Mercurial > repos > fubar > microsatbed
diff seqrequester/src/main.mk @ 1:1085e094cf5f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
| author | fubar |
|---|---|
| date | Sat, 13 Jul 2024 12:39:06 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqrequester/src/main.mk Sat Jul 13 12:39:06 2024 +0000 @@ -0,0 +1,155 @@ +MODULE := seqrequester +VERSION := snapshot v1.0 +VERSION_H := utility/src/version.H + +TARGET := libseqrequester.a +SOURCES := utility/src/align/align-ksw2-driver.C \ + utility/src/align/align-ksw2-extz.C \ + utility/src/align/align-ksw2-extz2-sse.C \ + utility/src/align/align-parasail-driver.C \ + utility/src/align/align-ssw-driver.C \ + utility/src/align/align-ssw.C \ + utility/src/align/edlib.C \ + \ + utility/src/bits/fibonacci-v1.C \ + utility/src/bits/hexDump-v1.C \ + utility/src/bits/stuffedBits-v1-binary.C \ + utility/src/bits/stuffedBits-v1-bits.C \ + utility/src/bits/stuffedBits-v1-delta.C \ + utility/src/bits/stuffedBits-v1-gamma.C \ + utility/src/bits/stuffedBits-v1-golomb.C \ + utility/src/bits/stuffedBits-v1-omega.C \ + utility/src/bits/stuffedBits-v1-unary.C \ + utility/src/bits/stuffedBits-v1-zeckendorf.C \ + utility/src/bits/stuffedBits-v1.C \ + utility/src/bits/wordArray-v1.C \ + \ + utility/src/datastructures/keyAndValue-v1.C \ + utility/src/datastructures/splitToWords-v1.C \ + utility/src/datastructures/stringList-v1.C \ + utility/src/datastructures/strings-v1.C \ + utility/src/datastructures/types-v1.C \ + \ + utility/src/files/accessing-v1.C \ + utility/src/files/buffered-v1-reading.C \ + utility/src/files/buffered-v1-writing.C \ + utility/src/files/compressed-v1-reading.C \ + utility/src/files/compressed-v1-writing.C \ + utility/src/files/compressed-v1.C \ + utility/src/files/fasta-fastq-v1.C \ + utility/src/files/files-v1.C \ + utility/src/files/memoryMapped-v1.C \ + utility/src/files/readLine-v0.C \ + utility/src/files/readLine-v1.C \ + utility/src/files/reading-v1.C \ + utility/src/files/writing-v1.C \ + \ + utility/src/kmers-v1/kmers-exact.C \ + utility/src/kmers-v1/kmers-files.C \ + utility/src/kmers-v1/kmers-histogram.C \ + utility/src/kmers-v1/kmers-reader.C \ + utility/src/kmers-v1/kmers-writer-block.C \ + utility/src/kmers-v1/kmers-writer-stream.C \ + utility/src/kmers-v1/kmers-writer.C \ + utility/src/kmers-v1/kmers.C \ + \ + utility/src/math/md5-v1.C \ + utility/src/math/mt19937ar-v1.C \ + utility/src/math/sampledDistribution-v1.C \ + \ + utility/src/sequence/dnaSeq-v1.C \ + utility/src/sequence/bufSeqFile-v1.C \ + utility/src/sequence/htsSeqFile-v1.C \ + utility/src/sequence/sequence-v1.C \ + \ + utility/src/system/logging-v1.C \ + utility/src/system/runtime-v1.C \ + utility/src/system/speedCounter-v1.C \ + utility/src/system/sweatShop-v1.C \ + utility/src/system/system-stackTrace-v1.C \ + utility/src/system/system-v1.C \ + utility/src/system/time-v1.C + +SOURCES += utility/src/htslib/hts/bcf_sr_sort.c \ + utility/src/htslib/hts/bgzf.c \ + utility/src/htslib/hts/errmod.c \ + utility/src/htslib/hts/faidx.c \ + utility/src/htslib/hts/header.c \ + utility/src/htslib/hts/hfile.c \ + utility/src/htslib/hts/hfile_libcurl.c \ + utility/src/htslib/hts/hfile_s3.c \ + utility/src/htslib/hts/hts.c \ + utility/src/htslib/hts/hts_expr.c \ + utility/src/htslib/hts/hts_os.c \ + utility/src/htslib/hts/kfunc.c \ + utility/src/htslib/hts/kstring.c \ + utility/src/htslib/hts/md5.c \ + utility/src/htslib/hts/multipart.c \ + utility/src/htslib/hts/probaln.c \ + utility/src/htslib/hts/realn.c \ + utility/src/htslib/hts/regidx.c \ + utility/src/htslib/hts/region.c \ + utility/src/htslib/hts/sam.c \ + utility/src/htslib/hts/synced_bcf_reader.c \ + utility/src/htslib/hts/tbx.c \ + utility/src/htslib/hts/textutils.c \ + utility/src/htslib/hts/thread_pool.c \ + utility/src/htslib/hts/vcf.c \ + utility/src/htslib/hts/vcf_sweep.c \ + utility/src/htslib/hts/vcfutils.c \ + utility/src/htslib/cram/cram_codecs.c \ + utility/src/htslib/cram/cram_decode.c \ + utility/src/htslib/cram/cram_encode.c \ + utility/src/htslib/cram/cram_external.c \ + utility/src/htslib/cram/cram_index.c \ + utility/src/htslib/cram/cram_io.c \ + utility/src/htslib/cram/cram_stats.c \ + utility/src/htslib/cram/mFILE.c \ + utility/src/htslib/cram/open_trace_file.c \ + utility/src/htslib/cram/pooled_alloc.c \ + utility/src/htslib/cram/string_alloc.c \ + utility/src/htslib/htscodecs/arith_dynamic.c \ + utility/src/htslib/htscodecs/fqzcomp_qual.c \ + utility/src/htslib/htscodecs/htscodecs.c \ + utility/src/htslib/htscodecs/pack.c \ + utility/src/htslib/htscodecs/rANS_static.c \ + utility/src/htslib/htscodecs/rANS_static32x16pr.c \ + utility/src/htslib/htscodecs/rANS_static32x16pr_neon.c \ + utility/src/htslib/htscodecs/rANS_static4x16pr.c \ + utility/src/htslib/htscodecs/rle.c \ + utility/src/htslib/htscodecs/tokenise_name3.c \ + utility/src/htslib/htscodecs/utils.c + +ifeq (${BUILDSTACKTRACE}, 1) +SOURCES += utility/src/system/libbacktrace/atomic.c \ + utility/src/system/libbacktrace/backtrace.c \ + utility/src/system/libbacktrace/dwarf.c \ + utility/src/system/libbacktrace/elf.c \ + utility/src/system/libbacktrace/fileline.c \ + utility/src/system/libbacktrace/mmap.c \ + utility/src/system/libbacktrace/mmapio.c \ + utility/src/system/libbacktrace/posix.c \ + utility/src/system/libbacktrace/print.c \ + utility/src/system/libbacktrace/simple.c \ + utility/src/system/libbacktrace/sort.c \ + utility/src/system/libbacktrace/state.c \ + utility/src/system/libbacktrace/unknown.c +endif + +SRC_INCDIRS := . \ + seqrequester \ + utility/src + +SYS_INCDIRS += $(shell pkg-config --cflags-only-I openssl libcurl liblzma | sed s:-I/:/:g) +LDFLAGS += $(shell pkg-config --libs-only-L openssl libcurl liblzma) +LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2 + +FILES += ../share/ultra-long-nanopore -> share/seqrequester/ultra-long-nanopore \ + ../share/pacbio -> share/seqrequester/pacbio \ + ../share/pacbio-hifi -> share/seqrequester/pacbio-hifi + +SUBMAKEFILES := seqrequester/seqrequester.mk + +ifeq ($(BUILDTESTS), 1) +SUBMAKEFILES += +endif