Mercurial > repos > fubar > microsatbed

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