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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 $perlenv_override to true if we've done this,
49 :     # so we can insert these fixes into the perl tool header.
50 :     #
51 :    
52 :     BEGIN {
53 :    
54 : olson 1.3 print "Here in the perl bootstrap. inc is:\n" . join("\n", @INC), "\n";
55 : olson 1.1
56 : parrello 1.29 my ($my_prefix, $prefix, $inc, @newInc);
57 : olson 1.1
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 : parrello 1.29
190 : olson 1.1 }
191 :    
192 :     sub compute_environment
193 :     {
194 :     #
195 :     # ReleaseTools configuration.
196 :     #
197 :    
198 :     push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);
199 :     push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);
200 : olson 1.23 push(@$Env, ["RTSITECONFIGDIR", "\$RTROOT/config", 0]);
201 : olson 1.1 push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);
202 : olson 1.2 push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);
203 : olson 1.1 push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);
204 :    
205 :     push(@$Env, ["BLASTMAT", "$ENV{FIG_HOME}/BLASTMAT", 0]);
206 :    
207 :     #
208 :     # Determine the path to use.
209 :     #
210 :     # This includes the path into the particular release we're configuring for,
211 :     # and to the environment's bin directory.
212 :     #
213 :    
214 :     my @path = ();
215 : olson 1.24 push(@path, $fig_bin);
216 : olson 1.1 push(@path, $env_bin);
217 :     push(@path, "$fig_disk/bin");
218 :    
219 :     push(@$Env, ["PATH", join(":", @path), 1]);
220 :    
221 : olson 1.26 #
222 :     # Compute LD_LIBRARY_PATH.
223 :     #
224 :     # Some packages, like mysql, place their shared libs in subdirectories
225 :     # of the libdir.
226 :     #
227 :    
228 :     my @ld_path = ($env_lib);
229 :    
230 :     my $dh;
231 :     if (!opendir($dh, $env_lib))
232 :     {
233 :     warn "Could not opendir $env_lib: $!";
234 :     }
235 :    
236 :     while ($_ = readdir($dh))
237 :     {
238 :     next if /^\./;
239 :    
240 :     my $path = "$env_lib/$_";
241 :     next unless -d $path;
242 :    
243 :     #
244 :     # See if there are any .so's in here.
245 :     #
246 :    
247 :     my @solist = <$path/*.so*>;
248 :     if (@solist > 0)
249 :     {
250 :     push(@ld_path, $path);
251 :     }
252 :     }
253 :     closedir($dh);
254 :    
255 :     #
256 :     # And if perl is dynamically linked, we need to add the perl core directory
257 :     # to the path too.
258 :     #
259 :    
260 :     my @coredir = <$env_lib/perl5/*/*/CORE>;
261 :     if (@coredir)
262 :     {
263 :     if ( -f "$coredir[0]/libperl.so" )
264 :     {
265 :     print "Found libperl in $coredir[0]\n";
266 :     push(@ld_path, $coredir[0]);
267 :     }
268 :     }
269 :    
270 :     my $ld_path = join(":", @ld_path);
271 :     $OtherConfig->{ld_library_path} = $ld_path;
272 :    
273 :     push(@$Env, ["LD_LIBRARY_PATH", $ld_path, 1]);
274 : olson 1.11
275 : olson 1.23 my @perllib = grep({ $_ ne "." } @INC,
276 :     $release_lib,
277 :     "$release_lib/FigKernelPackages",
278 :     "$fig_disk/config");
279 : olson 1.12
280 :     push(@$Env, ["PERL5LIB", join(":", @perllib), 1]);
281 : olson 1.1 }
282 :    
283 :     sub configure_python
284 :     {
285 :     #
286 :     # Determine the PYTHONPATH we're to use.
287 :     #
288 :     # Right now, we don't compute a replacement for the system path,
289 :     # but we're likely going to require that *if* python is
290 :     # distributed with the environment. We're currently not doing that.
291 :     #
292 :     # So we just need to point to any python packages in the release,
293 :     # and to packages that were installed in the environment dir.
294 :     #
295 :    
296 :     my $python = find_python();
297 :     print "Found python at $python\n";
298 :    
299 :     my $py_version = `$python -c 'import sys; print "%d.%d" % (sys.version_info[:2])'`;
300 :     chomp $py_version;
301 :     print "Python version $py_version\n";
302 :    
303 : olson 1.23 #
304 :     # Python figures this out for us.
305 :     #$OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
306 : olson 1.2
307 : olson 1.1 my @path = ();
308 : olson 1.23 #push(@path, $OtherConfig->{python_site_path});
309 : olson 1.2 push(@path, "$release_lib");
310 : olson 1.1 push(@path, "$fig_disk/config");
311 :     push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
312 :    
313 :     $OtherConfig->{pythonpath} = join(":", @path);
314 :     }
315 :    
316 :     sub find_in_path
317 :     {
318 : olson 1.5 my($file, @extra) = @_;
319 : olson 1.1 my(@path) = split(":", $ENV{PATH});
320 :    
321 : olson 1.5 for my $p (@path, @extra)
322 : olson 1.1 {
323 :     my $x = "$p/$file";
324 :     if (-x $x)
325 :     {
326 :     return $x;
327 :     }
328 :     }
329 :     return undef;
330 :     }
331 :    
332 :     #
333 :     # Find the name of the python executable we are to use.
334 :     #
335 :     sub find_python
336 :     {
337 :     my $python;
338 :    
339 :     #
340 :     # Special case for the mac.
341 :     #
342 : olson 1.11 # RDO 20040603 - don't do this any more; we want to pick up
343 :     # the python we ship.
344 :     #
345 : olson 1.1
346 : olson 1.11 if (0 && $ENV{FIGCONFIG_ENV} eq "mac")
347 : olson 1.1 {
348 : olson 1.7 #
349 :     # We'd like to use the MacPython that is installed
350 :     # as pythonw.
351 :     #
352 :     if ($python = find_in_path("pythonw", "/usr/local/bin"))
353 : olson 1.1 {
354 : olson 1.7 $OtherConfig->{python_require_poundbang_env} = 1;
355 : olson 1.1 return $python;
356 :     }
357 :    
358 :     #
359 : olson 1.7 # Otherwise, we can live with the regular python.
360 :     # Fall thru to the generic case.
361 : olson 1.1 #
362 : olson 1.7 }
363 :     #
364 :     # Non-mac, just look in the env dir or the path.
365 :     #
366 : olson 1.1
367 : olson 1.7 $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
368 :     if (-x $python)
369 :     {
370 : olson 1.13 #
371 :     # The mac doesn't seem to like the long #! lines, so we'll use poundbang env.
372 :     #
373 : olson 1.15 if ($ENV{FIGCONFIG_ENV} =~ /^mac/)
374 : olson 1.13 {
375 :     $OtherConfig->{python_require_poundbang_env} = 1;
376 :     }
377 : olson 1.7 return $python;
378 : olson 1.1 }
379 :    
380 : olson 1.7 return find_in_path("python");
381 : olson 1.1 }
382 :    
383 :     #
384 :     # Find the name of the perl executable we are to use.
385 :     #
386 :     sub find_perl
387 :     {
388 :     my $perl;
389 :    
390 :     $perl = "$ENV{FIGCONFIG_ENV_DIR}/bin/perl";
391 :     if (-x $perl)
392 :     {
393 :     return $perl;
394 :     }
395 :    
396 :     warn "We did not find a perl executable in the SEED distribution; some modules may not be found\n";
397 :     return find_in_path("perl");
398 :     }
399 :    
400 :     sub write_bash_init
401 :     {
402 :     my($fh, $env) = @_;
403 :    
404 :     foreach my $item (@$env)
405 :     {
406 :     my($name, $value, $append) = @$item;
407 :    
408 :     if ($append)
409 :     {
410 :     #
411 :     # Write code to detect if the value is set, and act accordingly.
412 :     #
413 :    
414 :     print $fh <<END;
415 :     DELIM=
416 :     if [ -n "\$$name" ] ; then
417 :     DELIM=:
418 :     fi
419 : olson 1.10 $name=$value\${DELIM}\${$name}
420 : olson 1.1 export $name
421 :     END
422 :     }
423 :     else
424 :     {
425 :     print $fh "$name=\"$value\"\n";
426 :     print $fh "export $name\n";
427 :     }
428 :     }
429 : olson 1.20 print $fh "alias rtpath='source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.sh'\n";
430 : olson 1.1 }
431 :    
432 :     sub write_csh_init
433 :     {
434 :     my($fh, $env) = @_;
435 :    
436 :     foreach my $item (@$env)
437 :     {
438 :     my($name, $value, $append) = @$item;
439 :    
440 :     if ($append)
441 :     {
442 :     #
443 :     # Write code to detect if the value is set, and act accordingly.
444 :     #
445 :    
446 :     print $fh <<END;
447 :     if (\$?$name) then
448 : olson 1.10 setenv $name $value:\${$name}
449 : olson 1.1 else
450 :     setenv $name $value
451 :     endif
452 :     END
453 :     }
454 :     else
455 :     {
456 :     print $fh "setenv $name \"$value\"\n";
457 :     }
458 :     }
459 :    
460 : olson 1.20 #
461 :     # Alias for RT stuff.
462 :     #
463 :     print $fh "alias rtpath 'source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.csh'\n";
464 : olson 1.1 }
465 :    
466 :     sub run_script
467 :     {
468 :     my($script) = @_;
469 :    
470 :    
471 :     unless (my $ret = do $script)
472 :     {
473 :     if ($@)
474 :     {
475 :     warn "Error parsing $script: $@\n";
476 :     }
477 :     elsif (!defined($ret))
478 :     {
479 :     warn "Couldn't do $script: $!\n";
480 :     }
481 :     else
482 :     {
483 :     warn "Counldn't run $script\n";
484 :     }
485 :     }
486 :    
487 :    
488 :     }
489 :    
490 :     sub configure_environment_specific
491 :     {
492 :     my $env_script = $ENV{FIGCONFIG_ENV_CONFIG};
493 :    
494 :     if (! -f $env_script)
495 :     {
496 :     warn "No environment-specific configuration file $env_script found, skipping\n";
497 :     return;
498 :     }
499 :    
500 :     run_script($env_script);
501 :     }
502 :    
503 :     #
504 :     # Create any directories that might be missing.
505 :     #
506 :    
507 :     sub setup_directories
508 :     {
509 :     my(@needed) = @_;
510 :    
511 :     for my $dir (@needed)
512 :     {
513 :     if (! -d $dir)
514 :     {
515 :     mkdir($dir) or warn "Could not create $dir: $!\n";
516 :     }
517 :     }
518 :     }
519 :    
520 :     sub setup_server_scripts
521 :     {
522 :     #
523 :     # Remove any start/stop servers scripts we might have, and write the stub
524 :     # start.
525 :     #
526 :    
527 :     unlink($start_servers);
528 :     unlink($stop_servers);
529 :    
530 :     open(F, ">$start_servers") or die "Cannot write $start_servers: $!";
531 :     print F "#!/bin/sh\n\n";
532 :     close(F);
533 :     chmod(0775, $start_servers);
534 :    
535 :     open(F, ">$stop_servers") or die "Cannot write $stop_servers: $!";
536 :     print F "#!/bin/sh\n\n";
537 :     close(F);
538 :     chmod(0775, $stop_servers);
539 :    
540 :     }
541 :    
542 : olson 1.7 sub finalize_server_scripts
543 :     {
544 :     #
545 :     # After any environment-specific stuff, call start_services and stop_services.
546 :     #
547 :    
548 :     open(F, ">>$start_servers") or die "Cannot write $start_servers: $!";
549 :     print F "\n$fig_bin/start_services\n";
550 :     close(F);
551 :     chmod(0775, $start_servers);
552 :    
553 :     open(F, ">>$stop_servers") or die "Cannot write $stop_servers: $!";
554 :     print F "\n$fig_bin/stop_services\n";
555 :     close(F);
556 :     chmod(0775, $stop_servers);
557 :    
558 :     }
559 :    
560 : olson 1.1 sub write_config_pm
561 :     {
562 :     my($fh, $config) = @_;
563 :    
564 :     print $fh "package FIG_Config;\n\n";
565 :    
566 :     foreach my $item (@$config)
567 :     {
568 :     my($name, $value, $quote) = @$item;
569 :    
570 :     my $q = $quote ? '"' : '';
571 :     printf $fh "\$%-15s = $q$value$q;\n", $name
572 :     }
573 :    
574 :     print $fh "\n1;\n";
575 :     }
576 :    
577 :     sub write_config_py
578 :     {
579 :     my($fh, $config) = @_;
580 :    
581 :     foreach my $item (@$config)
582 :     {
583 :     my($name, $value, $quote) = @$item;
584 :    
585 :     #
586 :     # Ugh. "global" is a keyword in python.
587 :     #
588 :    
589 :     $name = "global_dir" if $name eq "global";
590 :    
591 :     my $q = $quote ? '"' : '';
592 :     printf $fh "%-15s = $q$value$q\n", $name
593 :     }
594 :     }
595 :    
596 :     sub write_tool_hdr_perl
597 :     {
598 :     my($fh) = @_;
599 :    
600 :     my $perl = find_perl();
601 :    
602 :     print $fh "#!$perl\n";
603 :     print $fh "\n";
604 :    
605 :     if ($::perlenv_override)
606 :     {
607 :     #
608 :     # Write the tool header BEGIN block to reset the environment.
609 :     #
610 :    
611 :     print $fh "BEGIN {\n";
612 :     print $fh " \@INC = qw(\n";
613 :     for my $inc (@INC)
614 :     {
615 :     next if $inc eq '.';
616 :     print $fh "\t$inc\n";
617 :     }
618 : olson 1.2 print $fh ");\n";
619 : olson 1.1 print $fh "}\n";
620 :     }
621 :    
622 :     print $fh "use Data::Dumper;\n";
623 :     print $fh "use Carp;\n";
624 :    
625 : olson 1.2 #
626 :     # We generate a comment here that gets expanded by switch_to_release
627 :     # This is part of the effort in making the environment bootstrapping
628 :     # code independent of releases.
629 :     #
630 :    
631 :     #print $fh "use lib \"$release_lib\";\n";
632 :     #print $fh "use lib \"$release_lib/FigKernelPackages\";\n";
633 :    
634 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
635 :     print $fh "# to point at the correct locations in the release directory.\n";
636 :     print $fh "#BEGIN switch_to_release generated code\n";
637 :     print $fh "#END switch_to_release generated code\n";
638 :     print $fh "\n";
639 :    
640 : olson 1.1 print $fh "use lib \"$fig_disk/config\";\n";
641 :    
642 :     print $fh "use FIG_Config;\n";
643 :     print $fh "\n";
644 : olson 1.11 print $fh "#### END tool_hdr ####\n\n"
645 : olson 1.1 }
646 :    
647 :     sub write_tool_hdr_python
648 :     {
649 :     my($fh) = @_;
650 :    
651 :     my $python = find_python();
652 :    
653 : olson 1.4 if ($OtherConfig->{python_require_poundbang_env})
654 :     {
655 :     print $fh "#!/usr/bin/env $python\n";
656 :     }
657 :     else
658 :     {
659 :     print $fh "#!$python\n";
660 :     }
661 : olson 1.1 print $fh "\n";
662 :    
663 : olson 1.11 print $fh "import sys, os\n";
664 : olson 1.2
665 :    
666 :     print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
667 :    
668 : olson 1.11 #
669 :     # Append the perl path to the environment, for use later with CallPerl.
670 :     #
671 :    
672 : olson 1.23 my $perlpath = join(":", @INC, $release_lib, "$release_lib/FigKernelPackages", "$fig_disk/config");
673 : olson 1.11 print $fh <<END;
674 :     if os.getenv("PERL5LIB", "") != "":
675 :     _delim = ":"
676 :     else:
677 :     _delim = ""
678 :     os.environ["PERL5LIB"] = "$perlpath" + _delim + os.getenv("PERL5LIB", "")
679 :    
680 :     END
681 :    
682 : olson 1.2 print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
683 :     print $fh "# to point at the correct locations in the release directory.\n";
684 :     print $fh "#BEGIN switch_to_release generated code\n";
685 :     print $fh "#END switch_to_release generated code\n";
686 :     print $fh "\n";
687 :    
688 :     print $fh "sys.path.append('$fig_disk/config')\n";
689 :    
690 : olson 1.1 print $fh "import FIG_Config\n";
691 :     print $fh "\n";
692 : olson 1.11 print $fh "#### END tool_hdr_py ####\n\n"
693 : olson 1.1 }
694 :    
695 : olson 1.23 sub write_rtconfig
696 :     {
697 :     my($fh) = @_;
698 :    
699 :     my $python = find_python();
700 :     my $perl = find_perl();
701 :    
702 :     print $fh "RTPYTHON=$python\n";
703 :     print $fh "RTPERL=$perl\n";
704 :     print $fh "RTPYTHONPATH=$OtherConfig->{pythonpath}\n";
705 :    
706 : olson 1.25 my %seen;
707 :     my @perlpath;
708 :     for (@INC, "$fig_disk/config")
709 :     {
710 :     next if $seen{$_};
711 :     push(@perlpath, $_);
712 :     $seen{$_}++;
713 :     }
714 :     my $perlpath = join(":", @perlpath);
715 : olson 1.23
716 :     print $fh "RTPERL5LIB=$perlpath\n";
717 :    
718 :     print $fh "RTPYTHONIMPORTS=FIG_Config\n";
719 :     print $fh "RTPERLIMPORTS=FIG_Config\n";
720 : olson 1.25 print $fh "RTSETENV=BLASTMAT=$fig_disk/BLASTMAT\n";
721 :     print $fh "RTSETENV=FIG_HOME=$fig_disk\n";
722 : olson 1.27 print $fh "#RTLD_LDPATH=$OtherConfig->{ld_library_path}\n";
723 : olson 1.23 }
724 :    
725 : olson 1.1 setup_directories("$fig_disk/bin",
726 :     "$fig_disk/config");
727 :    
728 :     setup_server_scripts();
729 :    
730 :    
731 :     find_python();
732 :    
733 :     compute_environment();
734 :     configure_std_fig_environment();
735 :     configure_python();
736 :     configure_environment_specific();
737 : olson 1.19 # configure_database();
738 : olson 1.7
739 :     finalize_server_scripts();
740 : olson 1.1
741 :     #
742 :     # Write the shell startup to the figdisk.
743 :     #
744 :     open(FH, ">$fig_disk/config/fig-user-env.sh") or die "Cannot write $fig_disk/config/fig-user-env.sh: $!";
745 :     write_bash_init(\*FH, $Env);
746 :     close(FH);
747 :    
748 :     open(FH, ">$fig_disk/config/fig-user-env.csh") or die "Cannot write $fig_disk/config/fig-user-env.csh: $!";
749 :     write_csh_init(\*FH, $Env);
750 :     close(FH);
751 :    
752 :     #
753 :     # Write the FIG_Config file.
754 :     #
755 :    
756 :     open(FH, ">$fig_disk/config/FIG_Config.pm") or die "Cannot write $fig_disk/config/FIG_Config.pm: $!";
757 :     write_config_pm(\*FH, $Config);
758 :     close(FH);
759 :    
760 :     open(FH, ">$fig_disk/config/FIG_Config.py") or die "Cannot write $fig_disk/config/FIG_Config.py: $!";
761 :     write_config_py(\*FH, $Config);
762 :     close(FH);
763 :    
764 :     #
765 :     # Write the tool headers
766 :     #
767 :    
768 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr") or die "Cannot write $fig_disk/config/tool_hdr: $!";
769 : olson 1.1 write_tool_hdr_perl(\*FH);
770 :     close(FH);
771 :    
772 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr_py") or die "Cannot write $fig_disk/config/tool_hdr_py: $!";
773 : olson 1.1 write_tool_hdr_python(\*FH);
774 :     close(FH);
775 :    
776 : olson 1.23 open(FH, ">$fig_disk/config/RTConfig") or die "Cannot write $fig_disk/config/RTConfig: $!";
777 :     write_rtconfig(\*FH);
778 :     close(FH);
779 :    
780 : olson 1.2 unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
781 :    
782 :     require FigCommon::SwitchRelease;
783 : olson 1.1
784 : olson 1.16 #
785 :     # We need to tweak the current path and PERL5LIB environment to get bootstrapping to
786 :     # work correctly.
787 :     #
788 :    
789 :     $ENV{PATH} = "$ENV{FIGCONFIG_ENVDIR}/bin:$ENV{PATH}";
790 :    
791 : olson 1.17 $ENV{PERL5LIB} = (map { $_->[1] } grep { $_->[0] eq "PERL5LIB"} @$Env)[0];
792 : olson 1.16
793 : olson 1.2 &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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