit.package}.tools.misc.BuildWikipediaOntology))
$(eval $(call compile-htsjdk-cmd,bwamemdigest,${jvarkit.package}.tools.mem.BWAMemDigest))
$(eval $(call compile-htsjdk-cmd,bwamemnop,${jvarkit.package}.tools.mem.BWAMemNOp))
$(eval $(call compile-htsjdk-cmd,cmpbams,${jvarkit.package}.tools.cmpbams.CompareBams2,wiki_flag))
$(eval $(call compile-htsjdk-cmd,cmpbamsandbuild,${jvarkit.package}.tools.cmpbams.CompareBamAndBuild))
$(eval $(call compile-htsjdk-cmd,coveragenormalizer,${jvarkit.package}.tools.misc.CoverageNormalizer))
$(eval $(call compile-htsjdk-cmd,deseqcount,${jvarkit.package}.tools.bam4deseq.HtSeqCount))
$(eval $(call compile-htsjdk-cmd,downsamplevcf,${jvarkit.package}.tools.misc.DownSampleVcf))
$(eval $(call compile-htsjdk-cmd,evs2bed,${jvarkit.package}.tools.evs2bed.DumpExomeVariantServerData))
$(eval $(call compile-htsjdk-cmd,evs2vcf,${jvarkit.package}.tools.evs2bed.EvsToVcf,api.evs))
$(eval $(call compile-htsjdk-cmd,evs2xml,${jvarkit.package}.tools.evs2bed.EvsDumpXml,api.evs))
$(eval $(call compile-htsjdk-cmd,extendbed,${jvarkit.package}.tools.misc.ExtendBed))
$(eval $(call compile-htsjdk-cmd,fastq2fasta,${jvarkit.package}.tools.misc.FastqToFasta))
$(eval $(call compile-htsjdk-cmd,fastqentropy,${jvarkit.package}.tools.fastq.FastqEntropy))
$(eval $(call compile-htsjdk-cmd,fastqgrep,${jvarkit.package}.tools.misc.FastqGrep))
$(eval $(call compile-htsjdk-cmd,fastqjs,${jvarkit.package}.tools.fastq.FastqJavascript))
$(eval $(call compile-htsjdk-cmd,fastqphred64to33,${jvarkit.package}.tools.fastq.ConvertPhred64toFastq33))
$(eval $(call compile-htsjdk-cmd,fastqrecordtreepack,${jvarkit.package}.tools.treepack.FastqRecordTreePack,wiki_flag))
$(eval $(call compile-htsjdk-cmd,fastqrevcomp,${jvarkit.package}.tools.misc.FastqRevComp))
$(eval $(call compile-htsjdk-cmd,fastqshuffle,${jvarkit.package}.tools.fastq.FastqShuffle))
$(eval $(call compile-htsjdk-cmd,fastqsplitinterleaved,${jvarkit.package}.tools.fastq.FastqSplitInterleaved))
$(eval $(call compile-htsjdk-cmd,findallcoverageatposition,${jvarkit.package}.tools.misc.FindAllCoverageAtPosition,wiki_flag))
$(eval $(call compile-htsjdk-cmd,findavariation,${jvarkit.package}.tools.misc.FindAVariation,wiki_flag))
$(eval $(call compile-htsjdk-cmd,findcorruptedfiles,${jvarkit.package}.tools.misc.FindCorruptedFiles))
$(eval $(call compile-htsjdk-cmd,findmyvirus,${jvarkit.package}.tools.mem.FindMyVirus))
$(eval $(call compile-htsjdk-cmd,findnewsplicesites,${jvarkit.package}.tools.rnaseq.FindNewSpliceSites))
$(eval $(call compile-htsjdk-cmd,fixvarscanmissingheader,${jvarkit.package}.tools.misc.FixVarScanMissingVCFHeader))
$(eval $(call compile-htsjdk-cmd,fixvcf,${jvarkit.package}.tools.misc.FixVCF))
$(eval $(call compile-htsjdk-cmd,fixvcfformat,${jvarkit.package}.tools.misc.FixVcfFormat))
$(eval $(call compile-htsjdk-cmd,fixvcfmissinggenotypes,${jvarkit.package}.tools.misc.FixVcfMissingGenotypes))
$(eval $(call compile-htsjdk-cmd,gcanddepth,${jvarkit.package}.tools.misc.GcPercentAndDepth))
$(eval $(call compile-htsjdk-cmd,concatsam,${jvarkit.package}.tools.misc.ConcatSam,wiki_flag))
$(eval $(call compile-htsjdk-cmd,genomicjaspar,${jvarkit.package}.tools.jaspar.GenomicJaspar))
$(eval $(call compile-htsjdk-cmd,genscan,${jvarkit.package}.tools.genscan.GenScan))
$(eval $(call compile-htsjdk-cmd,groupbygene,${jvarkit.package}.tools.groupbygene.GroupByGene))
$(eval $(call compile-htsjdk-cmd,howmanybamdict,${jvarkit.package}.tools.misc.HowManyBamDict))
$(eval $(call compile-htsjdk-cmd,idea20130924,${jvarkit.package}.tools.bwamempcr.Idea20130924))
$(eval $(call compile-htsjdk-cmd,illuminadir,${jvarkit.package}.tools.misc.IlluminaDirectory,wiki_flag ${gson.jar}))
$(eval $(call compile-htsjdk-cmd,ilmnfastqstats,${jvarkit.package}.tools.misc.IlluminaStatsFastq))
$(eval $(call compile-htsjdk-cmd,impactofduplicates,${jvarkit.package}.tools.impactdup.ImpactOfDuplicates))
$(eval $(call compile-htsjdk-cmd,kg2bed,${jvarkit.package}.tools.misc.KnownGenesToBed, wiki_flag))
$(eval $(call compile-htsjdk-cmd,liftover2svg,${jvarkit.package}.tools.liftover.LiftOverToSVG))
$(eval $(call compile-htsjdk-cmd,mapuniprot,${jvarkit.package}.tools.misc.MapUniProtFeatures,${generated.dir}/java/org/uniprot/package-info.java))
$(eval $(call compile-htsjdk-cmd,mergesplittedblast,${jvarkit.package}.tools.blast.MergeSplittedBlast,api.ncbi.blast))
$(eval $(call compile-htsjdk-cmd,metrics2xml,${jvarkit.package}.tools.metrics2xml.PicardMetricsToXML))
$(eval $(call compile-htsjdk-cmd,ncbitaxonomy2xml,${jvarkit.package}.tools.misc.NcbiTaxonomyToXml))
$(eval $(call compile-htsjdk-cmd,ngsfilessummary,${jvarkit.package}.tools.ngsfiles.NgsFilesSummary))
$(eval $(call compile-htsjdk-cmd,noemptyvcf,${jvarkit.package}.tools.misc.NoEmptyVCF))
$(eval $(call compile-htsjdk-cmd,nozerovariationvcf,${jvarkit.package}.tools.misc.NoZeroVariationVCF))
$(eval $(call compile-htsjdk-cmd,pademptyfastq,${jvarkit.package}.tools.misc.PadEmptyFastq))
$(eval $(call compile-htsjdk-cmd,paintcontext,${jvarkit.package}.tools.bam2graphics.PaintContext))
$(eval $(call compile-htsjdk-cmd,pubmeddump,${jvarkit.package}.tools.pubmed.PubmedDump,wiki_flag))
$(eval $(call compile-htsjdk-cmd,pubmedgender,${jvarkit.package}.tools.pubmed.PubmedGender,wiki_flag))
$(eval $(call compile-htsjdk-cmd,pubmedmap,${jvarkit.package}.tools.pubmed.PubmedMap,wiki_flag))
$(eval $(call compile-htsjdk-cmd,pubmedgraph,${jvarkit.package}.tools.pubmed.PubmedGraph))
$(eval $(call compile-htsjdk-cmd,pubmedorcidgraph,${jvarkit.package}.tools.pubmed.PubmedOrcidGraph,wiki_flag ${gson.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedfilterjs,${jvarkit.package}.tools.pubmed.PubmedFilterJS,api.ncbi.pubmed))
$(eval $(call compile-htsjdk-cmd,referencetovcf,${jvarkit.package}.tools.misc.ReferenceToVCF))
$(eval $(call compile-htsjdk-cmd,sam2json,${jvarkit.package}.tools.misc.SamToJson,wiki_flag ${gson.jar} ))
$(eval $(call compile-htsjdk-cmd,sam2psl,${jvarkit.package}.tools.misc.SamToPsl,wiki_flag))
$(eval $(call compile-htsjdk-cmd,sam2tsv,${jvarkit.package}.tools.sam2tsv.Sam2Tsv,wiki_flag))
$(eval $(call compile-htsjdk-cmd,sam4weblogo,${jvarkit.package}.tools.sam4weblogo.SAM4WebLogo))
$(eval $(call compile-htsjdk-cmd,samclipindelfraction,${jvarkit.package}.tools.misc.SamClipIndelFraction))
$(eval $(call compile-htsjdk-cmd,samextractclip,${jvarkit.package}.tools.structvar.SamExtractClip,wiki_flag))
$(eval $(call compile-htsjdk-cmd,samfindclippedregions,${jvarkit.package}.tools.structvar.SamFindClippedRegions))
$(eval $(call compile-htsjdk-cmd,samfixcigar,${jvarkit.package}.tools.samfixcigar.SamFixCigar,wiki_flag))
$(eval $(call compile-htsjdk-cmd,samgrep,${jvarkit.package}.tools.samgrep.SamGrep,wiki_flag))
$(eval $(call compile-htsjdk-cmd,samjs,${jvarkit.package}.tools.samjs.SamJavascript))
$(eval $(call compile-htsjdk-cmd,samshortinvert,${jvarkit.package}.tools.structvar.SamShortInvertion))
$(eval $(call compile-htsjdk-cmd,samstats01,${jvarkit.package}.tools.bamstats01.BamStats01,wiki_flag))
$(eval $(call compile-htsjdk-cmd,scanshortinvert,${jvarkit.package}.tools.mem.ScanShortInvert))
$(eval $(call compile-htsjdk-cmd,sigframe,${jvarkit.package}.tools.sigframe.SigFrame))
$(eval $(call compile-htsjdk-cmd,sortvcfoninfo,${jvarkit.package}.tools.sortvcfonref.SortVcfOnInfo))
$(eval $(call compile-htsjdk-cmd,sortvcfonref2,${jvarkit.package}.tools.sortvcfonref.SortVcfOnRef2,wiki_flag))
$(eval $(call compile-htsjdk-cmd,splitbam3,${jvarkit.package}.tools.splitbam.SplitBam3,wiki_flag))
$(eval $(call compile-htsjdk-cmd,splitbytile,${jvarkit.package}.tools.splitbytitle.SplitByTile))
$(eval $(call compile-htsjdk-cmd,splitread,${jvarkit.package}.tools.splitread.SplitRead))
#$(eval $(call compile-htsjdk-cmd,tview,${jvarkit.package}.tools.tview.TViewCmd))
#$(eval $(call compile-cgi-cmd,tview.cgi))
$(eval $(call compile-htsjdk-cmd,vcf2hilbert,${jvarkit.package}.tools.misc.VcfToHilbert))
$(eval $(call compile-htsjdk-cmd,vcf2ps,${jvarkit.package}.tools.misc.VcfToPostscript))
$(eval $(call compile-htsjdk-cmd,vcf2rdf,${jvarkit.package}.tools.vcf2rdf.VcfToRdf,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcf2sql,${jvarkit.package}.tools.vcf2sql.VcfToSql))
$(eval $(call compile-htsjdk-cmd,vcf2xml,${jvarkit.package}.tools.vcf2xml.Vcf2Xml))
$(eval $(call compile-htsjdk-cmd,vcfannobam,${jvarkit.package}.tools.vcfannobam.VCFAnnoBam))
$(eval $(call compile-htsjdk-cmd,vcfbed,${jvarkit.package}.tools.vcfbed.VCFBed,wiki_flag galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcfbedjs,${jvarkit.package}.tools.vcfbed.VCFBed))
$(eval $(call compile-htsjdk-cmd,vcfbiomart,${jvarkit.package}.tools.vcfbiomart.VcfBiomart))
$(eval $(call compile-htsjdk-cmd,vcfcadd,${jvarkit.package}.tools.misc.VcfCadd))
$(eval $(call compile-htsjdk-cmd,vcfcmppred,${jvarkit.package}.tools.vcfcmp.VCFComparePredictions))
$(eval $(call compile-htsjdk-cmd,vcfcomm,${jvarkit.package}.tools.vcfcmp.VCFComm))
$(eval $(call compile-htsjdk-cmd,vcfcompare,${jvarkit.package}.tools.vcfcmp.VCFCompare))
$(eval $(call compile-htsjdk-cmd,vcfcomparegt,${jvarkit.package}.tools.vcfcmp.VCFCompareGT))
$(eval $(call compile-htsjdk-cmd,vcfconcat,${jvarkit.package}.tools.vcfconcat.VcfConcat))
$(eval $(call compile-htsjdk-cmd,vcf2zip,${jvarkit.package}.tools.vcfconcat.VcfToZip,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfcutsamples,${jvarkit.package}.tools.misc.VcfCutSamples))
$(eval $(call compile-htsjdk-cmd,vcfdas,${jvarkit.package}.tools.vcfdas.VcfDistributedAnnotationSystem, ${jetty.jars}))
$(eval $(call compile-htsjdk-cmd,vcffilterdoid,${jvarkit.package}.tools.vcfdo.VcfFilterDoid))
$(eval $(call compile-htsjdk-cmd,vcffilterjs,${jvarkit.package}.tools.vcffilterjs.VCFFilterJS,galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcffilterso,${jvarkit.package}.tools.misc.VcfFilterSequenceOntology,wiki_flag galaxy_flag vcfpredictions))
$(eval $(call compile-htsjdk-cmd,vcffixindels,${jvarkit.package}.tools.vcffixindels.VCFFixIndels,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfgo,${jvarkit.package}.tools.vcfgo.VcfGeneOntology))
$(eval $(call compile-htsjdk-cmd,vcfhead,${jvarkit.package}.tools.misc.VcfHead,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,splitvcf,${jvarkit.package}.tools.misc.SplitVcf,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,forkvcf,${jvarkit.package}.tools.misc.ForkVcf,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfin,${jvarkit.package}.tools.vcfcmp.VcfIn,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfjaspar,${jvarkit.package}.tools.jaspar.VcfJaspar))
$(eval $(call compile-htsjdk-cmd,vcfliftover,${jvarkit.package}.tools.liftover.VcfLiftOver))
$(eval $(call compile-htsjdk-cmd,vcfmapuniprot,${jvarkit.package}.tools.misc.VcfMapUniprot,${generated.dir}/java/org/uniprot/package-info.java))
$(eval $(call compile-htsjdk-cmd,vcfmerge,${jvarkit.package}.tools.vcfmerge.VCFMerge2))
$(eval $(call compile-htsjdk-cmd,vcfmulti2one,${jvarkit.package}.tools.onesamplevcf.VcfMultiToOne))
$(eval $(call compile-htsjdk-cmd,vcfpolyx,${jvarkit.package}.tools.misc.VCFPolyX,wiki_flag galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcfpredictions,${jvarkit.package}.tools.vcfannot.VCFPredictions,wiki_flag galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcfrebase,${jvarkit.package}.tools.vcfrebase.VcfRebase,wiki_flag))
$(eval $(call compile-cgi-cmd,vcfregistry.cgi))
$(eval $(call compile-htsjdk-cmd,vcfregulomedb,${jvarkit.package}.tools.misc.VcfRegulomeDB))
$(eval $(call compile-htsjdk-cmd,vcfrenamechr,${jvarkit.package}.tools.misc.ConvertVcfChromosomes))
$(eval $(call compile-htsjdk-cmd,vcfrenamesamples,${jvarkit.package}.tools.misc.VcfRenameSamples))
$(eval $(call compile-htsjdk-cmd,vcfresetvcf,${jvarkit.package}.tools.misc.VcfRemoveGenotypeIfInVcf))
$(eval $(call compile-htsjdk-cmd,vcfremovegenotypejs,${jvarkit.package}.tools.misc.VcfRemoveGenotypeJs))
$(eval $(call compile-htsjdk-cmd,vcfsetdict,${jvarkit.package}.tools.misc.VcfSetSequenceDictionary))
$(eval $(call compile-htsjdk-cmd,vcfshuffle,${jvarkit.package}.tools.misc.VCFShuffle,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfsimulator,${jvarkit.package}.tools.misc.VcfSimulator))
$(eval $(call compile-htsjdk-cmd,vcfstats,${jvarkit.package}.tools.vcfstats.VcfStats))
$(eval $(call compile-htsjdk-cmd,vcfcombinetwosnvs,${jvarkit.package}.tools.vcfannot.VCFCombineTwoSnvs))
$(eval $(call compile-htsjdk-cmd,vcfstripannot,${jvarkit.package}.tools.vcfstripannot.VCFStripAnnotations,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcftabixml,${jvarkit.package}.tools.vcftabixml.VCFTabixml))
$(eval $(call compile-htsjdk-cmd,vcftail,${jvarkit.package}.tools.misc.VcfTail,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcftreepack,${jvarkit.package}.tools.treepack.VcfTreePack,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcftrio,${jvarkit.package}.tools.vcftrios.VCFTrios))
$(eval $(call compile-htsjdk-cmd,vcfvcf,${jvarkit.package}.tools.vcfvcf.VcfVcf))
$(eval $(call compile-htsjdk-cmd,vcfviewgui,${jvarkit.package}.tools.vcfviewgui.VcfViewGui))
$(eval $(call compile-htsjdk-cmd,worldmapgenome,${jvarkit.package}.tools.circular.WorldMapGenome))
$(eval $(call compile-htsjdk-cmd,uniprotfilterjs,${jvarkit.package}.tools.misc.UniprotFilterJS,${generated.dir}/java/org/uniprot/package-info.java ))
$(eval $(call compile-htsjdk-cmd,blastfilterjs,${jvarkit.package}.tools.blast.BlastFilterJS,api.ncbi.blast))
$(eval $(call compile-htsjdk-cmd,skipxmlelements,${jvarkit.package}.tools.misc.SkipXmlElements))
$(eval $(call compile-htsjdk-cmd,minicaller,${jvarkit.package}.tools.calling.MiniCaller))
$(eval $(call compile-htsjdk-cmd,vcfcomparecallersonesample,${jvarkit.package}.tools.vcfcmp.VcfCompareCallersOneSample))
$(eval $(call compile-htsjdk-cmd,samretrieveseqandqual,${jvarkit.package}.tools.misc.SamRetrieveSeqAndQual))
$(eval $(call compile-htsjdk-cmd,vcfensemblvep,${jvarkit.package}.tools.ensembl.VcfEnsemblVepRest,api.ensembl.vep ${httpclient.libs}))
$(eval $(call compile-htsjdk-cmd,vcfgroupbypop,${jvarkit.package}.tools.misc.VcfGroupByPopulation))
$(eval $(call compile-htsjdk-cmd,vcfcomparecallers,${jvarkit.package}.tools.vcfcmp.VcfCompareCallers))
$(eval $(call compile-htsjdk-cmd,bamtile,${jvarkit.package}.tools.misc.BamTile))
$(eval $(call compile-htsjdk-cmd,xcontaminations,${jvarkit.package}.tools.xcontamination.XContaminations))
$(eval $(call compile-htsjdk-cmd,vcfjoinvcfjs,${jvarkit.package}.tools.vcffilterjs.VCFJoinVCFJS))
$(eval $(call compile_biostar_cmd,139647))
$(eval $(call compile-htsjdk-cmd,vcfburden,${jvarkit.package}.tools.misc.VcfBurden))
$(eval $(call compile-htsjdk-cmd,bioalcidae,${jvarkit.package}.tools.bioalcidae.BioAlcidae,${gson.jar} api.ncbi.blast api.ncbi.insdseq ${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/package-info.java wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfbedsetfilter,${jvarkit.package}.tools.vcfbed.VCFBedSetFilter,wiki_flag galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcfreplacetag,${jvarkit.package}.tools.vcfstripannot.VCFReplaceTag))
$(eval $(call compile-htsjdk-cmd,vcfindextabix,${jvarkit.package}.tools.misc.VcfIndexTabix))
$(eval $(call compile-htsjdk-cmd,vcfpeekvcf,${jvarkit.package}.tools.vcfvcf.VcfPeekVcf))
$(eval $(call compile-htsjdk-cmd,vcfgetvariantbyindex,${jvarkit.package}.tools.misc.VcfGetVariantByIndex))
$(eval $(call compile-htsjdk-cmd,vcfmulti2oneallele,${jvarkit.package}.tools.misc.VcfMultiToOneAllele,galaxy_flag))
$(eval $(call compile-htsjdk-cmd,vcfmulti2oneinfo,${jvarkit.package}.tools.misc.VcfMultiToOneInfo))
$(eval $(call compile-htsjdk-cmd,bedindextabix,${jvarkit.package}.tools.misc.BedIndexTabix))
$(eval $(call compile-htsjdk-cmd,vcf2bam,${jvarkit.package}.tools.misc.VcfToBam))
$(eval $(call compile-htsjdk-cmd,vcffilterxpath,${jvarkit.package}.tools.misc.VcfFilterXPath))
$(eval $(call compile-htsjdk-cmd,pcrclipreads,${jvarkit.package}.tools.pcr.PcrClipReads))
$(eval $(call compile-htsjdk-cmd,extendrefwithreads,${jvarkit.package}.tools.extendref.ExtendReferenceWithReads,wiki_flag))
$(eval $(call compile-htsjdk-cmd,pcrslicereads,${jvarkit.package}.tools.pcr.PcrSliceReads))
$(eval $(call compile-htsjdk-cmd,samjmx,${jvarkit.package}.tools.jmx.SamJmx))
$(eval $(call compile-htsjdk-cmd,vcfjmx,${jvarkit.package}.tools.jmx.VcfJmx))
$(eval $(call compile-htsjdk-cmd,gtf2xml,${jvarkit.package}.tools.misc.Gtf2Xml))
$(eval $(call compile-htsjdk-cmd,sortsamrefname,${jvarkit.package}.tools.misc.SortSamRefName))
$(eval $(call compile-htsjdk-cmd,bamclip2insertion,${jvarkit.package}.tools.misc.BamClipToInsertion))
$(eval $(call compile-htsjdk-cmd,localrealignreads,${jvarkit.package}.tools.misc.LocalRealignReads))
$(eval $(call compile-htsjdk-cmd,msa2vcf,${jvarkit.package}.tools.msa2vcf.MsaToVcf))
$(eval $(call compile-htsjdk-cmd,samslop,${jvarkit.package}.tools.misc.SamSlop,wiki_flag))
$(eval $(call compile-htsjdk-cmd,projectserver,${jvarkit.package}.tools.server.ProjectServer,${jetty.jars}))
$(eval $(call compile-htsjdk-cmd,vcfcalledwithanothermethod,${jvarkit.package}.tools.misc.VcfCalledWithAnotherMethod))
$(eval $(call compile-htsjdk-cmd,vcfderby01,${jvarkit.package}.tools.burden.VcfDerby01,wiki_flag ${derby.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdensplitter,${jvarkit.package}.tools.burden.VcfBurdenSplitter,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfburdenfisherh,${jvarkit.package}.tools.burden.VcfBurdenFisherH,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfburdenfisherv,${jvarkit.package}.tools.burden.VcfBurdenFisherV,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfburdenrscriptv,${jvarkit.package}.tools.burden.VcfBurdenRscriptV,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfdoest,${jvarkit.package}.tools.burden.VcfDoest,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcffilternotinpedigree,${jvarkit.package}.tools.burden.VcfFilterNotInPedigree,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfburdenmaf,${jvarkit.package}.tools.burden.VcfBurdenMAF,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfburdenexac,${jvarkit.package}.tools.burden.VcfBurdenFilterExac,galaxy_flag wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfgenesplitter,${jvarkit.package}.tools.misc.VcfGeneSplitter,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfsqltag,${jvarkit.package}.tools.sql.VcfSqlTag))
$(eval $(call compile-htsjdk-cmd,vcfburdenfiltergenes,${jvarkit.package}.tools.burden.VcfBurdenFilterGenes,wiki_flag galaxy_flag))
$(eval $(call compile-htsjdk-cmd,sammaskalignedbases,${jvarkit.package}.tools.misc.SamMaskAlignedBases,wiki_flag))
$(eval $(call compile-htsjdk-cmd,gff2kg,${jvarkit.package}.tools.misc.Gff2KnownGene,wiki_flag))
$(eval $(call compile-htsjdk-cmd,miniassembly,${jvarkit.package}.tools.misc.MiniAssembly,wiki_flag))
$(eval $(call compile-htsjdk-cmd,haloplexparasite,${jvarkit.package}.tools.haloplex.HaloplexParasite,wiki_flag))
$(eval $(call compile-htsjdk-cmd,bam2sql,${jvarkit.package}.tools.misc.BamToSql,wiki_flag))
$(eval $(call compile-htsjdk-cmd,vcfinjectpedigree,${jvarkit.package}.tools.burden.VcfInjectPedigree,wiki_flag))
$(eval $(call compile-htsjdk-cmd,gbrowserhtml,${jvarkit.package}.tools.misc.GBrowserHtml,wiki_flag ${gson.jar} copy.samtools.js))
$(eval $(call compile-htsjdk-cmd,bim2vcf,${jvarkit.package}.tools.misc.BimToVcf,wiki_flag))
$(eval $(call compile-htsjdk-cmd,samreadlengthdistribution,${jvarkit.package}.tools.misc.SamReadLengthDistribution,wiki_flag))
$(eval $(call compile-htsjdk-cmd,queue2make,${jvarkit.package}.tools.misc.QueueToMake,wiki_flag))
all-jnlp : $(addprefix ${dist.dir}/,$(addsuffix .jar,vcfviewgui buildwpontology batchigvpictures)) ${htsjdk.jars} \
./src/main/resources/jnlp/generic.jnlp .secret.keystore
mkdir -p ${tmp.dir}
cp $(filter %.jar,$^) ${tmp.dir}
$(foreach J, $(filter %.jar,$^) , jarsigner ${J} secret ; )
sed -e 's/__MAIN_JAR__/vcfviewgui/g' \
-e 's/__TITLE__/VcfViewGui/g' \
-e 's/__MAIN_CLASS__/${jvarkit.package}.tools.vcfviewgui.VcfViewGui/g' \
./src/main/resources/jnlp/generic.jnlp > ${tmp.dir}/vcfviewgui.jnlp
sed -e 's/__MAIN_JAR__/buildwpontology/g' \
-e 's/__TITLE__/BuildWikipediaOntology/g' \
-e 's/__MAIN_CLASS__/${jvarkit.package}.tools.misc.BuildWikipediaOntology/g' \
./src/main/resources/jnlp/generic.jnlp > ${tmp.dir}/buildwpontology.jnlp
sed -e 's/__MAIN_JAR__/batchigvpictures/g' \
-e 's/__TITLE__/BatchIGVPictures/g' \
-e 's/__MAIN_CLASS__/${jvarkit.package}.tools.batchpicts.BatchIGVPictures/g' \
./src/main/resources/jnlp/generic.jnlp > ${tmp.dir}/batchigvpictures.jnlp
.secret.keystore :
-keytool -genkeypair -keystore $@ -alias secret \
-keypass $(if ${keytool.keypass},${keytool.keypass},KEYTOOLPASS) \
-storepass $(if ${keytool.storepass},${keytool.storepass},KEYTOOLSTOREPASS) \
-dname CN=Pierre Lindenbaum, OU=INSERM, O=INSERM, L=Nantes, ST=Nantes, C=Fr
${generated.dir}/java/org/uniprot/package-info.java : api.uniprot
api.uniprot :
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p org.uniprot ${xjc.proxy} "http://www.uniprot.org/support/docs/uniprot.xsd"
api.ncbi.pubmed :
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.pubmed -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_150101.dtd"
api.evs:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p edu.washington.gs.evs ${xjc.proxy} -wsdl "http://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdl"
api.ncbi.blast:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.blast -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"
api.ncbi.esearch:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.esearch -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/corehtml/query/DTD/eSearch_020511.dtd"
api.ncbi.elink:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.elink -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/elink_020122.dtd"
api.ncbi.gb:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.gb -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd"
api.ncbi.taxonomy:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.taxonomy -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"
api.ncbi.tseq:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.tseq -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd"
api.ncbi.insdseq:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.insdseq -dtd ${xjc.proxy} "https://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd"
api.ncbi.dbsnp.gt:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.dbsnp.gt ${xjc.proxy} "https://ftp.ncbi.nlm.nih.gov/snp/specs/genoex_1_5.xsd"
${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/package-info.java : api.ncbi.dbsnp
api.ncbi.dbsnp:
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.dbsnp ${xjc.proxy} "https://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_current.xsd"
## API Ensembl
api.ensembl.vep :
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p org.ensembl.vep ./src/main/resources/xsd/ensembl/vep.xsd
api.printf:
mkdir -p ${generated.dir}/java/com/github/lindenb/jvarkit/util/printf && \
${JAVACC} -OUTPUT_DIRECTORY=${generated.dir}/java/com/github/lindenb/jvarkit/util/printf \
src/main/resources/javacc/com/github/lindenb/jvarkit/util/printf/Printf.jj
api.samfilter:
mkdir -p ${src.dir}/java/com/github/lindenb/jvarkit/util/bio/samfilter && \
${JAVACC} -OUTPUT_DIRECTORY=${src.dir}/com/github/lindenb/jvarkit/util/bio/samfilter \
src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj
copy.opendoc.odp.resources :
mkdir -p ${tmp.dir}/META-INF/opendocument/odp
cp src/main/resources/opendocument/thumbnail.png ${tmp.dir}/META-INF/opendocument/odp/
cp $(addprefix src/main/resources/opendocument/odp/, meta.xml content.xml settings.xml styles.xml mimetype ) ${tmp.dir}/META-INF/opendocument/odp/
copy.samtools.js:
mkdir -p ${tmp.dir}/META-INF/js
$(foreach J,gbrowse.js hershey.js samtools.js com.github.lindenb.jvarkit.tools.misc.GBrowserHtml.js,cp src/main/js/${J} ${tmp.dir}/META-INF/js/ ; )
## jvarkit-library (used in knime)
library: ${dist.dir}/jvarkit-${htsjdk.version}.jar
${dist.dir}/jvarkit-${htsjdk.version}.jar : ${htsjdk.jars} ${bigwig.jars} \
${generated.dir}/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java \
${src.dir}/com/github/lindenb/jvarkit/util/Library.java
mkdir -p ${tmp.dir}/META-INF $(dir $@)
cp src/main/resources/messages/messages.properties ${tmp.dir}
${JAVAC} -d ${tmp.dir} -g -classpath "$(subst $(SPACE),:,$(filter %.jar,$^))" -sourcepath ${src.dir}:${generated.dir}/java $(filter %.java,$^)
${JAR} cf $@ -C ${tmp.dir} .
rm -rf ${tmp.dir}
##
## Download mysql connector for java
##
${mysql.jar} :
echo "Downloading mysql connector for java version ${mysql.version} from oracle"
mkdir -p $(dir $@)
curl -Lk ${curl.proxy} -o jeter.tar.gz "http://dev.mysql.com/get/Downloads/Connector-J/mysql-connector-java-${mysql.version}.tar.gz"
tar xvfz jeter.tar.gz --strip-components=1 "mysql-connector-java-${mysql.version}/mysql-connector-java-${mysql.version}-bin.jar"
mv mysql-connector-java-${mysql.version}-bin.jar $@
rm jeter.tar.gz
##
## BerkeleyDB
##
${berkeleydb.jar}:
echo "Downloading berkeleydb for java version ${berkeleydb.version} from oracle"
mkdir -p $(dir $@)
curl -Lk ${curl.proxy} -o $@ "http://download.oracle.com/maven/com/sleepycat/je/${berkeleydb.version}/je-${berkeleydb.version}.jar"
##
## Broad BigWig
##
${bigwig.log4j.jar} : ${bigwig.jar}
touch -c $@
${bigwig.jar} xx :
echo "Downloading bigwig library for java."
mkdir -p lib
rm -rf bigwig.zip bigwig-${bigwig.version}
curl -k ${curl.proxy} -o bigwig.zip -L "https://github.com/lindenb/bigwig/archive/${bigwig.version}.zip"
unzip bigwig.zip
rm -rf bigwig.zip
echo "Compiling, using apache ant"
(cd bigwig-${bigwig.version} && ${ANT} )
mv bigwig-${bigwig.version}/lib/$(notdir ${bigwig.log4j.jar}) ${bigwig.log4j.jar}
mv bigwig-${bigwig.version}/dist/BigWig.jar ${bigwig.jar}
rm -rf bigwig-${bigwig.version}
##
## Common math
##
${common.math.jar} :
echo "Downloading common math"
mkdir -p $(dir $@)
curl -Lk ${curl.proxy} -o jeter.tar.gz "http://www.us.apache.org/dist/commons/math/binaries/commons-math3-${common.math.version}-bin.tar.gz"
tar xvfz jeter.tar.gz --strip-components=1 "commons-math3-${common.math.version}/commons-math3-${common.math.version}.jar"
mv commons-math3-${common.math.version}.jar $@
rm jeter.tar.gz
##
## Apache Stuf
##
$(addprefix lib/, commons-validator/commons-validator/1.4.0/commons-validator-1.4.0.jar commons-beanutils/commons-beanutils/1.8.3/commons-beanutils-1.8.3.jar ):
mkdir -p $(dir $@) && curl -Lk ${curl.proxy} -o $@ "http://central.maven.org/maven2/$(patsubst lib/%,%,$@)"
${generated.dir}/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java :
mkdir -p $(dir $@)
echo "package ${jvarkit.package}.util.htsjdk;" > $@
echo '@javax.annotation.Generated("jvarkit")' >> $@
echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> $@
echo 'public static String getVersion() {return "${htsjdk.version}";}' >> $@
echo 'public static String getHash() {return "${htsjdk.version}";}' >> $@
echo 'public static String getHome() {return "$(word 1,${htsjdk.jars})";}' >> $@
echo 'public static String getJavadocUrl(Class<?> clazz) {return "https://samtools.github.io/htsjdk/javadoc/htsjdk/"+clazz.getName().replaceAll("\\.","/")+".html";}' >> $@
echo '}' >> $@
## API EVS
src/main/generated-sources/java/edu/washington/gs/evs/package-info.java :
mkdir -p ${generated.dir}/java
${JAVA_HOME}/bin/xjc ${xjc.proxy} -d ${generated.dir}/java \
-p edu.washington.gs.evs \
"http://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdl"
#
# ga4gh schema, see
# http://plindenbaum.blogspot.fr/2015/06/playing-with-ga4gh-schemas-and-avro-my.html
#
ga4gh.schemas.version ?= 0.5.1
ga4gh.schemas.avpr = $(addsuffix .avpr,$(addprefix ${generated.dir}/resources/avro/ga4gh/schemas-${ga4gh.schemas.version}/src/main/resources/avro/,beacon common readmethods reads referencemethods references variantmethods variants wip/metadata wip/metadatamethods wip/variationReference ))
ga4gh.schemas.sources : lib/org/ga4gh/ga4gh-${ga4gh.schemas.version}.jar
lib/org/ga4gh/ga4gh-${ga4gh.schemas.version}.jar: ${avro.libs} ${ga4gh.schemas.avpr}
mkdir -p ${generated.dir}/java _tmp.avro${ga4gh.schemas.version} lib/org/ga4gh
java -jar $< compile protocol \
${generated.dir}/resources/avro/ga4gh/schemas-${ga4gh.schemas.version}/src/main/resources/avro \
${generated.dir}/resources/avro/ga4gh/schemas-${ga4gh.schemas.version}/src/main/resources/avro/wip \
${generated.dir}/java
javac -d _tmp.avro${ga4gh.schemas.version} -cp ${avro.libs} -sourcepath ${generated.dir}/java ${generated.dir}/java/org/ga4gh/*.java
jar cvf lib/org/ga4gh/ga4gh-${ga4gh.schemas.version}.jar -C _tmp.avro${ga4gh.schemas.version} .
rm -rf _tmp.avro${ga4gh.schemas.version}
$(filter-out $(word 1,${ga4gh.schemas.avpr}),${ga4gh.schemas.avpr}) : $(word 1,${ga4gh.schemas.avpr})
$(word 1,${ga4gh.schemas.avpr}) : ${avro.libs}
rm -rf ${generated.dir}/resources/avro/ga4gh/schemas-${ga4gh.schemas.version}
mkdir -p $(dir $@)
curl -Lk ${curl.proxy} -o schema.zip "https://github.com/ga4gh/schemas/archive/v${ga4gh.schemas.version}.zip"
unzip schema.zip -d ${generated.dir}/resources/avro/ga4gh
rm schema.zip
$(foreach P,${ga4gh.schemas.avpr}, java -jar ${avro.libs} idl $(patsubst %.avpr,%.avdl,${P}) ${P} ; )
touch $@
#
# end of ga4gh schema
#
#
clean:
rm -rf ${dist.dir}