File: BUILD.html

package info (click to toggle)
epcr 2.3.12-1-9
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 916 kB
  • sloc: cpp: 5,730; ansic: 231; makefile: 31; python: 26; sh: 12
file content (331 lines) | stat: -rw-r--r-- 9,271 bytes parent folder | download | duplicates (6)
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
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Electronic PCR commandline tools: build instructions</title>
<meta name="
            author
          " content="Greg Schuler, NCBI
              ;
            Kirill Rotmistrovsky, NCBI
              ;
            ">
<style>
          body {
          }
          hr.section-sep {
            width: 100% ;
            noshade: noshade ;
          }
          div.subsection {
            margin-left: 8px ;
          }
          div.subsubsection {
            margin-left: 16px ;
          }
          div.section h2.title {
            font-weight:  bold ;
            font-size: 144% ; 
          }
          div.subsection h3.title { 
            font-weight:  bold ;
            font-size: 120% ; 
          }
          div.subsubsection h4.title { 
            font-weight:  bold ;
            font-size: 109% ; 
          }
          div.abstract {
            font-style: italic ;
          }
          dt {
            font-weight: bold ;
          }
          h1.title {
            text-align: center ;
            font-weight: bold ;
            font-size: 180% ; }
          }
        </style>
</head>
<body bgcolor="#FFFFFF">
<h1 class="title">Electronic PCR commandline tools: build instructions</h1>
<p align="right">Version: 2.3.12</p>
<ol>
<li>
<a href="#build">Build</a><ol>
<li>
<a href="#bld-unix">Unix/gcc instructions</a><ol>
<li><a href="#bld-unix-args">Make arguments</a></li>
<li><a href="#bld-unix-macosx">Mac OS/X with gcc</a></li>
</ol>
</li>
<li><a href="#bld-bcc">Windows/BorlandC++ instructions</a></li>
<li><a href="#bld-vc8">Windows/MS-VisualC++8.0 instructions</a></li>
</ol>
</li>
<li>
<a href="#files">Files</a><ol>
<li><a href="#files-common">Sources common to forward and reverse e-PCR binaries</a></li>
<li><a href="#files-forward">Forward e-PCR source files</a></li>
<li><a href="#files-reverse">Reverse e-PCR source files</a></li>
<li><a href="#files-extra">Extra files</a></li>
<li><a href="#files-build">Build files</a></li>
</ol>
</li>
</ol>
    <div class="abstract">
<hr class="section-sep">
      Build e-PCR and reverse e-PCR (re-PCR, famap) binaries with GNU
      make and GCC.
    </div>

    <hr class="setion-sep">
<div class="section">
<a name="build"></a><h2 class="title">Build</h2>
      

      <div class="subsection">
<a name="bld-unix"></a><h3 class="title">Unix/gcc instructions</h3>
	    
	    <ol>
<li>Unpack archive</li>
<li>Edit stand/config.mk if nesessary</li>
<li>run <u>gmake links depend all OPTIMIZE=6</u>
</li>
</ol>
	
		<div class="subsubsection">
<a name="bld-unix-args"></a><h4 class="title">Make arguments</h4>
		  
		  <p>One can use following arguments to make:</p>
		  <dl>
<dt>OPTIMIZE=[0-9]</dt>
<dd>to pass with -O argument to
		    compiler (default is build debug version)</dd>
<dt>srcdir={path-to-src}</dt>
<dd>to set path to sources</dd>
<dt>objdir={path-to-obj}</dt>
<dd>to set path where to
		    place .o</dd>
<dt>tgtdir={target-path}</dt>
<dd>to set path where to put
		    targets (libepcr.a and executable files)</dd>
</dl>
		</div>

		<div class="subsubsection">
<a name="bld-unix-macosx"></a><h4 class="title">Mac OS/X with gcc</h4>
		  
		  <p>Use LF64LDFLAGS= LF64CCFLAGS=-DNATIVE_LARGEFILES (yes, 
		    space after first "=") argument 
		    with gmake since Mac OS/2 does not have (and does not need) *64 file
		    functions and off64_t</p>
		</div>
      </div>

      <div class="subsection">
<a name="bld-bcc"></a><h3 class="title">Windows/BorlandC++ instructions</h3>
		
		<ol>
<li>Unpack archive</li>
<li>Edit stand/Makefile.bcc55-w32 if nesessary</li>
<li>run <u>make all -f stand/Makefile.bcc55-w32</u>
</li>
</ol>
	
      </div>

      <div class="subsection">
<a name="bld-vc8"></a><h3 class="title">Windows/MS-VisualC++8.0 instructions</h3>
		
		<ol>
<li>Unpack archive</li>
<li>Edit stand/Makefile.vc8 if nesessary</li>
<li>run <u>nmake all -f stand/Makefile.vc8</u>
</li>
</ol>
	
      </div>
    </div>

    <hr class="setion-sep">
<div class="section">
<a name="files"></a><h2 class="title">Files</h2>
      

      <p><u>e-PCR</u> package includes two tool sets: forward
      e-PCR (e-PCR) and reverse e-PCR (re-PCR, fahash and famap). These
      binaries share some source files, that are compiled as
      <u>libepcr.a</u> library.</p> 

      <p>Directory <u>stand/</u> contains makefiles to use
      with GCC. Change <u>stand/config.mk</u> to update compiler
      and compiling options. Makefiles should be OK for GNU
      make.</p>

      <div class="subsection">
<a name="files-common"></a><h3 class="title">Sources common to forward and reverse e-PCR binaries</h3>
	

	<dl>
<dt>build_cfg.h</dt>
<dd>macroses that control compilation
	  with/without <u>NCBI</u> toolkit</dd>
<dt>defaults.h</dt>
<dd>defaults for e-PCR program (used also in library)</dd>
<dt>mswin.h</dt>
<dd>windows compatibility defines and declarations</dd>
<dt>native64.h</dt>
<dd>native 64bit file access compatibility defines and declarations</dd>
<dt>strref.hpp</dt>
<dd>class for passing reference to string data</dd>
<dt>sts_i.hpp</dt>
<dd>generic STS interface class</dd>
<dt>hashset.hpp</dt>
<dd>hash calculating class
	  declaration (allows set of discontiguos words)</dd>
<dt>hashset.cpp</dt>
<dd>hash calculating class
	  implementation</dd>
<dt>align.hpp</dt>
<dd>align or compare two sequences allowing
	  mismatches and gaps, declarations</dd>
<dt>align.cpp</dt>
<dd>align or compare two sequences allowing
	  mismatches and gaps, implementation</dd>
<dt>minilcs.hpp</dt>
<dd>align two sequences templat class</dd>
<dt>faread.hpp</dt>
<dd>read fasta files, declarations</dd>
<dt>faread.cpp</dt>
<dd>read fasta files, implementation</dd>
<dt>mmap.hpp</dt>
<dd>mmap(2) wrapper for huge files and no
	  page boundary restriction, declarations</dd>
<dt>mmap.cpp</dt>
<dd>mmap(2) wrapper for huge files and no
	  page boundary restriction, implementation</dd>
<dt>getopt.c</dt>
<dd>getopt implementation -- to compile for
          windows</dd>
</dl>
      </div>

      <div class="subsection">
<a name="files-forward"></a><h3 class="title">Forward e-PCR source files</h3>
	
	<dl>
<dt>e-PCR_main.cpp</dt>
<dd>main for e-PCR commandline program</dd>
<dt>stsmatch_i.hpp</dt>
<dd>STS lookup algorithm declarations</dd>
<dt>stsmatch_i.cpp</dt>
<dd>STS lookup algorithm implementation</dd>
<dt>stsfilter.cpp</dt>
<dd>Postprocessor for STS lookup</dd>
<dt>stsmatch_m.hpp</dt>
<dd>STS and STS hash table
	  implementation for mmapable UniSTS file, declarations</dd>
<dt>stsmatch_m.cpp</dt>
<dd>STS and STS hash table
	  implementation for mmapable UniSTS file, implementation</dd>
<dt>stsmatch.hpp</dt>
<dd>Some useful callbacks
	  declarations</dd>
<dt>stsmatch.cpp</dt>
<dd>Some useful callbacks,
	  implementation</dd>
</dl>
      </div>

      <div class="subsection">
<a name="files-reverse"></a><h3 class="title">Reverse e-PCR source files</h3>
	
	<dl>
<dt>bin-io.hpp</dt>
<dd>Generic read/write integers and strings</dd>
<dt>fahash_defines.h</dt>
<dd>Internal defines for fahash</dd>
<dt>fahash_internal.hpp</dt>
<dd>Internal defines for fahash</dd>
<dt>fahash.hpp</dt>
<dd>Hash sequence words in file, declarations</dd>
<dt>fahash_create.cpp</dt>
<dd>Hash sequence words in file,
	  creating hash file, abstract</dd>
<dt>fahash_create1.cpp</dt>
<dd>Hash sequence words in file,
	  creating hash file version 1 implementation</dd>
<dt>fahash_create2.cpp</dt>
<dd>Hash sequence words in file,
	  creating hash file version 2 implementation</dd>
<dt>fahash_lookup.cpp</dt>
<dd>Hash sequence words in file,
	  lookup algorithm implementation</dd>
<dt>fast_seqio.hpp</dt>
<dd>Fast access to regions of
	  sequences, declarations</dd>
<dt>fast_seqio_read.cpp</dt>
<dd>Fast access to regions of
	  sequences, implementation</dd>
<dt>fast_seqio_write.cpp</dt>
<dd>Fast access to regions of
	  sequences, create sequence file implementation</dd>
<dt>famap_main.cpp</dt>
<dd>main for commandline tool to
	  create/dump mmapable file</dd>
<dt>fahash_main.cpp</dt>
<dd>main for commandline tool to
	  create hash file</dd>
<dt>sts.hpp</dt>
<dd>simple implementation for STS class</dd>
<dt>re-PCR_main.cpp</dt>
<dd>main for reverse e-PCR commandline tool</dd>
</dl>
      </div>


      <div class="subsection">
<a name="files-extra"></a><h3 class="title">Extra files</h3>
	
	<dl>
<dt>seqcmp_main.cpp</dt>
<dd>Main file for align.?pp
	  test</dd>
</dl>
      </div>

      <div class="subsection">
<a name="files-build"></a><h3 class="title">Build files</h3>
	
	<dl>
<dt>Makefile</dt>
<dd>Master makefile</dd>
<dt>stand/version.mk</dt>
<dd>Version definitions</dd>
<dt>stand/config.mk</dt>
<dd>Compiler options</dd>
<dt>stand/Makefile.libepcr</dt>
<dd>libepcr makefile</dd>
<dt>stand/Makefile.cmd_epcr</dt>
<dd>e-PCR makefile</dd>
<dt>stand/Makefile.cmd_repcr</dt>
<dd>re-PCR makefile</dd>
<dt>stand/Makefile.cmd_famap</dt>
<dd>famap makefile</dd>
<dt>stand/Makefile.cmd_fahash</dt>
<dd>fahash makefile</dd>
<dt>stand/Makefile.cmd_seqcmp</dt>
<dd>seqcmp makefile</dd>
<dt>stand/Makefile.bcc55-w32</dt>
<dd>makefile for BorlandC++/win32</dd>
<dt>stand/Makefile.vc8</dt>
<dd>makefile for MS Visual C++ 8.0</dd>
</dl>
      </div>

    </div>

  <hr class="section-sep">
</body>
</html>