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revision 1.10, Thu Apr 1 12:59:40 2004 UTC revision 1.28, Mon Dec 5 19:10:06 2005 UTC
# Line 1  Line 1 
1  #  #
2    # 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  # FIG bootstrap script.  # FIG bootstrap script.
20  #  #
21  # Control is passed here from the toplevel configure (or dists/releases/install depending  # Control is passed here from the toplevel configure (or dists/releases/install depending
# Line 131  Line 148 
148    
149      my $fig = "$fig_disk/FIG";      my $fig = "$fig_disk/FIG";
150      my $data = "$fig/Data";      my $data = "$fig/Data";
151        my $sproutData = "$fig/SproutData";
152    
153      my $hostname = `hostname`;      my $hostname = `hostname`;
154      chomp $hostname;      chomp $hostname;
# Line 140  Line 158 
158      push(@$Config, ["fig", $fig, 1]);      push(@$Config, ["fig", $fig, 1]);
159      push(@$Config, ["bin", $fig_bin, 1]);      push(@$Config, ["bin", $fig_bin, 1]);
160      push(@$Config, ["ext_bin", $env_bin, 1]);      push(@$Config, ["ext_bin", $env_bin, 1]);
161        push(@$Config, ["common_runtime", $env_dir, 1]);
162        push(@$Config, ["arch", $ENV{FIGCONFIG_ENV}, 1]);
163        push(@$Config, ["var", "$fig/var", 1]);
164      push(@$Config, ["data", $data, 1]);      push(@$Config, ["data", $data, 1]);
165      push(@$Config, ["global", "$data/Global", 1]);      push(@$Config, ["global", "$data/Global", 1]);
166      push(@$Config, ["organisms", "$data/Organisms", 1]);      push(@$Config, ["organisms", "$data/Organisms", 1]);
167      push(@$Config, ["RC", "$fig_disk/FIG/ResolutionCenter", 1]);      push(@$Config, ["RC", "$fig_disk/FIG/ResolutionCenter", 1]);
168      push(@$Config, ["NR", "$fig_disk/FIG/NR", 1]);      push(@$Config, ["NR", "$fig_disk/FIG/NR", 1]);
169      push(@$Config, ["temp", "$fig_disk/FIG/Tmp", 1]);      push(@$Config, ["temp", "$fig_disk/FIG/Tmp", 1]);
170      push(@$Config, ["temp_url", "http://$hostname/FIG-Tmp", 1]);      push(@$Config, ["sproutData", $sproutData, 1]);
171      push(@$Config, ["cgi_url", "http://$hostname/FIG", 1]);  
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    
181      #      #
182      # Add values for a relative base href of temp and CGI pages.  The latter      # Add values for a relative base href of temp and CGI pages.  The latter
# Line 155  Line 184 
184      # sense to derive the above 2 values from these.  -- GJO      # sense to derive the above 2 values from these.  -- GJO
185      #      #
186    
187      push(@$Config, ["temp_base", "/FIG-Tmp/", 1]);      push(@$Config, ["temp_base", "$sandbox/FIG-Tmp/", 1]);
188      push(@$Config, ["cgi_base", "/FIG/", 1]);      push(@$Config, ["cgi_base", "$sandbox/FIG/", 1]);
189  }  }
190    
191  sub compute_environment  sub compute_environment
# Line 167  Line 196 
196    
197      push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);      push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);
198      push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);      push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);
199        push(@$Env, ["RTSITECONFIGDIR", "\$RTROOT/config", 0]);
200      push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);      push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);
201      push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);      push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);
202      push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);      push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);
# Line 181  Line 211 
211      #      #
212    
213      my @path = ();      my @path = ();
     push(@path, $env_bin);  
214      push(@path, $fig_bin);      push(@path, $fig_bin);
215        push(@path, $env_bin);
216      push(@path, "$fig_disk/bin");      push(@path, "$fig_disk/bin");
217    
218      push(@$Env, ["PATH", join(":", @path), 1]);      push(@$Env, ["PATH", join(":", @path), 1]);
219    
220      push(@$Env, ["LD_LIBRARY_PATH", "${env_lib}", 1]);      #
221        # Compute  LD_LIBRARY_PATH.
222        #
223        # Some packages, like mysql, place their shared libs in subdirectories
224        # of the libdir.
225        #
226    
227        my @ld_path = ($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    
274        my @perllib = grep({ $_ ne "." } @INC,
275                           $release_lib,
276                           "$release_lib/FigKernelPackages",
277                           "$fig_disk/config");
278    
279        push(@$Env, ["PERL5LIB", join(":", @perllib), 1]);
280  }  }
281    
282  sub configure_python  sub configure_python
# Line 210  Line 299 
299      chomp $py_version;      chomp $py_version;
300      print "Python version $py_version\n";      print "Python version $py_version\n";
301    
302      $OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";      #
303        # Python figures this out for us.
304        #$OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
305    
306      my @path = ();      my @path = ();
307      push(@path, $OtherConfig->{python_site_path});      #push(@path, $OtherConfig->{python_site_path});
308      push(@path, "$release_lib");      push(@path, "$release_lib");
309      push(@path, "$fig_disk/config");      push(@path, "$fig_disk/config");
310      push(@$Env, ["PYTHONPATH", join(":", @path), 1]);      push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
# Line 247  Line 338 
338      #      #
339      # Special case for the mac.      # Special case for the mac.
340      #      #
341        # RDO 20040603 - don't do this any more; we want to pick up
342        # the python we ship.
343        #
344    
345      if ($ENV{FIGCONFIG_ENV} eq "mac")      if (0 && $ENV{FIGCONFIG_ENV} eq "mac")
346      {      {
347          #          #
348          # We'd like to use the MacPython that is installed          # We'd like to use the MacPython that is installed
# Line 272  Line 366 
366      $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";      $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
367      if (-x $python)      if (-x $python)
368      {      {
369            #
370            # The mac doesn't seem to like the long #! lines, so we'll use poundbang env.
371            #
372            if ($ENV{FIGCONFIG_ENV} =~ /^mac/)
373            {
374                $OtherConfig->{python_require_poundbang_env} = 1;
375            }
376          return $python;          return $python;
377      }      }
378    
# Line 324  Line 425 
425              print $fh "export $name\n";              print $fh "export $name\n";
426          }          }
427      }      }
428        print $fh "alias rtpath='source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.sh'\n";
429  }  }
430    
431  sub write_csh_init  sub write_csh_init
# Line 354  Line 456 
456          }          }
457      }      }
458    
459        #
460        # Alias for RT stuff.
461        #
462        print $fh "alias rtpath 'source \$RTDIST/releases/\$RTCURRENT/ReleaseTools/RTPath.csh'\n";
463  }  }
464    
465  sub run_script  sub run_script
# Line 534  Line 640 
640    
641      print $fh "use FIG_Config;\n";      print $fh "use FIG_Config;\n";
642      print $fh "\n";      print $fh "\n";
643        print $fh "#### END tool_hdr ####\n\n"
644  }  }
645    
646  sub write_tool_hdr_python  sub write_tool_hdr_python
# Line 552  Line 659 
659      }      }
660      print $fh "\n";      print $fh "\n";
661    
662      print $fh "import sys\n";      print $fh "import sys, os\n";
663    
664    
665      print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";      print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
666    
667        #
668        # Append the perl path to the environment, for use later with CallPerl.
669        #
670    
671        my $perlpath = join(":", @INC, $release_lib, "$release_lib/FigKernelPackages", "$fig_disk/config");
672        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      print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";      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";      print $fh "# to point at the correct locations in the release directory.\n";
683      print $fh "#BEGIN switch_to_release generated code\n";      print $fh "#BEGIN switch_to_release generated code\n";
# Line 567  Line 688 
688    
689      print $fh "import FIG_Config\n";      print $fh "import FIG_Config\n";
690      print $fh "\n";      print $fh "\n";
691        print $fh "#### END tool_hdr_py ####\n\n"
692    }
693    
694    sub write_rtconfig
695    {
696        my($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        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    
715        print $fh "RTPERL5LIB=$perlpath\n";
716    
717        print $fh "RTPYTHONIMPORTS=FIG_Config\n";
718        print $fh "RTPERLIMPORTS=FIG_Config\n";
719        print $fh "RTSETENV=BLASTMAT=$fig_disk/BLASTMAT\n";
720        print $fh "RTSETENV=FIG_HOME=$fig_disk\n";
721        print $fh "#RTLD_LDPATH=$OtherConfig->{ld_library_path}\n";
722  }  }
723    
724  setup_directories("$fig_disk/bin",  setup_directories("$fig_disk/bin",
# Line 581  Line 733 
733  configure_std_fig_environment();  configure_std_fig_environment();
734  configure_python();  configure_python();
735  configure_environment_specific();  configure_environment_specific();
736    # configure_database();
737    
738  finalize_server_scripts();  finalize_server_scripts();
739    
# Line 619  Line 772 
772  write_tool_hdr_python(\*FH);  write_tool_hdr_python(\*FH);
773  close(FH);  close(FH);
774    
775    open(FH, ">$fig_disk/config/RTConfig") or die "Cannot write $fig_disk/config/RTConfig: $!";
776    write_rtconfig(\*FH);
777    close(FH);
778    
779  unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");  unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
780    
781  require FigCommon::SwitchRelease;  require FigCommon::SwitchRelease;
782    
783    #
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    $ENV{PERL5LIB} = (map { $_->[1] } grep { $_->[0] eq "PERL5LIB"} @$Env)[0];
791    
792  &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});  &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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