-
Notifications
You must be signed in to change notification settings - Fork 131
/
Makefile.legacy
896 lines (771 loc) · 60.9 KB
/
Makefile.legacy
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
#
# Makefile for jvarkit
#
SHELL=/bin/bash
this.makefile=$(lastword $(MAKEFILE_LIST))
this.dir=$(dir $(realpath ${this.makefile}))
top:
@echo "This is the top target. Run 'make name-of-target' to build the desired target. Run 'make all' if you're Pierre Lindenbaum. See http://lindenb.github.io/jvarkit/ for a list of the available tools."
#need local settings ? create a file 'local.mk' in this directory
ifneq ($(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
JAVAH?=javah
JAVA?=java
JAVACC?=javacc
JAR?=jar
#
# include java libraries from Maven
#
include maven.mk
XJC?=$(JAVA) -cp "$(subst $(SPACE),:,${xjc_jars})" -DenableExternalEntityProcessing=true com.sun.tools.xjc.XJCFacade
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
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}
jvarkit.package=com.github.lindenb.jvarkit
## http://stackoverflow.com/questions/9551416
EMPTY :=
SPACE := $(EMPTY) $(EMPTY)
define CRLF
endef
gatk.tools = org_broadinstitute_gatk_engine_CommandLineGATK \
org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants \
org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator \
org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration
define make_gatk_code
${generated.dir}/resources/json/gatk/$$(lastword $$(subst _, ,$(1))).json :
mkdir -p $$(dir $$@)
curl -Lk $${curl.proxy} -o "$$(addsuffix .tmp,$$@)" "https://software.broadinstitute.org/gatk/gatkdocs/$(1).php.json"
mv $$(addsuffix .tmp,$$@) $$@
${generated.dir}/java/com/github/lindenb/jvarkit/gatk/commands/Abstract$$(lastword $$(subst _, ,$(1))).java :${generated.dir}/resources/json/gatk/$$(lastword $$(subst _, ,$(1))).json gatkcodegen ${this.dir}src/main/resources/velocity/gatkcmd.vm
mkdir -p $$(dir $$@) && ${JAVA} -jar ${dist.dir}/gatkcodegen.jar -T $$(word 3,$$^) $$< > $$@
endef
define compile-htsjdk-cmd
## 1 : target name
## 2 : qualified main class name
## 3 : other deps
$(1) : ${htsjdk.jars} \
$(addsuffix .java,$(addprefix ${src.dir}/,$(subst .,/,$(2)))) \
$(3)
echo "### COMPILING $(1) ######"
mkdir -p ${tmp.dir}/META-INF ${dist.dir}
mkdir -p ${tmp.dir}/$(dir $(subst .,/,$(2)))
cp -v "$(addsuffix .java,$(addprefix ${src.dir}/,$(subst .,/,$(2))))" "${tmp.dir}/$(dir $(subst .,/,$(2)))"
echo '### Printing javac version : it should be OpenJdk 11. if Not, check your $$$${PATH}.'
${JAVAC} -version 2>&1 > $$(addsuffix .jdkversion,$$@) && \
cat $$(addsuffix .jdkversion,$$@) && \
grep -E '11\.[0-9_]+\.[0-9_]+' $$(addsuffix .jdkversion,$$@) && \
rm $$(addsuffix .jdkversion,$$@)
#information about the java jre/sdk.
echo -n "javac=" > "${tmp.dir}/META-INF/jdk.properties"
which ${JAVAC} >> "${tmp.dir}/META-INF/jdk.properties"
echo -n "jar=" >> "${tmp.dir}/META-INF/jdk.properties"
which ${JAR} >> "${tmp.dir}/META-INF/jdk.properties"
echo -n "java=" >> "${tmp.dir}/META-INF/jdk.properties"
which ${JAVA} >> "${tmp.dir}/META-INF/jdk.properties"
echo "classpath=$$(subst $$(SPACE),:,$$(filter %.jar,$$^))" >> "${tmp.dir}/META-INF/jdk.properties"
echo -n "self=" >> "${tmp.dir}/META-INF/jdk.properties"
echo "${dist.dir}/$(1)$(if ${standalone},-fat).jar" >> "${tmp.dir}/META-INF/jdk.properties"
#compile
${JAVAC} \
-J-Djvarkit.libs.jars='$$(subst $$(SPACE),:,$$(filter %.jar,$$^))' \
-J-Djvarkit.main.class='$(2)' \
-J-Djvarkit.this.dir='${this.dir}' \
-d ${tmp.dir} \
-g -classpath "$$(subst $$(SPACE),:,$$(filter %.jar,$$^))" \
-sourcepath ${src.dir}:${generated.dir}/java $$(filter %.java,$$^)
ifeq (${standalone},yes)
$$(foreach J,$$(filter %.jar,$$^),unzip -o $${J} -d ${tmp.dir};)
endif
#create META-INF/MANIFEST.MF
echo "Manifest-Version: 1.0" > ${tmp.mft}
echo "Main-Class: $(2)" >> ${tmp.mft}
echo "Htsjdk-Version: ${htsjdk.version}" >> ${tmp.mft}
ifneq (${standalone},yes)
echo "Class-Path: $$(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)$(if ${standalone},-fat).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 ${http.proxy.host},-Dhttp.proxyHost=${http.proxy.host}) $(if ${http.proxy.port},-Dhttp.proxyPort=${http.proxy.port}) ' >> ${dist.dir}/$(1)
ifeq (${standalone},yes)
echo -n ' -jar "${dist.dir}/$(1)-fat.jar" ' >> ${dist.dir}/$(1)
else
echo -n ' -cp "$$(subst $$(SPACE),:,$$(realpath $$(filter %.jar,$$^))):${dist.dir}/$(1).jar" $(2) ' >> ${dist.dir}/$(1)
endif
echo '"$$$$@"' >> ${dist.dir}/$(1)
chmod ugo+rx ${dist.dir}/$(1)
# generate markdown if needed
-if [ "${TRAVIS}" != "true" ] && [ "${standalone}" != "yes" ] ; then \
${JAVA} -Djvarkit.doc.dir=${this.dir}docs -Djvarkit.src.dir=${this.dir}src/main/java -jar "${dist.dir}/$(1)$(if ${standalone},-fat).jar" --help --helpFormat make-doc ;\
fi
#cleanup
rm -rf "${tmp.dir}"
endef
##
## Creates a CGI script for java app
##
define compile-cgi-cmd
${dist.dir}/$(1).cgi : $(1)
echo "#!/bin/bash" > $$@
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
gatk_apps:$(if ${gatk.jar},gatkwalkers,)
APPS= vcffixindels vcftail vcfhead vcfburdenfisherh vcfburdenfisherv vcfburdenmaf \
vcfmulti2oneallele vcfin vcffilterso vcffilterjs vcfburdensplitter vcfpredictions \
vcfpolyx vcfburdenfiltergenes vcfbed vcfbedsetfilter gatk_apps vcftrio vcffamilies groupbygene \
addlinearindextobed allelefreqcalc almostsortedvcf backlocate bam2fastq lowresbam2raster bam2raster bam2svg \
bam2xml bam2wig bamcmpcoverage bamindexreadnames bamliftover bamqueryreadnames \
bamrenamechr bamsnvwig bamstats04 bamstats05 bamtreepack batchigvpictures bedliftover \
bedrenamechr biostar103303 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 \
downsamplevcf evs2vcf evs2xml 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 \
liftover2svg mapuniprot mergesplittedblast ncbitaxonomy2xml metrics2xml ngsfilessummary noemptyvcf \
nozerovariationvcf pademptyfastq pubmeddump pubmedorcidgraph pubmedfilterjs referencetovcf sam2json \
sam2psl sam2tsv sam4weblogo samclipindelfraction samextractclip samfindclippedregions samfixcigar \
samgrep samjs samshortinvert samstats01 sigframe sortvcfoninfo \
sortvcfonref2 splitbam3 splitbytile splitread \
vcf2hilbert vcf2ps vcf2rdf vcf2sql vcf2xml vcfannobam \
vcfbiomart vcfcadd vcfcmppred vcfcomm vcfcompare vcfcomparegt \
vcfconcat vcfcutsamples \
vcfjaspar vcfliftover vcfmerge vcfmulti2one \
vcfrebase vcfregistry.cgi vcfregulomedb vcfrenamechr vcfrenamesamples \
vcfresetvcf vcfsetdict vcfmakedict vcfshuffle vcfsimulator vcfstats vcfcombinetwosnvs vcfstripannot \
vcftabixml vcftreepack vcfvcf worldmapgenome \
uniprotfilterjs skipxmlelements vcfensemblvep vcfgroupbypop bamtile xcontaminations \
biostar3654 bioalcidae bioalcidaejdk 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 \
vcfmovefilterstoinfo gatkcodegen cmpbams4 vcfeigen01 biostar234081 biostar234230 vcfgnomad vcf2svg mergeblastxml \
vcfannotwithbeacon commbams samscansplitreads samretrieveseqandqual pubmedcodinglang biostar251649 samcolortag vcf2table \
variantsinwindow knime2txt lumpyvcf2circos vcfucsc xsltstream vcfloopovergenes vcffilterjdk samjdk vcfnocall2homref \
vcfserver tviewserver vcftrap prettysam vcfremoveunusedalt lumpysort samaddpi goutils gb2gff \
indexcov2vcf samcustomsortjdk
.PHONY: all tests $(APPS) clean download_all_maven library top burden
all: $(APPS)
burden: vcfburden vcfburdensplitter vcfburdenfisherh vcfburdenfisherv vcfburdenmaf vcfburdenfiltergenes vcfinjectpedigree vcfburdenrscriptv vcffilternotinpedigree vcfderby01 vcfmovefilterstoinfo
${dist.dir}/testsng.jar: testsng
tests: ${testng.jars} ${dist.dir}/testsng.jar
-${JAVA} \
$(if ${http.proxy.host},-Dhttp.proxyHost=${http.proxy.host} -Dhttps.proxyHost=${http.proxy.host}) \
$(if ${http.proxy.port},-Dhttp.proxyPort=${http.proxy.port} -Dhttps.proxyPort=${http.proxy.port}) \
-cp "$(subst $(SPACE),:,$(filter %.jar,$^))" org.testng.TestNG -parallel false \
-suitename "jvarkit" -testname "jvarkit" \
-log 2 -d "test-output" -testjar ${dist.dir}/testsng.jar
rm -vf ${dist.dir}/testsng.jar
tests2: ${testng.jars} ${htsjdk.jars} ${httpclient.libs} api.ncbi.gb ${bigwig.jars} ${mysql.jar} ${jetty.jars} ${common.math3.libs} ${gson.jar} ${berkeleydb.jar} ${jaxb.jars}
rm -rf "${tmp.dir}"
mkdir -p "${tmp.dir}"
${JAVAC} -d ${tmp.dir} -cp "$(subst $(SPACE),:,$(filter %.jar,$^))" -sourcepath ${generated.dir}/java:src/test/java:src/main/java `find src/test/java -type f -name "*.java" | grep -i -v jfx | grep -v SimplePlotTest`
${JAVA} \
-Dhttp.nonProxyHosts="localhost" \
$(if ${http.proxy.host},-Dhttp.proxyHost=${http.proxy.host} -Dhttps.proxyHost=${http.proxy.host}) \
$(if ${http.proxy.port},-Dhttp.proxyPort=${http.proxy.port} -Dhttps.proxyPort=${http.proxy.port}) \
-cp "$(subst $(SPACE),:,$(filter %.jar,$^)):${tmp.dir}" org.testng.TestNG -parallel false -d "test-output" ./src/test/resources/testng.xml
rm -rf "${tmp.dir}"
#bigwig
$(eval $(call compile-htsjdk-cmd,vcfbigwig,${jvarkit.package}.tools.vcfbigwig.VCFBigWig,${jcommander.jar} ${bigwig.jars} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfensemblreg, ${jvarkit.package}.tools.ensemblreg.VcfEnsemblReg,${bigwig.jars} ${jcommander.jar}))
$(eval $(call compile_biostar_cmd,105754,${bigwig.jar} ${jcommander.jar} ))
# common math
$(eval $(call compile-htsjdk-cmd,naivecnvdetector,${jvarkit.package}.tools.structvar.NaiveCnvDetector,${jcommander.jar} ${common.math3.libs} ${bigwig.jars}))
#berkeley
$(eval $(call compile-htsjdk-cmd,vcfphylotree,${jvarkit.package}.tools.phylo.VcfPhyloTree,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,ngsfilesscanner,${jvarkit.package}.tools.ngsfiles.NgsFilesScanner,${jcommander.jar} ${berkeleydb.jar}))
$(eval $(call compile_biostar_cmd,92368,${jcommander.jar} ${berkeleydb.jar}))
#mysql
$(eval $(call compile-htsjdk-cmd,vcfucsc,${jvarkit.package}.tools.vcfucsc.VcfUcsc,${jcommander.jar} ${mysql.jar}))
$(eval $(call compile-htsjdk-cmd,addlinearindextobed,${jvarkit.package}.tools.misc.AddLinearIndexToBed,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,allelefreqcalc,${jvarkit.package}.tools.misc.AlleleFrequencyCalculator,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bam2xml,${jvarkit.package}.tools.bam2xml.Bam2Xml,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,almostsortedvcf,${jvarkit.package}.tools.sortvcfonref.AlmostSortedVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,backlocate,${jvarkit.package}.tools.backlocate.BackLocate,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bam2fastq,${jvarkit.package}.tools.fastq.BamToFastq,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bam2raster,${jvarkit.package}.tools.bam2graphics.Bam2Raster,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,lowresbam2raster,${jvarkit.package}.tools.bam2graphics.LowResBam2Raster,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bam2svg,${jvarkit.package}.tools.bam2svg.BamToSVG,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,sv2svg,${jvarkit.package}.tools.bam2svg.SvToSVG,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bam2wig,${jvarkit.package}.tools.bam2wig.Bam2Wig,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamcmpcoverage,${jvarkit.package}.tools.misc.BamCmpCoverage,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samaddpi,${jvarkit.package}.tools.misc.SamAddPI,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamindexreadnames,${jvarkit.package}.tools.bamindexnames.BamIndexReadNames,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamliftover,${jvarkit.package}.tools.liftover.BamLiftOver,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,bamqueryreadnames,${jvarkit.package}.tools.bamindexnames.BamQueryReadNames,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamrenamechr,${jvarkit.package}.tools.misc.ConvertBamChromosomes,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamstatsjfx,${jvarkit.package}.tools.bamstats01.BamStatsJfx,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,bamstats02,${jvarkit.package}.tools.bamstats01.BamStats02,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,bamstats02view,${jvarkit.package}.tools.bamstats01.BamStats02View,${jcommander.jar} bamstats02 ))
$(eval $(call compile-htsjdk-cmd,bamstats04,${jvarkit.package}.tools.bamstats04.BamStats04,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamstats05,${jvarkit.package}.tools.bamstats04.BamStats05,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamtreepack,${jvarkit.package}.tools.treepack.BamTreePack,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,batchigvpictures,${jvarkit.package}.tools.batchpicts.BatchIGVPictures,${jcommander.jar} copy.opendoc.odp.resources))
$(eval $(call compile-htsjdk-cmd,bedliftover,${jvarkit.package}.tools.liftover.BedLiftOver,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bedrenamechr,${jvarkit.package}.tools.misc.ConvertBedChromosomes,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,103303,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,130456,${jcommander.jar} ))
$(eval $(call compile_biostar_cmd,145820,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,59647,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,76892,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,77288,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,77828,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,78285,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,78400,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile_biostar_cmd,81455,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,84452,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,84786,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,86363,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,86480,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,90204,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,95652,${jcommander.jar} ${jaxb.jars} api.ncbi.gb))
$(eval $(call compile_biostar_cmd,3654,${jcommander.jar} ${jaxb.jars} api.ncbi.insdseq api.ncbi.blast))
$(eval $(call compile_biostar_cmd,154220,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,140111,${jcommander.jar} ${jaxb.jars} api.ncbi.dbsnp.gt ${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/gt/package-info.java))
$(eval $(call compile_biostar_cmd,160470,${jcommander.jar} ${jaxb.jars} api.ncbi.blast ))
$(eval $(call compile_biostar_cmd,165777,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,170742,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,172515,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,173114,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,175929,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,178713,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,214299,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,234081,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,234230,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,251649,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,322664,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,332826,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,336589,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,352930,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,blast2sam,${jvarkit.package}.tools.blast2sam.BlastToSam,${jcommander.jar} ${jaxb.jars} api.ncbi.blast ))
$(eval $(call compile-htsjdk-cmd,gb2gff,${jvarkit.package}.tools.genbank.GenbankToGff3,${jcommander.jar} ${jaxb.jars} api.ncbi.gb ))
$(eval $(call compile-htsjdk-cmd,blastmapannots,${jvarkit.package}.tools.blastmapannots.BlastMapAnnotations,${jcommander.jar} ${jaxb.jars} 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,${jcommander.jar} ${jaxb.jars} api.ncbi.blast ))
$(eval $(call compile-htsjdk-cmd,reduceblast,${jvarkit.package}.tools.blast.ReduceBlast,${jcommander.jar} ${jaxb.jars} api.ncbi.blast ))
$(eval $(call compile-htsjdk-cmd,mergeblastxml,${jvarkit.package}.tools.blast.MergeBlastXml,${jcommander.jar} ${jaxb.jars} api.ncbi.blast))
$(eval $(call compile-htsjdk-cmd,buildwpontology,${jvarkit.package}.tools.misc.BuildWikipediaOntology,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bwamemdigest,${jvarkit.package}.tools.mem.BWAMemDigest,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bwamemnop,${jvarkit.package}.tools.mem.BWAMemNOp,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,cmpbams,${jvarkit.package}.tools.cmpbams.CompareBams,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,cmpbams4,${jvarkit.package}.tools.cmpbams.CompareBams4,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,commbams,${jvarkit.package}.tools.cmpbams.CommBams,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,cmpbamsandbuild,${jvarkit.package}.tools.cmpbams.CompareBamAndBuild,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,coveragenormalizer,${jvarkit.package}.tools.misc.CoverageNormalizer,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,downsamplevcf,${jvarkit.package}.tools.misc.DownSampleVcf,${jcommander.jar}))
###$(eval $(call compile-htsjdk-cmd,evs2bed,${jvarkit.package}.tools.evs2bed.DumpExomeVariantServerData,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,evs2vcf,${jvarkit.package}.tools.evs2bed.EvsToVcf,${jcommander.jar} ${jaxb.jars} api.evs))
$(eval $(call compile-htsjdk-cmd,evs2xml,${jvarkit.package}.tools.evs2bed.EvsDumpXml,${jcommander.jar} ${jaxb.jars} api.evs))
$(eval $(call compile-htsjdk-cmd,fastq2fasta,${jvarkit.package}.tools.misc.FastqToFasta,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqentropy,${jvarkit.package}.tools.fastq.FastqEntropy,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqgrep,${jvarkit.package}.tools.misc.FastqGrep,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqjs,${jvarkit.package}.tools.fastq.FastqJavascript,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqphred64to33,${jvarkit.package}.tools.fastq.ConvertPhred64toFastq33,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqrecordtreepack,${jvarkit.package}.tools.treepack.FastqRecordTreePack,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,fastqrevcomp,${jvarkit.package}.tools.misc.FastqRevComp,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqshuffle,${jvarkit.package}.tools.fastq.FastqShuffle,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fastqsplitinterleaved,${jvarkit.package}.tools.fastq.FastqSplitInterleaved,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,findallcoverageatposition,${jvarkit.package}.tools.misc.FindAllCoverageAtPosition,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,findavariation,${jvarkit.package}.tools.misc.FindAVariation,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,findcorruptedfiles,${jvarkit.package}.tools.misc.FindCorruptedFiles,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,findmyvirus,${jvarkit.package}.tools.mem.FindMyVirus,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,findnewsplicesites,${jvarkit.package}.tools.rnaseq.FindNewSpliceSites,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fixvarscanmissingheader,${jvarkit.package}.tools.misc.FixVarScanMissingVCFHeader,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fixvcf,${jvarkit.package}.tools.misc.FixVCF,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fixvcfformat,${jvarkit.package}.tools.misc.FixVcfFormat,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,fixvcfmissinggenotypes,${jvarkit.package}.tools.misc.FixVcfMissingGenotypes,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,gcanddepth,${jvarkit.package}.tools.misc.GcPercentAndDepth,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,concatsam,${jvarkit.package}.tools.misc.ConcatSam,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,genomicjaspar,${jvarkit.package}.tools.jaspar.GenomicJaspar,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,genscan,${jvarkit.package}.tools.genscan.GenScan,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,groupbygene,${jvarkit.package}.tools.groupbygene.GroupByGene,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,howmanybamdict,${jvarkit.package}.tools.misc.HowManyBamDict,${jcommander.jar}))
####$(eval $(call compile-htsjdk-cmd,idea20130924,${jvarkit.package}.tools.bwamempcr.Idea20130924))
$(eval $(call compile-htsjdk-cmd,illuminadir,${jvarkit.package}.tools.misc.IlluminaDirectory,${jcommander.jar} ${gson.jar}))
$(eval $(call compile-htsjdk-cmd,ilmnfastqstats,${jvarkit.package}.tools.misc.IlluminaStatsFastq,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,impactofduplicates,${jvarkit.package}.tools.impactdup.ImpactOfDuplicates,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,kg2bed,${jvarkit.package}.tools.misc.KnownGenesToBed,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,liftover2svg,${jvarkit.package}.tools.liftover.LiftOverToSVG,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,mapuniprot,${jvarkit.package}.tools.misc.MapUniProtFeatures,${jcommander.jar} ${jaxb.jars} ${generated.dir}/java/org/uniprot/package-info.java))
$(eval $(call compile-htsjdk-cmd,mergesplittedblast,${jvarkit.package}.tools.blast.MergeSplittedBlast,${jcommander.jar} ${jaxb.jars} api.ncbi.blast))
$(eval $(call compile-htsjdk-cmd,metrics2xml,${jvarkit.package}.tools.metrics2xml.PicardMetricsToXML,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,ncbitaxonomy2xml,${jvarkit.package}.tools.misc.NcbiTaxonomyToXml,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,ngsfilessummary,${jvarkit.package}.tools.ngsfiles.NgsFilesSummary,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,noemptyvcf,${jvarkit.package}.tools.misc.NoEmptyVCF,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,nozerovariationvcf,${jvarkit.package}.tools.misc.NoZeroVariationVCF,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pademptyfastq,${jvarkit.package}.tools.misc.PadEmptyFastq,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmeddump,${jvarkit.package}.tools.pubmed.PubmedDump,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmed404,${jvarkit.package}.tools.pubmed.Pubmed404,${jcommander.jar} ${httpclient.libs}))
$(eval $(call compile-htsjdk-cmd,ncbigenedump,${jvarkit.package}.tools.misc.NcbiGeneDump,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedcodinglang,${jvarkit.package}.tools.pubmed.PubmedCodingLanguages,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedgender,${jvarkit.package}.tools.pubmed.PubmedGender,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedmap,${jvarkit.package}.tools.pubmed.PubmedMap,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedgraph,${jvarkit.package}.tools.pubmed.PubmedGraph,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedorcidgraph,${jvarkit.package}.tools.pubmed.PubmedOrcidGraph,${jcommander.jar} ${berkeleydb.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedauthorgraph,${jvarkit.package}.tools.pubmed.PubmedAuthorGraph,${jcommander.jar} ${berkeleydb.jar}))
$(eval $(call compile-htsjdk-cmd,pubmedfilterjs,${jvarkit.package}.tools.pubmed.PubmedFilterJS,${jcommander.jar} ${jaxb.jars} api.ncbi.pubmed))
$(eval $(call compile-htsjdk-cmd,referencetovcf,${jvarkit.package}.tools.misc.ReferenceToVCF,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,sam2json,${jvarkit.package}.tools.misc.SamToJson,${jcommander.jar} ${gson.jar} ))
$(eval $(call compile-htsjdk-cmd,sam2psl,${jvarkit.package}.tools.misc.SamToPsl,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,sam2tsv,${jvarkit.package}.tools.sam2tsv.Sam2Tsv,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,wescnvtview,${jvarkit.package}.tools.sam2tsv.WesCnvTView,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,prettysam,${jvarkit.package}.tools.sam2tsv.PrettySam,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,sam4weblogo,${jvarkit.package}.tools.sam4weblogo.SAM4WebLogo,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samclipindelfraction,${jvarkit.package}.tools.misc.SamClipIndelFraction,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samextractclip,${jvarkit.package}.tools.structvar.SamExtractClip,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfstrechofgt,${jvarkit.package}.tools.structvar.VcfStretchOfGt,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,samscansplitreads,${jvarkit.package}.tools.structvar.SamScanSplitReads,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,samfindclippedregions,${jvarkit.package}.tools.structvar.SamFindClippedRegions,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samfixcigar,${jvarkit.package}.tools.samfixcigar.SamFixCigar,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,samgrep,${jvarkit.package}.tools.samgrep.SamGrep,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,samjs,${jvarkit.package}.tools.samjs.SamJavascript,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samcolortag,${jvarkit.package}.tools.samjs.SamColorTag,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samshortinvert,${jvarkit.package}.tools.structvar.SamShortInvertion,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samstats01,${jvarkit.package}.tools.bamstats01.BamStats01,${jcommander.jar} ))
##$(eval $(call compile-htsjdk-cmd,scanshortinvert,${jvarkit.package}.tools.mem.ScanShortInvert))
$(eval $(call compile-htsjdk-cmd,sigframe,${jvarkit.package}.tools.sigframe.SigFrame,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,sortvcfoninfo,${jvarkit.package}.tools.sortvcfonref.SortVcfOnInfo,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,sortvcfonref2,${jvarkit.package}.tools.sortvcfonref.SortVcfOnRef2,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,splitbam3,${jvarkit.package}.tools.splitbam.SplitBam3,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,splitbytile,${jvarkit.package}.tools.splitbytitle.SplitByTile,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,splitread,${jvarkit.package}.tools.splitread.SplitRead,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,tview,${jvarkit.package}.tools.tview.TViewCmd,${jcommander.jar}))
#$(eval $(call compile-cgi-cmd,tview.cgi))
$(eval $(call compile-htsjdk-cmd,vcf2hilbert,${jvarkit.package}.tools.hilbert.VcfToHilbert,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2ps,${jvarkit.package}.tools.misc.VcfToPostscript,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2svg,${jvarkit.package}.tools.misc.VcfToSvg,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2rdf,${jvarkit.package}.tools.vcf2rdf.VcfToRdf,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcf2sql,${jvarkit.package}.tools.vcf2sql.VcfToSql,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2xml,${jvarkit.package}.tools.vcf2xml.Vcf2Xml,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfannobam,${jvarkit.package}.tools.vcfannobam.VCFAnnoBam,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfbed,${jvarkit.package}.tools.vcfbed.VCFBed,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfbiomart,${jvarkit.package}.tools.ensembl.VcfBiomart,${jcommander.jar} ${httpclient.libs}))
$(eval $(call compile-htsjdk-cmd,vcfcadd,${jvarkit.package}.tools.misc.VcfCadd,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfallelebalance,${jvarkit.package}.tools.misc.VcfAlleleBalance,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfnocall2homref,${jvarkit.package}.tools.misc.VcfNoCallToHomRef,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcmppred,${jvarkit.package}.tools.vcfcmp.VCFComparePredictions,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcomm,${jvarkit.package}.tools.vcfcmp.VCFComm,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcompare,${jvarkit.package}.tools.vcfcmp.VCFCompare,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcomparegt,${jvarkit.package}.tools.vcfcmp.VCFCompareGT,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfconcat,${jvarkit.package}.tools.vcfconcat.VcfConcat,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2zip,${jvarkit.package}.tools.vcfconcat.VcfToZip,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfcutsamples,${jvarkit.package}.tools.misc.VcfCutSamples,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfdas,${jvarkit.package}.tools.vcfdas.VcfDistributedAnnotationSystem,${jcommander.jar} ${jetty.jars} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcffilterjs,${jvarkit.package}.tools.vcffilterjs.VCFFilterJS,${jcommander.jar} ${gson.jar} ))
$(eval $(call compile-htsjdk-cmd,vcffilterso,${jvarkit.package}.tools.vcffilterso.VcfFilterSequenceOntology,${jcommander.jar} ${jaxb.jars} vcfpredictions))
$(eval $(call compile-htsjdk-cmd,vcffixindels,${jvarkit.package}.tools.vcffixindels.VCFFixIndels,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfgo,${jvarkit.package}.tools.vcfgo.VcfGeneOntology,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfhead,${jvarkit.package}.tools.misc.VcfHead,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2bed,${jvarkit.package}.tools.misc.VcfToBed,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,splitvcf,${jvarkit.package}.tools.misc.SplitVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,forkvcf,${jvarkit.package}.tools.misc.ForkVcf,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfin,${jvarkit.package}.tools.vcfcmp.VcfIn,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfjaspar,${jvarkit.package}.tools.jaspar.VcfJaspar,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfliftover,${jvarkit.package}.tools.liftover.VcfLiftOver,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfmerge,${jvarkit.package}.tools.vcfmerge.VCFMerge,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfmulti2one,${jvarkit.package}.tools.onesamplevcf.VcfMultiToOne,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfpolyx,${jvarkit.package}.tools.misc.VCFPolyX,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfpredictions,${jvarkit.package}.tools.vcfannot.VCFPredictions,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfrebase,${jvarkit.package}.tools.vcfrebase.VcfRebase,${jcommander.jar} ${jaxb.jars}) )
$(eval $(call compile-cgi-cmd,vcfregistry.cgi,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfregulomedb,${jvarkit.package}.tools.misc.VcfRegulomeDB,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfrenamechr,${jvarkit.package}.tools.misc.ConvertVcfChromosomes,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfrenamesamples,${jvarkit.package}.tools.misc.VcfRenameSamples,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfresetvcf,${jvarkit.package}.tools.misc.VcfRemoveGenotypeIfInVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfremoveunusedalt,${jvarkit.package}.tools.misc.VcfRemoveUnusedAlt,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfremovegenotypejs,${jvarkit.package}.tools.misc.VcfRemoveGenotypeJs,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfsetdict,${jvarkit.package}.tools.misc.VcfSetSequenceDictionary,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfmakedict,${jvarkit.package}.tools.misc.VcfCreateDictionary,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfshuffle,${jvarkit.package}.tools.misc.VCFShuffle,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfsimulator,${jvarkit.package}.tools.misc.VcfSimulator,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfstats,${jvarkit.package}.tools.vcfstats.VcfStats,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfstatsjfx,${jvarkit.package}.tools.vcfstats.VcfStatsJfx,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcombinetwosnvs,${jvarkit.package}.tools.vcfannot.VCFCombineTwoSnvs,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfstripannot,${jvarkit.package}.tools.vcfstripannot.VCFStripAnnotations,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcftabixml,${jvarkit.package}.tools.vcftabixml.VCFTabixml,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcftail,${jvarkit.package}.tools.misc.VcfTail,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcftreepack,${jvarkit.package}.tools.treepack.VcfTreePack,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcftrio,${jvarkit.package}.tools.vcftrios.VCFTrios,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcffamilies,${jvarkit.package}.tools.vcftrios.VCFFamilies,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfvcf,${jvarkit.package}.tools.vcfvcf.VcfVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,worldmapgenome,${jvarkit.package}.tools.circular.WorldMapGenome,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,uniprotfilterjs,${jvarkit.package}.tools.misc.UniprotFilterJS,${jcommander.jar} ${jaxb.jars} ${generated.dir}/java/org/uniprot/package-info.java ))
$(eval $(call compile-htsjdk-cmd,blastfilterjs,${jvarkit.package}.tools.blast.BlastFilterJS,${jcommander.jar} ${jaxb.jars} api.ncbi.blast))
$(eval $(call compile-htsjdk-cmd,skipxmlelements,${jvarkit.package}.tools.misc.SkipXmlElements,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,minicaller,${jvarkit.package}.tools.calling.MiniCaller,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcomparecallersonesample,${jvarkit.package}.tools.vcfcmp.VcfCompareCallersOneSample,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samretrieveseqandqual,${jvarkit.package}.tools.misc.SamRetrieveSeqAndQual,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfensemblvep,${jvarkit.package}.tools.ensembl.VcfEnsemblVepRest,${jcommander.jar} ${httpclient.libs}))
$(eval $(call compile-htsjdk-cmd,vcfgroupbypop,${jvarkit.package}.tools.misc.VcfGroupByPopulation,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcomparecallers,${jvarkit.package}.tools.vcfcmp.VcfCompareCallers,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamtile,${jvarkit.package}.tools.misc.BamTile,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,xcontaminations,${jvarkit.package}.tools.xcontamination.XContaminations,${jcommander.jar}))
$(eval $(call compile_biostar_cmd,139647,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfburden,${jvarkit.package}.tools.misc.VcfBurden,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bioalcidae,${jvarkit.package}.tools.bioalcidae.BioAlcidae,${jcommander.jar} ${gson.jar} ${jaxb.jars} api.ncbi.blast api.ncbi.insdseq ${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/package-info.java ))
$(eval $(call compile-htsjdk-cmd,bioalcidaejdk,${jvarkit.package}.tools.bioalcidae.BioAlcidaeJdk,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfbedsetfilter,${jvarkit.package}.tools.vcfbed.VCFBedSetFilter,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfreplacetag,${jvarkit.package}.tools.vcfstripannot.VCFReplaceTag,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfindextabix,${jvarkit.package}.tools.misc.VcfIndexTabix,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfpeekvcf,${jvarkit.package}.tools.vcfvcf.VcfPeekVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfgetvariantbyindex,${jvarkit.package}.tools.misc.VcfGetVariantByIndex,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfmulti2oneallele,${jvarkit.package}.tools.misc.VcfMultiToOneAllele,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfmulti2oneinfo,${jvarkit.package}.tools.misc.VcfMultiToOneInfo,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bedindextabix,${jvarkit.package}.tools.misc.BedIndexTabix,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcf2bam,${jvarkit.package}.tools.misc.VcfToBam,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcffilterxpath,${jvarkit.package}.tools.misc.VcfFilterXPath,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pcrclipreads,${jvarkit.package}.tools.pcr.PcrClipReads,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamslicebed,${jvarkit.package}.tools.pcr.BamSliceBed,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,extendrefwithreads,${jvarkit.package}.tools.extendref.ExtendReferenceWithReads,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,pcrslicereads,${jvarkit.package}.tools.pcr.PcrSliceReads,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samjmx,${jvarkit.package}.tools.jmx.SamJmx,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfjmx,${jvarkit.package}.tools.jmx.VcfJmx,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,gtf2xml,${jvarkit.package}.tools.misc.Gtf2Xml,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,sortsamrefname,${jvarkit.package}.tools.misc.SortSamRefName,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bamclip2insertion,${jvarkit.package}.tools.misc.BamClipToInsertion,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,localrealignreads,${jvarkit.package}.tools.misc.LocalRealignReads,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,msa2vcf,${jvarkit.package}.tools.msa2vcf.MsaToVcf,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samslop,${jvarkit.package}.tools.misc.SamSlop,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,projectserver,${jvarkit.package}.tools.server.ProjectServer,${jcommander.jar} ${jetty.jars}))
$(eval $(call compile-htsjdk-cmd,vcfcalledwithanothermethod,${jvarkit.package}.tools.misc.VcfCalledWithAnotherMethod,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfderby01,${jvarkit.package}.tools.burden.VcfDerby01,${jcommander.jar} ${derby.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdensplitter,${jvarkit.package}.tools.burden.VcfBurdenSplitter,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,casectrljfx,${jvarkit.package}.tools.burden.CaseControlJfx,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,indexcovjfx,${jvarkit.package}.tools.structvar.IndexCovJfx,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,indexcov2vcf,${jvarkit.package}.tools.structvar.IndexCovToVcf,${jcommander.jar} ${common.math3.libs}))
$(eval $(call compile-htsjdk-cmd,validatecnv,${jvarkit.package}.tools.structvar.ValidateCnv,${jcommander.jar} ${common.math3.libs}))
$(eval $(call compile-htsjdk-cmd,vcfburdensplitter2,${jvarkit.package}.tools.burden.VcfBurdenSplitter2,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfburdenfisherh,${jvarkit.package}.tools.burden.VcfBurdenFisherH,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdenfisherv,${jvarkit.package}.tools.burden.VcfBurdenFisherV,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdenrscriptv,${jvarkit.package}.tools.burden.VcfBurdenRscriptV,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfdoest,${jvarkit.package}.tools.burden.VcfDoest,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcffilternotinpedigree,${jvarkit.package}.tools.burden.VcfFilterNotInPedigree,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdenmaf,${jvarkit.package}.tools.burden.VcfBurdenMAF,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfburdenexac,${jvarkit.package}.tools.burden.VcfBurdenFilterExac,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfgenesplitter,${jvarkit.package}.tools.misc.VcfGeneSplitter,${jcommander.jar} ))
#$(eval $(call compile-htsjdk-cmd,vcfsqltag,${jvarkit.package}.tools.sql.VcfSqlTag))
$(eval $(call compile-htsjdk-cmd,vcfburdenfiltergenes,${jvarkit.package}.tools.burden.VcfBurdenFilterGenes,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,sammaskalignedbases,${jvarkit.package}.tools.misc.SamMaskAlignedBases,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,gff2kg,${jvarkit.package}.tools.misc.Gff2KnownGene,${jcommander.jar} ))
#$(eval $(call compile-htsjdk-cmd,miniassembly,${jvarkit.package}.tools.misc.MiniAssembly,))
$(eval $(call compile-htsjdk-cmd,haloplexparasite,${jvarkit.package}.tools.haloplex.HaloplexParasite,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,bam2sql,${jvarkit.package}.tools.misc.BamToSql,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfinjectpedigree,${jvarkit.package}.tools.burden.VcfInjectPedigree,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,gbrowserhtml,${jvarkit.package}.tools.misc.GBrowserHtml,${jcommander.jar} ${gson.jar} copy.samtools.js))
$(eval $(call compile-htsjdk-cmd,bim2vcf,${jvarkit.package}.tools.misc.BimToVcf,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,samreadlengthdistribution,${jvarkit.package}.tools.misc.SamReadLengthDistribution,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,queue2make,${jvarkit.package}.tools.misc.QueueToMake,${jcommander.jar} ))
$(eval $(call compile-htsjdk-cmd,vcfmovefilterstoinfo,${jvarkit.package}.tools.burden.VcfMoveFiltersToInfo,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,gatkcodegen,${jvarkit.package}.tools.gatk.codegen.GATKCodeGenerator,${jcommander.jar} ${gson.jar} ${velocity.jars} ))
$(eval $(call compile-htsjdk-cmd,vcfeigen01,${jvarkit.package}.tools.vcfeigen.VcfEigen01,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,jfxngs,${jvarkit.package}.tools.vcfviewgui.JfxNgs,${jcommander.jar} jfxngs-resources))
$(eval $(call compile-htsjdk-cmd,ngsworkflow,${jvarkit.package}.tools.workflow.NgsWorkflow,${gson.jar} ${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfgnomad,${jvarkit.package}.tools.gnomad.VcfGnomad,${gson.jar} ${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfcomposite,${jvarkit.package}.tools.vcfcomposite.VCFComposite,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfannotwithbeacon,${jvarkit.package}.tools.ga4gh.VcfAnnotWithBeacon,${jcommander.jar} ${gson.jar} ${berkeleydb.jar} ${httpclient.libs} ))
$(eval $(call compile-htsjdk-cmd,vcf2table,${jvarkit.package}.tools.misc.VcfToTable,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,prettytable,${jvarkit.package}.tools.misc.PrettyTable,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,goutils,${jvarkit.package}.tools.misc.GoUtils,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,variantsinwindow,${jvarkit.package}.tools.misc.VariantsInWindow,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,casectrlcanvas,${jvarkit.package}.tools.burden.CaseControlCanvas,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,knime2txt,${jvarkit.package}.tools.misc.KnimeToText,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,lumpyvcf2circos,${jvarkit.package}.tools.lumpysv.LumpyVcfToCircos,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,lumpysort,${jvarkit.package}.tools.lumpysv.LumpySort,${jcommander.jar} ${berkeleydb.jar}))
$(eval $(call compile-htsjdk-cmd,fastgenotypegvcfs,${jvarkit.package}.tools.gvcf.FastGenotypeGVCFs,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,xsltstream,${jvarkit.package}.tools.misc.XsltStream,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfloopovergenes,${jvarkit.package}.tools.burden.VcfLoopOverGenes,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcffilterjdk,${jvarkit.package}.tools.vcffilterjs.VcfFilterJdk,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,samjdk,${jvarkit.package}.tools.samjs.SamJdk,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samcustomsortjdk,${jvarkit.package}.tools.samjs.SamCustomSortJdk,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,optimizer,${jvarkit.package}.tools.optimizer.Optimizer,${jcommander.jar} ${gson.jar}))
##$(eval $(call compile-htsjdk-cmd,vcfamalgamation,${jvarkit.package}.tools.vcfamalgation.VcfXmlAmalgamation,${jcommander.jar} ${gson.jar} ${bigwig.jars}))
$(eval $(call compile-htsjdk-cmd,vcfserver,${jvarkit.package}.tools.vcfserver.VcfServer,${jcommander.jar} ${jetty.jars}))
$(eval $(call compile-htsjdk-cmd,tviewserver,${jvarkit.package}.tools.tview.TViewServer,${jcommander.jar} ${jetty.jars}))
$(eval $(call compile-htsjdk-cmd,trapindexer,${jvarkit.package}.tools.trap.TrapIndexer,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcftrap,${jvarkit.package}.tools.trap.VcfTrap,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfepistatis01,${jvarkit.package}.tools.epistasis.VcfEpistatis01,${jcommander.jar}))
#$(eval $(call compile-htsjdk-cmd,subcloneit,${jvarkit.package}.tools.cloneit.SubCloneIt,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,igvreview,${jvarkit.package}.tools.igvreview.IgvReview,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,samtranslocations,${jvarkit.package}.tools.structvar.SamTranslocations,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfafinfofilter,${jvarkit.package}.tools.misc.VcfAfInfoFilter,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,faidxsplitter,${jvarkit.package}.tools.misc.FaidxSplitter,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfclusteredreadedge,${jvarkit.package}.tools.misc.VcfClusteredReadEdge,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfgapfrequent,${jvarkit.package}.tools.structvar.VcfGapFrequent,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,mergecnvnator,${jvarkit.package}.tools.structvar.MergeCnvNator,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,mergesv,${jvarkit.package}.tools.structvar.MergeStructuralVariants,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfburdengoenrichment,${jvarkit.package}.tools.burden.VcfBurdenGoEnrichment,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfoptimizeped4skat,${jvarkit.package}.tools.skat.VcfOptimizePedForSkat,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfskatslidingwindow,${jvarkit.package}.tools.skat.VcfSkatSlidingWindow,${jcommander.jar} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,vcfskat,${jvarkit.package}.tools.skat.VcfSkat,${jcommander.jar} ${jaxb.jars}))
##$(eval $(call compile-htsjdk-cmd,vcfspringfilter,${jvarkit.package}.tools.misc.VcfSpringFilter,${jcommander.jar} ${spring-beans.jars}))
##$(eval $(call compile-htsjdk-cmd,testsng,${jvarkit.package}.tools.tests.TestNg01,${testng.jars} ${bigwig.jars} ${jaxb.jars}))
$(eval $(call compile-htsjdk-cmd,simpleplot,${jvarkit.package}.tools.misc.SimplePlot,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,cytoband2svg,${jvarkit.package}.tools.misc.CytobandToSvg,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,vcfancestralalleles,${jvarkit.package}.tools.onekgenomes.VcfAncestralAllele,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,bednonoverlappingset,${jvarkit.package}.tools.misc.BedNonOverlappingSet,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,wescnvsvg,${jvarkit.package}.tools.bam2svg.WesCnvSvg,${jcommander.jar}))
$(eval $(call compile-htsjdk-cmd,gexftr,${jvarkit.package}.tools.gephi.GexfTransformer,${jcommander.jar}))
$(lib.dir)/org/gephi/gephi.jar:
test -f "${gephi_home}/bin/gephi"
rm -rf "${tmp.dir}"
mkdir -p "${tmp.dir}" "$(dir $@)"
find "${gephi_home}/gephi/modules" \
"${gephi_home}/platform/core" \
"${gephi_home}/platform/lib" -type f -name "*.jar" | while read F; do echo "$$F" && unzip -o "$$F" -d "${tmp.dir}" ; done
jar cf $@ -C "${tmp.dir}" .
rm -rf "${tmp.dir}"
jar tvf $@ | head
$(eval $(call compile-htsjdk-cmd,gephicmd,${jvarkit.package}.tools.gephi.GephiCmd,${jcommander.jar} $(lib.dir)/org/gephi/gephi.jar ))
ij: ${dist.dir}/ij
${dist.dir}/ij : $(sort ${derby.jars} ${derby-tools.jar})
mkdir -p $(dir $@)org.gephi.preview.api
echo '#!/bin/bash' > @
echo -n '${JAVA} -Dfile.encoding=UTF8 -cp "$(subst $(SPACE),:,$(filter %.jar,$^))" org.apache.derby.tools.ij $$*' >> $@
chmod ugo+rx $@
javacc: ${dist.dir}/javacc
${dist.dir}/javacc : ${javacc.jar}
mkdir -p $(dir $@)
echo '#!/bin/bash' > @
echo -n '${JAVA} -Dfile.encoding=UTF8 -cp "$(subst $(SPACE),:,$(filter %.jar,$^))" javacc $$*' >> $@
chmod ugo+rx $@
GATKWALKERS_SRC=$(addsuffix .java,$(addprefix ${src.dir}/com/github/lindenb/jvarkit/tools/gatk/, variants/SoftClipAnnotator variants/GroupByVariants variants/GroupByGenotypes variants/EigenVariants variants/WindowVariants))
gatkwalkers:
mkdir -p ${tmp.dir} ${dist.dir}
${JAVAC} -d ${tmp.dir} -g -classpath ${gatk.jar} -sourcepath ${src.dir}:${generated.dir}/java ${GATKWALKERS_SRC}
##$(foreach F,${GATKWALKERS_SRC}, cp ${F} ${tmp.dir}$(subst ${src.dir},,${F});)
${JAR} cf ${dist.dir}/mygatk.jar -C ${tmp.dir} .
rm -rf ${tmp.dir}
echo '#!/bin/bash' > ${dist.dir}/mygatk
echo -n '${JAVA} -Dfile.encoding=UTF8 -Xmx3g ' >> ${dist.dir}/mygatk
echo -n ' -cp "$(realpath ${gatk.jar}):$(realpath ${dist.dir}/mygatk.jar)" org.broadinstitute.gatk.engine.CommandLineGATK ' >> ${dist.dir}/mygatk
echo '$$*' >> ${dist.dir}/mygatk
chmod ugo+rx ${dist.dir}/mygatk
all-jnlp : $(addprefix ${dist.dir}/,$(addsuffix .jar, 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 ${J} secret ; )
sed -e 's/__MAIN_JAR__/buildwpontology/g' \
-e 's/__TITLE__/BuildWikipediaOntology/g' \
-e 's/__MAIN_CLASS__/${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 : ${xjc_jars}
rm -rf ${generated.dir}/java/org/uniprot/
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p org.uniprot ${xjc.proxy} "https://www.uniprot.org/docs/uniprot.xsd"
api.ncbi.pubmed : ${xjc_jars}
rm -rf ${generated.dir}/java/gov/nih/nlm/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_100101.dtd"
api.evs: ${xjc_jars}
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: ${xjc_jars}
rm -rf ${generated.dir}/gov/nih/nlm/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: ${xjc_jars}
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/corehtml/query/DTD/eLink_020511.dtd"
api.ncbi.gb: ${generated.dir}/java/gov/nih/nlm/ncbi/gb/ObjectFactory.java
${generated.dir}/java/gov/nih/nlm/ncbi/gb/ObjectFactory.java : ${xjc_jars}
rm -rf ${generated.dir}/gov/nih/nlm/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: ${xjc_jars}
rm -rf ${generated.dir}/gov/nih/nlm/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: ${xjc_jars}
rm -rf ${generated.dir}/gov/nih/nlm/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: ${xjc_jars}
rm -rf ${generated.dir}/gov/nih/nlm/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: ${this.dir}src/main/resources/xsd/ncbi/genoex_1_5.xsd ${jaxb.jars }
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.dbsnp.gt ${xjc.proxy} $<
${generated.dir}/java/gov/nih/nlm/ncbi/dbsnp/package-info.java : api.ncbi.dbsnp
touch -c $@
api.ncbi.dbsnp: ${this.dir}src/main/resources/xsd/ncbi/docsum_3.4.xsd ${xjc_jars}
mkdir -p ${generated.dir}/java
${XJC} -d ${generated.dir}/java -p gov.nih.nlm.ncbi.dbsnp ${xjc.proxy} $<
## 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.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/ ; )
## GATK code generation using php.json URLs
gatk_code: $(foreach U,${gatk.tools},${generated.dir}/java/com/github/lindenb/jvarkit/gatk/commands/Abstract$(lastword $(subst _, ,$U)).java)
$(eval $(foreach U,${gatk.tools},$(call make_gatk_code,${U})))
## jvarkit-library (used in knime)
library: ${dist.dir}/jvarkit-${htsjdk.version}.jar
${dist.dir}/jvarkit-${htsjdk.version}.jar : ${htsjdk.jars} ${bigwig.jars} \
${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}
##
## 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}
##
## 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/%,%,$@)"
## API EVS
src/main/generated-sources/java/edu/washington/gs/evs/package-info.java : ${xjc_jars}
mkdir -p ${generated.dir}/java
${XJC} ${xjc.proxy} -d ${generated.dir}/java \
-p edu.washington.gs.evs \
"http://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdl"
## copy resources for jxngs
jfxngs-resources:
mkdir -p ${tmp.dir}/com/github/lindenb/jvarkit/tools/vcfviewgui
$(foreach S,bam vcf, cp -v src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/${S}.snippets.xml ${tmp.dir}/com/github/lindenb/jvarkit/tools/vcfviewgui/;)
#
# 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
#
#
#
# begin jni+htslib
#
#
HTSLIB_VERSION=1.6
htslib.jar : ${dist.dir}/libhtslibjni.so
${dist.dir}/libhtslibjni.so : ${dist.dir}/htslib.jar
touch -c $@
${dist.dir}/htslib.jar : $(addsuffix .java,$(addprefix ${src.dir}/com/github/lindenb/jvarkit/htslib/,HtsFile KString Bcf1)) \
${this.dir}src/main/cpp/htslib/libhts.so \
${this.dir}src/main/cpp/htslibjni.c
rm -rf "${tmp.dir}" "${dist.dir}/libhtslibjni.so"
mkdir -p $(dir $@) "${tmp.dir}"
$(JAVAC) -d ${tmp.dir} -g -classpath "$(subst $(SPACE),:,$(filter %.jar,$^))" -sourcepath ${src.dir}:${generated.dir}/java $(filter %.java,$^)
$(JAVAH) -o "${generated.dir}/cpp/htslibjni.h" -jni -classpath "${tmp.dir}" $(subst /,.,$(subst ${src.dir}/,,$(basename $(filter %.java,$^))))
gcc -Wall -fPIC -shared -I /home/lindenb/package/jdk1.8.0_152/include -I /home/lindenb/package/jdk1.8.0_152/include/linux $(addprefix -I,$(sort $(dir $(shell find "${JAVA_HOME}/include" -type f -name "*.h")))) -I ${this.dir}src/main/cpp/htslib -I "${generated.dir}/cpp" -o ${dist.dir}/libhtslibjni.so $(filter %.c,$^)
${JAR} cf $@ -C ${tmp.dir} .
rm -rf "${tmp.dir}"
${this.dir}src/main/cpp/htslib/libhts.so : ${this.dir}src/main/cpp/htslib/Makefile
cd $(dir $@) && make
${this.dir}src/main/cpp/htslib/Makefile:
rm -rf "$(dir $@)"
wget -O "${HTSLIB_VERSION}.tar.gz" "https://github.com/samtools/htslib/archive/${HTSLIB_VERSION}.tar.gz"
tar xfz "${HTSLIB_VERSION}.tar.gz"
mv -v "htslib-${HTSLIB_VERSION}" "$(dir $@)"
rm -vf "${HTSLIB_VERSION}.tar.gz"
touch -c "$@"
#
# end of jni+htslib
#
#
include jfx.mk
## Knime helper
knimehelper: ${dist.dir}/knimehelper.jar
@echo -n "KnimeHelper-";date +%Y-%m-%d
@echo -n "KnimeHelper: A java library to be used in the java nodes of [http://knime.org](http://knime.org). See [http://lindenb.github.io/jvarkit/KnimeIntegration.html](http://lindenb.github.io/jvarkit/KnimeIntegration.html). This library was compiled on "; LANG=en_UTF-8 date | tr -d "\n"; echo "."
${dist.dir}/knimehelper.jar: ${src.dir}/com/github/lindenb/jvarkit/knime/KnimeVariantHelper.java ${htsjdk.jars} ${jcommander.jar}
mkdir -p ${tmp.dir}/META-INF/services
${JAVAC} -cp "$(subst $(SPACE),:,$(realpath $(filter %.jar,$^)))" -d ${tmp.dir} -sourcepath ${src.dir}:${generated.dir}/java $<
$(foreach J,$(filter %.jar,$^),unzip -o ${J} -d ${tmp.dir};)
${JAR} cvf $@ -C ${tmp.dir} .
rm -rf "${tmp.dir}"
clean:
rm -rf ${dist.dir}