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comparison seqrequester/src/main.mk @ 1:1085e094cf5f draft

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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
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0:dd71d3167476 1:1085e094cf5f
1 MODULE := seqrequester
2 VERSION := snapshot v1.0
3 VERSION_H := utility/src/version.H
4
5 TARGET := libseqrequester.a
6 SOURCES := utility/src/align/align-ksw2-driver.C \
7 utility/src/align/align-ksw2-extz.C \
8 utility/src/align/align-ksw2-extz2-sse.C \
9 utility/src/align/align-parasail-driver.C \
10 utility/src/align/align-ssw-driver.C \
11 utility/src/align/align-ssw.C \
12 utility/src/align/edlib.C \
13 \
14 utility/src/bits/fibonacci-v1.C \
15 utility/src/bits/hexDump-v1.C \
16 utility/src/bits/stuffedBits-v1-binary.C \
17 utility/src/bits/stuffedBits-v1-bits.C \
18 utility/src/bits/stuffedBits-v1-delta.C \
19 utility/src/bits/stuffedBits-v1-gamma.C \
20 utility/src/bits/stuffedBits-v1-golomb.C \
21 utility/src/bits/stuffedBits-v1-omega.C \
22 utility/src/bits/stuffedBits-v1-unary.C \
23 utility/src/bits/stuffedBits-v1-zeckendorf.C \
24 utility/src/bits/stuffedBits-v1.C \
25 utility/src/bits/wordArray-v1.C \
26 \
27 utility/src/datastructures/keyAndValue-v1.C \
28 utility/src/datastructures/splitToWords-v1.C \
29 utility/src/datastructures/stringList-v1.C \
30 utility/src/datastructures/strings-v1.C \
31 utility/src/datastructures/types-v1.C \
32 \
33 utility/src/files/accessing-v1.C \
34 utility/src/files/buffered-v1-reading.C \
35 utility/src/files/buffered-v1-writing.C \
36 utility/src/files/compressed-v1-reading.C \
37 utility/src/files/compressed-v1-writing.C \
38 utility/src/files/compressed-v1.C \
39 utility/src/files/fasta-fastq-v1.C \
40 utility/src/files/files-v1.C \
41 utility/src/files/memoryMapped-v1.C \
42 utility/src/files/readLine-v0.C \
43 utility/src/files/readLine-v1.C \
44 utility/src/files/reading-v1.C \
45 utility/src/files/writing-v1.C \
46 \
47 utility/src/kmers-v1/kmers-exact.C \
48 utility/src/kmers-v1/kmers-files.C \
49 utility/src/kmers-v1/kmers-histogram.C \
50 utility/src/kmers-v1/kmers-reader.C \
51 utility/src/kmers-v1/kmers-writer-block.C \
52 utility/src/kmers-v1/kmers-writer-stream.C \
53 utility/src/kmers-v1/kmers-writer.C \
54 utility/src/kmers-v1/kmers.C \
55 \
56 utility/src/math/md5-v1.C \
57 utility/src/math/mt19937ar-v1.C \
58 utility/src/math/sampledDistribution-v1.C \
59 \
60 utility/src/sequence/dnaSeq-v1.C \
61 utility/src/sequence/bufSeqFile-v1.C \
62 utility/src/sequence/htsSeqFile-v1.C \
63 utility/src/sequence/sequence-v1.C \
64 \
65 utility/src/system/logging-v1.C \
66 utility/src/system/runtime-v1.C \
67 utility/src/system/speedCounter-v1.C \
68 utility/src/system/sweatShop-v1.C \
69 utility/src/system/system-stackTrace-v1.C \
70 utility/src/system/system-v1.C \
71 utility/src/system/time-v1.C
72
73 SOURCES += utility/src/htslib/hts/bcf_sr_sort.c \
74 utility/src/htslib/hts/bgzf.c \
75 utility/src/htslib/hts/errmod.c \
76 utility/src/htslib/hts/faidx.c \
77 utility/src/htslib/hts/header.c \
78 utility/src/htslib/hts/hfile.c \
79 utility/src/htslib/hts/hfile_libcurl.c \
80 utility/src/htslib/hts/hfile_s3.c \
81 utility/src/htslib/hts/hts.c \
82 utility/src/htslib/hts/hts_expr.c \
83 utility/src/htslib/hts/hts_os.c \
84 utility/src/htslib/hts/kfunc.c \
85 utility/src/htslib/hts/kstring.c \
86 utility/src/htslib/hts/md5.c \
87 utility/src/htslib/hts/multipart.c \
88 utility/src/htslib/hts/probaln.c \
89 utility/src/htslib/hts/realn.c \
90 utility/src/htslib/hts/regidx.c \
91 utility/src/htslib/hts/region.c \
92 utility/src/htslib/hts/sam.c \
93 utility/src/htslib/hts/synced_bcf_reader.c \
94 utility/src/htslib/hts/tbx.c \
95 utility/src/htslib/hts/textutils.c \
96 utility/src/htslib/hts/thread_pool.c \
97 utility/src/htslib/hts/vcf.c \
98 utility/src/htslib/hts/vcf_sweep.c \
99 utility/src/htslib/hts/vcfutils.c \
100 utility/src/htslib/cram/cram_codecs.c \
101 utility/src/htslib/cram/cram_decode.c \
102 utility/src/htslib/cram/cram_encode.c \
103 utility/src/htslib/cram/cram_external.c \
104 utility/src/htslib/cram/cram_index.c \
105 utility/src/htslib/cram/cram_io.c \
106 utility/src/htslib/cram/cram_stats.c \
107 utility/src/htslib/cram/mFILE.c \
108 utility/src/htslib/cram/open_trace_file.c \
109 utility/src/htslib/cram/pooled_alloc.c \
110 utility/src/htslib/cram/string_alloc.c \
111 utility/src/htslib/htscodecs/arith_dynamic.c \
112 utility/src/htslib/htscodecs/fqzcomp_qual.c \
113 utility/src/htslib/htscodecs/htscodecs.c \
114 utility/src/htslib/htscodecs/pack.c \
115 utility/src/htslib/htscodecs/rANS_static.c \
116 utility/src/htslib/htscodecs/rANS_static32x16pr.c \
117 utility/src/htslib/htscodecs/rANS_static32x16pr_neon.c \
118 utility/src/htslib/htscodecs/rANS_static4x16pr.c \
119 utility/src/htslib/htscodecs/rle.c \
120 utility/src/htslib/htscodecs/tokenise_name3.c \
121 utility/src/htslib/htscodecs/utils.c
122
123 ifeq (${BUILDSTACKTRACE}, 1)
124 SOURCES += utility/src/system/libbacktrace/atomic.c \
125 utility/src/system/libbacktrace/backtrace.c \
126 utility/src/system/libbacktrace/dwarf.c \
127 utility/src/system/libbacktrace/elf.c \
128 utility/src/system/libbacktrace/fileline.c \
129 utility/src/system/libbacktrace/mmap.c \
130 utility/src/system/libbacktrace/mmapio.c \
131 utility/src/system/libbacktrace/posix.c \
132 utility/src/system/libbacktrace/print.c \
133 utility/src/system/libbacktrace/simple.c \
134 utility/src/system/libbacktrace/sort.c \
135 utility/src/system/libbacktrace/state.c \
136 utility/src/system/libbacktrace/unknown.c
137 endif
138
139 SRC_INCDIRS := . \
140 seqrequester \
141 utility/src
142
143 SYS_INCDIRS += $(shell pkg-config --cflags-only-I openssl libcurl liblzma | sed s:-I/:/:g)
144 LDFLAGS += $(shell pkg-config --libs-only-L openssl libcurl liblzma)
145 LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2
146
147 FILES += ../share/ultra-long-nanopore -> share/seqrequester/ultra-long-nanopore \
148 ../share/pacbio -> share/seqrequester/pacbio \
149 ../share/pacbio-hifi -> share/seqrequester/pacbio-hifi
150
151 SUBMAKEFILES := seqrequester/seqrequester.mk
152
153 ifeq ($(BUILDTESTS), 1)
154 SUBMAKEFILES +=
155 endif