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1 : olson 1.1 #
2 : olson 1.28 # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 :     #
7 :     # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 :     # Public License.
10 :     #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :    
18 :     #
19 : olson 1.1 # FIG bootstrap script.
20 :     #
21 :     # Control is passed here from the toplevel configure (or dists/releases/install depending
22 :     # on how far we've gotten in the process).
23 :     #
24 :     # The configure has set the following environment variables for our use:
25 :     #
26 :     # FIG_HOME Root of the FIGdisk tree we're setting up
27 :     # FIGCONFIG_ENV Name of the environment we're configuring for
28 :     # FIGCONFIG_ENV_DIR Directory in which the binary install tree for $FIGCONFIG_ENV lives
29 :     # FIGCONFIG_RELEASE Release number we're configuring
30 :     # FIGCONFIG_RELEASE_DIR Directory in which that release lives
31 :     #
32 :     # Important note: perl system libraries may not be available when this
33 :     # script is running, if the FIGCONFIG_ENV_DIR is different than it was
34 :     # when the binaries were created. Part of the task of this
35 :     # script is to recognize this case and configure the process
36 :     # environment correctly so that the post-install process as
37 :     # handled by the Makefiles can use perl properly, without concern for paths.
38 :     #
39 :    
40 :     #
41 :     # Look into the FIGCONFIG_ENV_DIR for the PREFIX that this
42 :     # environment was compiled on. If that directory is different
43 :     # than the one we're currently using, rewrite @INC accordingly.
44 :     #
45 :     # We put this into a BEGIN block so that we can later use "use"
46 :     # without worrying about paths.
47 :     #
48 :     # We also set the $perlenv_override to true if we've done this,
49 :     # so we can insert these fixes into the perl tool header.
50 :     #
51 :    
52 :     BEGIN {
53 :    
54 : olson 1.3 print "Here in the perl bootstrap. inc is:\n" . join("\n", @INC), "\n";
55 : olson 1.1
56 :     my $my_prefix, $prefix, $inc, @newInc;
57 :    
58 :     $my_prefix = $ENV{FIGCONFIG_ENV_DIR};
59 :     open(P, "<$my_prefix/PREFIX");
60 :     $prefix = <P>;
61 :     chomp $prefix;
62 :    
63 :    
64 :     # print "Prefix is $prefix myprefix=$my_prefix\n";
65 :    
66 :     if ($prefix ne $my_prefix)
67 :     {
68 :     @newInc = ();
69 :     for $inc (@INC)
70 :     {
71 :     $inc =~ s,^$prefix,$my_prefix,;
72 :     push(@newInc, $inc);
73 :     }
74 :    
75 :     $::perlenv_override = 1;
76 : olson 1.3 @INC = @newInc;
77 : olson 1.1 }
78 :     }
79 :    
80 :    
81 :     use FileHandle;
82 :     use strict;
83 :    
84 :     #
85 :     # Environment definition
86 :     #
87 :     # This list contains triples
88 :     # ($name, $value, $appendFlag). $name is the name of the
89 :     # variable; $value is the value to set, and $appendFlag
90 :     # is nonzero if we need to append this value to an existing
91 :     # environment variable.
92 :     #
93 :    
94 :     our $Env = [];
95 :    
96 :     #
97 :     # FIG configuration information.
98 :     # This list contains tuples [$name, $value, $quote]
99 :     # which are to be set in the FIG_Config modules for
100 :     # both python and perl. $quote is 1 for things that need
101 :     # to be quoted, 0 otherwise.
102 :     #
103 :     our $Config = [];
104 :    
105 :     #
106 :     # Other key/value pairs of stuff we may need to pass
107 :     # to and from the environment-specific configuration modules.
108 :     #
109 :     # Known keys:
110 :     #
111 :     # pythonpath
112 :     #
113 :    
114 :     our $OtherConfig = {};
115 :    
116 :     #
117 :     # Cache values of the various places we may be installing things.
118 :     #
119 :    
120 :     our $fig_disk = $ENV{FIG_HOME};
121 :     our $env_name = $ENV{FIGCONFIG_ENV};
122 : olson 1.7 our $env_dir = "$ENV{FIGCONFIG_ENV_DIR}";
123 : olson 1.1 our $env_bin = "$ENV{FIGCONFIG_ENV_DIR}/bin";
124 :     our $env_lib = "$ENV{FIGCONFIG_ENV_DIR}/lib";
125 : olson 1.2 #
126 :     # We are moving to use a symlink in dist/releases/current for these.
127 :     # This symlink is managed by switch_to_release.
128 :     #
129 :     #our $release_bin = "$ENV{FIGCONFIG_RELEASE_DIR}/bin/$ENV{FIGCONFIG_ENV}";
130 :     #our $release_lib = "$ENV{FIGCONFIG_RELEASE_DIR}/lib/$ENV{FIGCONFIG_ENV}";
131 :    
132 : olson 1.8 our $release_bin = "$fig_disk/dist/releases/current/$ENV{FIGCONFIG_ENV}/bin";
133 :     our $release_lib = "$fig_disk/dist/releases/current/$ENV{FIGCONFIG_ENV}/lib";
134 : olson 1.2
135 :     our $fig_bin = "$fig_disk/FIG/bin";
136 : olson 1.1
137 :     #
138 :     # Location of start/stop servers scripts.
139 :     #
140 :     our $start_servers = "$fig_disk/bin/start-servers";
141 :     our $stop_servers = "$fig_disk/bin/stop-servers";
142 :    
143 :     sub configure_std_fig_environment
144 :     {
145 :     #
146 :     # Populate the Config with the usual stuff we need in FIG_Config.pm.
147 :     #
148 :    
149 :     my $fig = "$fig_disk/FIG";
150 :     my $data = "$fig/Data";
151 : olson 1.21 my $sproutData = "$fig/SproutData";
152 : olson 1.1
153 :     my $hostname = `hostname`;
154 :     chomp $hostname;
155 :    
156 :     push(@$Config, ["fig_disk", $fig_disk, 1]);
157 : olson 1.6 push(@$Config, ["blastmat", "$fig_disk/BLASTMAT", 1]);
158 : olson 1.1 push(@$Config, ["fig", $fig, 1]);
159 : olson 1.2 push(@$Config, ["bin", $fig_bin, 1]);
160 : olson 1.1 push(@$Config, ["ext_bin", $env_bin, 1]);
161 : olson 1.18 push(@$Config, ["common_runtime", $env_dir, 1]);
162 :     push(@$Config, ["arch", $ENV{FIGCONFIG_ENV}, 1]);
163 : olson 1.22 push(@$Config, ["var", "$fig/var", 1]);
164 : olson 1.1 push(@$Config, ["data", $data, 1]);
165 :     push(@$Config, ["global", "$data/Global", 1]);
166 :     push(@$Config, ["organisms", "$data/Organisms", 1]);
167 :     push(@$Config, ["RC", "$fig_disk/FIG/ResolutionCenter", 1]);
168 :     push(@$Config, ["NR", "$fig_disk/FIG/NR", 1]);
169 :     push(@$Config, ["temp", "$fig_disk/FIG/Tmp", 1]);
170 : olson 1.21 push(@$Config, ["sproutData", $sproutData, 1]);
171 : olson 1.11
172 :     my $sandbox;
173 :     if ($ENV{FIGCONFIG_SANDBOX})
174 :     {
175 :     $sandbox = "/$ENV{FIGCONFIG_SANDBOX}";
176 :     }
177 :    
178 :     push(@$Config, ["temp_url", "http://$hostname$sandbox/FIG-Tmp", 1]);
179 :     push(@$Config, ["cgi_url", "http://$hostname$sandbox/FIG", 1]);
180 : golsen 1.9
181 :     #
182 :     # Add values for a relative base href of temp and CGI pages. The latter
183 :     # is used by HHTP.pm to write common page start. It would make the most
184 :     # sense to derive the above 2 values from these. -- GJO
185 :     #
186 :    
187 : olson 1.11 push(@$Config, ["temp_base", "$sandbox/FIG-Tmp/", 1]);
188 :     push(@$Config, ["cgi_base", "$sandbox/FIG/", 1]);
189 : olson 1.1 }
190 :    
191 :     sub compute_environment
192 :     {
193 :     #
194 :     # ReleaseTools configuration.
195 :     #
196 :    
197 :     push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);
198 :     push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);
199 : olson 1.23 push(@$Env, ["RTSITECONFIGDIR", "\$RTROOT/config", 0]);
200 : olson 1.1 push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);
201 : olson 1.2 push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);
202 : olson 1.1 push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);
203 :    
204 :     push(@$Env, ["BLASTMAT", "$ENV{FIG_HOME}/BLASTMAT", 0]);
205 :    
206 :     #
207 :     # Determine the path to use.
208 :     #
209 :     # This includes the path into the particular release we're configuring for,
210 :     # and to the environment's bin directory.
211 :     #
212 :    
213 :     my @path = ();
214 : olson 1.24 push(@path, $fig_bin);
215 : olson 1.1 push(@path, $env_bin);
216 :     push(@path, "$fig_disk/bin");
217 :    
218 :     push(@$Env, ["PATH", join(":", @path), 1]);
219 :    
220 : olson 1.26 #
221 :     # Compute LD_LIBRARY_PATH.
222 :     #
223 :     # Some packages, like mysql, place their shared libs in subdirectories
224 :     # of the libdir.
225 :     #
226 :    
227 :     my @ld_path = ($env_lib);
228 :    
229 :     my $dh;
230 :     if (!opendir($dh, $env_lib))
231 :     {
232 :     warn "Could not opendir $env_lib: $!";
233 :     }
234 :    
235 :     while ($_ = readdir($dh))
236 :     {
237 :     next if /^\./;
238 :    
239 :     my $path = "$env_lib/$_";
240 :     next unless -d $path;
241 :    
242 :     #
243 :     # See if there are any .so's in here.
244 :     #
245 :    
246 :     my @solist = <$path/*.so*>;
247 :     if (@solist > 0)
248 :     {
249 :     push(@ld_path, $path);
250 :     }
251 :     }
252 :     closedir($dh);
253 :    
254 :     #
255 :     # And if perl is dynamically linked, we need to add the perl core directory
256 :     # to the path too.
257 :     #
258 :    
259 :     my @coredir = <$env_lib/perl5/*/*/CORE>;
260 :     if (@coredir)
261 :     {
262 :     if ( -f "$coredir[0]/libperl.so" )
263 :     {
264 :     print "Found libperl in $coredir[0]\n";
265 :     push(@ld_path, $coredir[0]);
266 :     }
267 :     }
268 :    
269 :     my $ld_path = join(":", @ld_path);
270 :     $OtherConfig->{ld_library_path} = $ld_path;
271 :    
272 :     push(@$Env, ["LD_LIBRARY_PATH", $ld_path, 1]);
273 : olson 1.11
274 : olson 1.23 my @perllib = grep({ $_ ne "." } @INC,
275 :     $release_lib,
276 :     "$release_lib/FigKernelPackages",
277 :     "$fig_disk/config");
278 : olson 1.12
279 :     push(@$Env, ["PERL5LIB", join(":", @perllib), 1]);
280 : olson 1.1 }
281 :    
282 :     sub configure_python
283 :     {
284 :     #
285 :     # Determine the PYTHONPATH we're to use.
286 :     #
287 :     # Right now, we don't compute a replacement for the system path,
288 :     # but we're likely going to require that *if* python is
289 :     # distributed with the environment. We're currently not doing that.
290 :     #
291 :     # So we just need to point to any python packages in the release,
292 :     # and to packages that were installed in the environment dir.
293 :     #
294 :    
295 :     my $python = find_python();
296 :     print "Found python at $python\n";
297 :    
298 :     my $py_version = `$python -c 'import sys; print "%d.%d" % (sys.version_info[:2])'`;
299 :     chomp $py_version;
300 :     print "Python version $py_version\n";
301 :    
302 : olson 1.23 #
303 :     # Python figures this out for us.
304 :     #$OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
305 : olson 1.2
306 : olson 1.1 my @path = ();
307 : olson 1.23 #push(@path, $OtherConfig->{python_site_path});
308 : olson 1.2 push(@path, "$release_lib");
309 : olson 1.1 push(@path, "$fig_disk/config");
310 :     push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
311 :    
312 :     $OtherConfig->{pythonpath} = join(":", @path);
313 :     }
314 :    
315 :     sub find_in_path
316 :     {
317 : olson 1.5 my($file, @extra) = @_;
318 : olson 1.1 my(@path) = split(":", $ENV{PATH});
319 :    
320 : olson 1.5 for my $p (@path, @extra)
321 : olson 1.1 {
322 :     my $x = "$p/$file";
323 :     if (-x $x)
324 :     {
325 :     return $x;
326 :     }
327 :     }
328 :     return undef;
329 :     }
330 :    
331 :     #
332 :     # Find the name of the python executable we are to use.
333 :     #
334 :     sub find_python
335 :     {
336 :     my $python;
337 :    
338 :     #
339 :     # Special case for the mac.
340 :     #
341 : olson 1.11 # RDO 20040603 - don't do this any more; we want to pick up
342 :     # the python we ship.
343 :     #
344 : olson 1.1
345 : olson 1.11 if (0 && $ENV{FIGCONFIG_ENV} eq "mac")
346 : olson 1.1 {
347 : olson 1.7 #
348 :     # We'd like to use the MacPython that is installed
349 :     # as pythonw.
350 :     #
351 :     if ($python = find_in_path("pythonw", "/usr/local/bin"))
352 : olson 1.1 {
353 : olson 1.7 $OtherConfig->{python_require_poundbang_env} = 1;
354 : olson 1.1 return $python;
355 :     }
356 :    
357 :     #
358 : olson 1.7 # Otherwise, we can live with the regular python.
359 :     # Fall thru to the generic case.
360 : olson 1.1 #
361 : olson 1.7 }
362 :     #
363 :     # Non-mac, just look in the env dir or the path.
364 :     #
365 : olson 1.1
366 : olson 1.7 $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
367 :     if (-x $python)
368 :     {
369 : olson 1.13 #
370 :     # The mac doesn't seem to like the long #! lines, so we'll use poundbang env.
371 :     #
372 : olson 1.15 if ($ENV{FIGCONFIG_ENV} =~ /^mac/)
373 : olson 1.13 {
374 :     $OtherConfig->{python_require_poundbang_env} = 1;
375 :     }
376 : olson 1.7 return $python;
377 : olson 1.1 }
378 :    
379 : olson 1.7 return find_in_path("python");
380 : olson 1.1 }
381 :    
382 :     #
383 :     # Find the name of the perl executable we are to use.
384 :     #
385 :     sub find_perl
386 :     {
387 :     my $perl;
388 :    
389 :     $perl = "$ENV{FIGCONFIG_ENV_DIR}/bin/perl";
390 :     if (-x $perl)
391 :     {
392 :     return $perl;
393 :     }
394 :    
395 :     warn "We did not find a perl executable in the SEED distribution; some modules may not be found\n";
396 :     return find_in_path("perl");
397 :     }
398 :    
399 :     sub write_bash_init
400 :     {
401 :     my($fh, $env) = @_;
402 :    
403 :     foreach my $item (@$env)
404 :     {
405 :     my($name, $value, $append) = @$item;
406 :    
407 :     if ($append)
408 :     {
409 :     #
410 :     # Write code to detect if the value is set, and act accordingly.
411 :     #
412 :    
413 :     print $fh <<END;
414 :     DELIM=
415 :     if [ -n "\$$name" ] ; then
416 :     DELIM=:
417 :     fi
418 : olson 1.10 $name=$value\${DELIM}\${$name}
419 : olson 1.1 export $name
420 :     END
421 :     }
422 :     else
423 :     {
424 :     print $fh "$name=\"$value\"\n";
425 :     print $fh "export $name\n";
426 :     }
427 :     }
428 : olson 1.20 print $fh "alias rtpath='source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.sh'\n";
429 : olson 1.1 }
430 :    
431 :     sub write_csh_init
432 :     {
433 :     my($fh, $env) = @_;
434 :    
435 :     foreach my $item (@$env)
436 :     {
437 :     my($name, $value, $append) = @$item;
438 :    
439 :     if ($append)
440 :     {
441 :     #
442 :     # Write code to detect if the value is set, and act accordingly.
443 :     #
444 :    
445 :     print $fh <<END;
446 :     if (\$?$name) then
447 : olson 1.10 setenv $name $value:\${$name}
448 : olson 1.1 else
449 :     setenv $name $value
450 :     endif
451 :     END
452 :     }
453 :     else
454 :     {
455 :     print $fh "setenv $name \"$value\"\n";
456 :     }
457 :     }
458 :    
459 : olson 1.20 #
460 :     # Alias for RT stuff.
461 :     #
462 :     print $fh "alias rtpath 'source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.csh'\n";
463 : olson 1.1 }
464 :    
465 :     sub run_script
466 :     {
467 :     my($script) = @_;
468 :    
469 :    
470 :     unless (my $ret = do $script)
471 :     {
472 :     if ($@)
473 :     {
474 :     warn "Error parsing $script: $@\n";
475 :     }
476 :     elsif (!defined($ret))
477 :     {
478 :     warn "Couldn't do $script: $!\n";
479 :     }
480 :     else
481 :     {
482 :     warn "Counldn't run $script\n";
483 :     }
484 :     }
485 :    
486 :    
487 :     }
488 :    
489 :     sub configure_environment_specific
490 :     {
491 :     my $env_script = $ENV{FIGCONFIG_ENV_CONFIG};
492 :    
493 :     if (! -f $env_script)
494 :     {
495 :     warn "No environment-specific configuration file $env_script found, skipping\n";
496 :     return;
497 :     }
498 :    
499 :     run_script($env_script);
500 :     }
501 :    
502 :     #
503 :     # Create any directories that might be missing.
504 :     #
505 :    
506 :     sub setup_directories
507 :     {
508 :     my(@needed) = @_;
509 :    
510 :     for my $dir (@needed)
511 :     {
512 :     if (! -d $dir)
513 :     {
514 :     mkdir($dir) or warn "Could not create $dir: $!\n";
515 :     }
516 :     }
517 :     }
518 :    
519 :     sub setup_server_scripts
520 :     {
521 :     #
522 :     # Remove any start/stop servers scripts we might have, and write the stub
523 :     # start.
524 :     #
525 :    
526 :     unlink($start_servers);
527 :     unlink($stop_servers);
528 :    
529 :     open(F, ">$start_servers") or die "Cannot write $start_servers: $!";
530 :     print F "#!/bin/sh\n\n";
531 :     close(F);
532 :     chmod(0775, $start_servers);
533 :    
534 :     open(F, ">$stop_servers") or die "Cannot write $stop_servers: $!";
535 :     print F "#!/bin/sh\n\n";
536 :     close(F);
537 :     chmod(0775, $stop_servers);
538 :    
539 :     }
540 :    
541 : olson 1.7 sub finalize_server_scripts
542 :     {
543 :     #
544 :     # After any environment-specific stuff, call start_services and stop_services.
545 :     #
546 :    
547 :     open(F, ">>$start_servers") or die "Cannot write $start_servers: $!";
548 :     print F "\n$fig_bin/start_services\n";
549 :     close(F);
550 :     chmod(0775, $start_servers);
551 :    
552 :     open(F, ">>$stop_servers") or die "Cannot write $stop_servers: $!";
553 :     print F "\n$fig_bin/stop_services\n";
554 :     close(F);
555 :     chmod(0775, $stop_servers);
556 :    
557 :     }
558 :    
559 : olson 1.1 sub write_config_pm
560 :     {
561 :     my($fh, $config) = @_;
562 :    
563 :     print $fh "package FIG_Config;\n\n";
564 :    
565 :     foreach my $item (@$config)
566 :     {
567 :     my($name, $value, $quote) = @$item;
568 :    
569 :     my $q = $quote ? '"' : '';
570 :     printf $fh "\$%-15s = $q$value$q;\n", $name
571 :     }
572 :    
573 :     print $fh "\n1;\n";
574 :     }
575 :    
576 :     sub write_config_py
577 :     {
578 :     my($fh, $config) = @_;
579 :    
580 :     foreach my $item (@$config)
581 :     {
582 :     my($name, $value, $quote) = @$item;
583 :    
584 :     #
585 :     # Ugh. "global" is a keyword in python.
586 :     #
587 :    
588 :     $name = "global_dir" if $name eq "global";
589 :    
590 :     my $q = $quote ? '"' : '';
591 :     printf $fh "%-15s = $q$value$q\n", $name
592 :     }
593 :     }
594 :    
595 :     sub write_tool_hdr_perl
596 :     {
597 :     my($fh) = @_;
598 :    
599 :     my $perl = find_perl();
600 :    
601 :     print $fh "#!$perl\n";
602 :     print $fh "\n";
603 :    
604 :     if ($::perlenv_override)
605 :     {
606 :     #
607 :     # Write the tool header BEGIN block to reset the environment.
608 :     #
609 :    
610 :     print $fh "BEGIN {\n";
611 :     print $fh " \@INC = qw(\n";
612 :     for my $inc (@INC)
613 :     {
614 :     next if $inc eq '.';
615 :     print $fh "\t$inc\n";
616 :     }
617 : olson 1.2 print $fh ");\n";
618 : olson 1.1 print $fh "}\n";
619 :     }
620 :    
621 :     print $fh "use Data::Dumper;\n";
622 :     print $fh "use Carp;\n";
623 :    
624 : olson 1.2 #
625 :     # We generate a comment here that gets expanded by switch_to_release
626 :     # This is part of the effort in making the environment bootstrapping
627 :     # code independent of releases.
628 :     #
629 :    
630 :     #print $fh "use lib \"$release_lib\";\n";
631 :     #print $fh "use lib \"$release_lib/FigKernelPackages\";\n";
632 :    
633 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
634 :     print $fh "# to point at the correct locations in the release directory.\n";
635 :     print $fh "#BEGIN switch_to_release generated code\n";
636 :     print $fh "#END switch_to_release generated code\n";
637 :     print $fh "\n";
638 :    
639 : olson 1.1 print $fh "use lib \"$fig_disk/config\";\n";
640 :    
641 :     print $fh "use FIG_Config;\n";
642 :     print $fh "\n";
643 : olson 1.11 print $fh "#### END tool_hdr ####\n\n"
644 : olson 1.1 }
645 :    
646 :     sub write_tool_hdr_python
647 :     {
648 :     my($fh) = @_;
649 :    
650 :     my $python = find_python();
651 :    
652 : olson 1.4 if ($OtherConfig->{python_require_poundbang_env})
653 :     {
654 :     print $fh "#!/usr/bin/env $python\n";
655 :     }
656 :     else
657 :     {
658 :     print $fh "#!$python\n";
659 :     }
660 : olson 1.1 print $fh "\n";
661 :    
662 : olson 1.11 print $fh "import sys, os\n";
663 : olson 1.2
664 :    
665 :     print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
666 :    
667 : olson 1.11 #
668 :     # Append the perl path to the environment, for use later with CallPerl.
669 :     #
670 :    
671 : olson 1.23 my $perlpath = join(":", @INC, $release_lib, "$release_lib/FigKernelPackages", "$fig_disk/config");
672 : olson 1.11 print $fh <<END;
673 :     if os.getenv("PERL5LIB", "") != "":
674 :     _delim = ":"
675 :     else:
676 :     _delim = ""
677 :     os.environ["PERL5LIB"] = "$perlpath" + _delim + os.getenv("PERL5LIB", "")
678 :    
679 :     END
680 :    
681 : olson 1.2 print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
682 :     print $fh "# to point at the correct locations in the release directory.\n";
683 :     print $fh "#BEGIN switch_to_release generated code\n";
684 :     print $fh "#END switch_to_release generated code\n";
685 :     print $fh "\n";
686 :    
687 :     print $fh "sys.path.append('$fig_disk/config')\n";
688 :    
689 : olson 1.1 print $fh "import FIG_Config\n";
690 :     print $fh "\n";
691 : olson 1.11 print $fh "#### END tool_hdr_py ####\n\n"
692 : olson 1.1 }
693 :    
694 : olson 1.23 sub write_rtconfig
695 :     {
696 :     my($fh) = @_;
697 :    
698 :     my $python = find_python();
699 :     my $perl = find_perl();
700 :    
701 :     print $fh "RTPYTHON=$python\n";
702 :     print $fh "RTPERL=$perl\n";
703 :     print $fh "RTPYTHONPATH=$OtherConfig->{pythonpath}\n";
704 :    
705 : olson 1.25 my %seen;
706 :     my @perlpath;
707 :     for (@INC, "$fig_disk/config")
708 :     {
709 :     next if $seen{$_};
710 :     push(@perlpath, $_);
711 :     $seen{$_}++;
712 :     }
713 :     my $perlpath = join(":", @perlpath);
714 : olson 1.23
715 :     print $fh "RTPERL5LIB=$perlpath\n";
716 :    
717 :     print $fh "RTPYTHONIMPORTS=FIG_Config\n";
718 :     print $fh "RTPERLIMPORTS=FIG_Config\n";
719 : olson 1.25 print $fh "RTSETENV=BLASTMAT=$fig_disk/BLASTMAT\n";
720 :     print $fh "RTSETENV=FIG_HOME=$fig_disk\n";
721 : olson 1.27 print $fh "#RTLD_LDPATH=$OtherConfig->{ld_library_path}\n";
722 : olson 1.23 }
723 :    
724 : olson 1.1 setup_directories("$fig_disk/bin",
725 :     "$fig_disk/config");
726 :    
727 :     setup_server_scripts();
728 :    
729 :    
730 :     find_python();
731 :    
732 :     compute_environment();
733 :     configure_std_fig_environment();
734 :     configure_python();
735 :     configure_environment_specific();
736 : olson 1.19 # configure_database();
737 : olson 1.7
738 :     finalize_server_scripts();
739 : olson 1.1
740 :     #
741 :     # Write the shell startup to the figdisk.
742 :     #
743 :     open(FH, ">$fig_disk/config/fig-user-env.sh") or die "Cannot write $fig_disk/config/fig-user-env.sh: $!";
744 :     write_bash_init(\*FH, $Env);
745 :     close(FH);
746 :    
747 :     open(FH, ">$fig_disk/config/fig-user-env.csh") or die "Cannot write $fig_disk/config/fig-user-env.csh: $!";
748 :     write_csh_init(\*FH, $Env);
749 :     close(FH);
750 :    
751 :     #
752 :     # Write the FIG_Config file.
753 :     #
754 :    
755 :     open(FH, ">$fig_disk/config/FIG_Config.pm") or die "Cannot write $fig_disk/config/FIG_Config.pm: $!";
756 :     write_config_pm(\*FH, $Config);
757 :     close(FH);
758 :    
759 :     open(FH, ">$fig_disk/config/FIG_Config.py") or die "Cannot write $fig_disk/config/FIG_Config.py: $!";
760 :     write_config_py(\*FH, $Config);
761 :     close(FH);
762 :    
763 :     #
764 :     # Write the tool headers
765 :     #
766 :    
767 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr") or die "Cannot write $fig_disk/config/tool_hdr: $!";
768 : olson 1.1 write_tool_hdr_perl(\*FH);
769 :     close(FH);
770 :    
771 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr_py") or die "Cannot write $fig_disk/config/tool_hdr_py: $!";
772 : olson 1.1 write_tool_hdr_python(\*FH);
773 :     close(FH);
774 :    
775 : olson 1.23 open(FH, ">$fig_disk/config/RTConfig") or die "Cannot write $fig_disk/config/RTConfig: $!";
776 :     write_rtconfig(\*FH);
777 :     close(FH);
778 :    
779 : olson 1.2 unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
780 :    
781 :     require FigCommon::SwitchRelease;
782 : olson 1.1
783 : olson 1.16 #
784 :     # We need to tweak the current path and PERL5LIB environment to get bootstrapping to
785 :     # work correctly.
786 :     #
787 :    
788 :     $ENV{PATH} = "$ENV{FIGCONFIG_ENVDIR}/bin:$ENV{PATH}";
789 :    
790 : olson 1.17 $ENV{PERL5LIB} = (map { $_->[1] } grep { $_->[0] eq "PERL5LIB"} @$Env)[0];
791 : olson 1.16
792 : olson 1.2 &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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