Commit b82571e8 authored by cvs2git's avatar cvs2git
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This commit was manufactured by cvs2svn to create tag 'mergepoint-vega-49

-dev-head'.

Sprout from master 2009-04-20 12:53:38 UTC Susan Fairley <sf7@sanger.ac.uk> 'Remaining part of db_display_name added for Tgut_symbol.'
Cherrypick from master 2010-02-04 11:06:22 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Remove unimplemented methods from synopsis.':
    misc-scripts/add_species_aliases.pl
    misc-scripts/alternative_splicing/AltSplicingToolkit/AUTHORS
    misc-scripts/alternative_splicing/AltSplicingToolkit/BUGS
    misc-scripts/alternative_splicing/AltSplicingToolkit/COPYING
    misc-scripts/alternative_splicing/AltSplicingToolkit/ChangeLog
    misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL
    misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL.configure
    misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.am
    misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.in
    misc-scripts/alternative_splicing/AltSplicingToolkit/NEWS
    misc-scripts/alternative_splicing/AltSplicingToolkit/README
    misc-scripts/alternative_splicing/AltSplicingToolkit/THANKS
    misc-scripts/alternative_splicing/AltSplicingToolkit/aclocal.m4
    misc-scripts/alternative_splicing/AltSplicingToolkit/configure.ac
    misc-scripts/alternative_splicing/AltSplicingToolkit/depcomp
    misc-scripts/alternative_splicing/AltSplicingToolkit/release_notes.txt
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/Constants.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/Main.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.in
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.h
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp
    misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
    misc-scripts/alternative_splicing/Fetch_gff.pl
    misc-scripts/alternative_splicing/README.txt
    misc-scripts/alternative_splicing/load_alt_slice_gff.pl
    misc-scripts/assembly/cleanup_tmp_tables.sql
    misc-scripts/constitutive_exon.pl
    misc-scripts/id_mapping/myRun.ksh
    misc-scripts/id_mapping/utils/myManager.ksh
    misc-scripts/ontology/README
    misc-scripts/ontology/scripts/add_subset_maps.pl
    misc-scripts/ontology/scripts/compute_closure.pl
    misc-scripts/ontology/scripts/demo1.pl
    misc-scripts/ontology/scripts/demo2.pl
    misc-scripts/ontology/scripts/load_OBO_file.pl
    misc-scripts/ontology/sql/table.sql
    misc-scripts/overlapping_regions.pl
    misc-scripts/xref_mapping/FAQ.txt
    misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
    misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm
    misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
    misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
    misc-scripts/xref_mapping/XrefParser/FantomParser.pm
    misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
    misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm
    misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm
    misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
    misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
    misc-scripts/xref_mapping/xrefs_detailed_docs.txt
    modules/Bio/EnsEMBL/DBSQL/SOTermAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm
    modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
    modules/Bio/EnsEMBL/LRGSlice.pm
    modules/Bio/EnsEMBL/SplicingEvent.pm
    modules/Bio/EnsEMBL/SplicingEventFeature.pm
    modules/Bio/EnsEMBL/SplicingTranscriptPair.pm
    sql/patch_54_55_a.sql
    sql/patch_54_55_b.sql
    sql/patch_54_55_c.sql
    sql/patch_54_55_d.sql
    sql/patch_54_55_e.sql
    sql/patch_54_55_f.sql
    sql/patch_54_55_g.sql
    sql/patch_54_55_h.sql
    sql/patch_55_56_a.sql
    sql/patch_55_56_b.sql
    sql/patch_55_56_c.sql
    sql/patch_55_56_d.sql
    sql/patch_56_57_a.sql
    sql/patch_56_57_b.sql
    sql/patch_56_57_c.sql
    sql/patch_56_57_d.sql
    sql/patch_56_57_e.sql
    sql/patch_56_57_f.sql
Delete:
    misc-scripts/protein_match/process_pmach.pl
parent f09f3df0
#!/usr/local/ensembl/bin/perl -w
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
use Getopt::Long qw( :config no_ignore_case );
#-----------------------------------------------------------------------
sub usage {
print("Info:\n");
print <<EOT;
Script to populate the meta table with species aliases.
>> The Release Coordinator runs this script <<
>> when all databases have been copied over <<
>> to the staging severs. <<
The script reads the already existing aliases from the
meta table (meta_key 'species.alias') and adds to this
aliases computed from the species name. It also uses the
information stored for the meta_keys species.taxonomy_id,
species.common_name, species.ensembl_common_name, and
species.ensembl_alias_name as aliases.
If the -n or --dryrun options are *not* specified, the existing
list of aliases is appended with any missing aliases. In any
case, the list of aliases will be displayed on the console.
The database will not be written to if there are no new aliases
to be written to the meta table.
If the -d or --dbname options are *not* used, the script will
iterate over all Core databases. If the -d or --dbname option
*is* used, only that Core database will be examined.
This script assumes that the database is a single-species
database.
This script does not check for alias duplications between
species.
EOT
print("Usage:\n");
printf( "\t%s\t[-n] -h dbhost [-P dbport] \\\n"
. "\t%s\t-u dbuser [-p dbpass] \\\n"
. "\t%2\$s\t[-d dbname]\n",
$0, ' ' x length($0) );
print("\n");
printf( "\t%s\t-?\n", $0 );
print("\n");
print("Arguments:\n");
print("\t-n/--dryrun\t\tDry run, don't write to database\n");
print("\t-h/--host dbhost\tDatabase server host name\n");
print("\t-P/--port dbport\tDatabase server port (optional)\n");
print("\t-u/--user dbuser\tDatabase user name\n");
print("\t-p/--pass dbpass\tUser password (optional)\n");
print("\t-d/--name dbname\tDatabase name (optional)\n");
print("\t-?/--help\t\tDisplays this information\n");
} ## end sub usage
#-----------------------------------------------------------------------
my $dryrun;
my ( $dbhost, $dbport );
my ( $dbuser, $dbpass );
my $dbname;
if (
!GetOptions(
'dryrun|n' => \$dryrun,
'dbhost|host|h=s' => \$dbhost,
'dbport|port|P=i' => \$dbport,
'dbuser|user|u=s' => \$dbuser,
'dbpass|pass|p=s' => \$dbpass,
'dbname|name|d=s' => \$dbname,
'help|?' => sub { usage(); exit } )
|| !defined($dbhost)
|| !defined($dbuser) )
{
usage();
exit;
}
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
'-host' => $dbhost,
'-port' => $dbport,
'-user' => $dbuser,
'-pass' => $dbpass,
);
my $select_stmt = qq(
SELECT DISTINCT LCASE(meta_value)
FROM meta
WHERE meta_key IN (
'species.taxonomy_id', 'species.common_name',
'species.ensembl_common_name', 'species.ensembl_alias_name'
)
AND species_id = 1
);
my $select_aliases_stmt = qq(
SELECT DISTINCT LCASE(meta_value)
FROM meta
WHERE meta_key = 'species.alias'
AND species_id = 1
);
my @dbas = @{ $registry->get_all_DBAdaptors( '-group' => 'Core' ) };
foreach my $dba ( sort { $a->species() cmp $b->species() } @dbas ) {
my $dbh = $dba->dbc()->db_handle();
if ( defined($dbname) && $dbname ne $dba->dbc()->dbname() ) { next }
my $species = $dba->species();
if ( $species =~ /^Ancestral/ ) { next }
printf( "%s{ %s }--\n",
'-' x ( 80 - ( 6 + length($species) ) ), $species );
printf( "Database = %s\n", $dba->dbc()->dbname() );
my %automatic_aliases;
my @existing_aliases;
my $alias = $species;
$automatic_aliases{$alias} = 1;
$alias =~ tr [_] [ ];
$automatic_aliases{$alias} = 1;
$species =~ /^(.)[^_]*_(.*)$/;
$alias = $1 . $2;
$automatic_aliases{$alias} = 1;
$species =~ /^(.)[^_]*_(...).*$/;
$alias = $1 . $2;
$automatic_aliases{$alias} = 1;
$species =~ /^(...)[^_]*_(...).*$/;
$alias = $1 . $2;
$automatic_aliases{$alias} = 1;
{
my $select_sth = $dbh->prepare($select_stmt);
$select_sth->execute();
my $meta_value;
$select_sth->bind_columns( \$meta_value );
while ( $select_sth->fetch() ) {
$automatic_aliases{$meta_value} = 1;
}
}
{
my $select_sth = $dbh->prepare($select_aliases_stmt);
$select_sth->execute();
my $meta_value;
$select_sth->bind_columns( \$meta_value );
while ( $select_sth->fetch() ) {
push( @existing_aliases, $meta_value );
}
}
my @old_aliases;
print("Aliases =\n");
foreach my $existing_alias ( sort(@existing_aliases) ) {
if ( exists( $automatic_aliases{$existing_alias} ) ) {
printf( "\t'%s' (automatic, in database)\n", $existing_alias );
push( @old_aliases, $existing_alias );
} else {
printf( "\t'%s' (in database)\n", $existing_alias );
}
}
map { delete( $automatic_aliases{$_} ) } @old_aliases;
my @new_aliases =
sort { length($a) <=> length($b) || $a cmp $b }
keys(%automatic_aliases);
if (@new_aliases) {
foreach my $new_alias (@new_aliases) {
printf( "\t'%s' (new automatic alias)\n", $new_alias );
}
my $insert_stmt = sprintf(
"INSERT IGNORE INTO meta (species_id, meta_key, meta_value) "
. "VALUES %s",
join(
', ',
map {
sprintf( "( 1, 'species.alias', %s )", $dbh->quote( lc($_) ) )
} @new_aliases
) );
if ( !$dryrun ) {
# Insert new aliases.
$dbh->do($insert_stmt);
print("Status = wrote new aliases to database\n");
} else {
print("Status = dry-run, not writing to database\n");
}
} else {
print("Status = no new aliases to write to database\n");
}
} ## end foreach my $dba ( sort { $a...})
Authors of AltSplicingToolkit.
Gautier Koscielny koscieln@ebi.ac.uk 2008-10-01
========================================================================
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited, and others. All rights reserved.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
Ensembl License for more details.
You should have received a copy of the Ensembl License
along with this program. If not, see <http://www.ensembl.org/info/about/code_licence.html>.
-*- outline -*-
This file lists the bugs you must be aware of. Be sure to check this
file before using programs from the AltSplicingToolkit.
altSpliceFinder must not be used in production if there are ``Serious'' bugs.
* Status: sane
* No known serious or important bugs so far.
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited, and others. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer
in the documentation and/or other materials provided with the
distribution.
3. The name "Ensembl" must not be used to endorse or promote products
derived from this software without prior written permission. For
written permission, please contact helpdesk@ensembl.org
4. Products derived from this software may not be called "Ensembl"
nor may "Ensembl" appear in their names without prior written
permission of the Ensembl developers.
5. Redistributions in any form whatsoever must retain the following
acknowledgement:
"This product includes software developed by Ensembl
(http://www.ensembl.org/)"
THIS SOFTWARE IS PROVIDED BY THE ENSEMBL GROUP ``AS IS'' AND ANY
EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ENSEMBL GROUP OR ITS
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2010-02-03 Gautier Koscielny <koscieln@ebi.ac.uk>
Part of Ensembl release 57
2010-01-15 Gautier Koscielny <koscieln@ebi.ac.uk>
altSpliceFinder modification.
Corrected options to compute statistics (--statistiscs|-s)
2009-12-08 Gautier Koscielny <koscieln@ebi.ac.uk>
altSpliceFinder modification.
* relax mode: option ``-relax|-r'' to compute cassette exons
and mutually exclusive events with relaxed constraints on
flanking exons.
In this mode, flanking exons are required to overlap but the
constraints on the same 3p or 5p end are removed.
* bug on A5SS computation fixed.
* remove spurious STDERR logs on intron retention event
computations.
2009-05-13 Gautier Koscielny <koscieln@ebi.ac.uk>
Release Version 0.4.
* NEWS: Mention the release.
2009-05-12 Gautier Koscielny <koscieln@ebi.ac.uk>
Add constitutives option:
* modify Main.cpp: add an option to compute constitutive exons.
* modify gff/SplicingEventGffGenerator.cpp to compute constitutive
exons only if the constitutives flag is on
Fix bug on constitutive exon computations. An exonic region is said
to be constitutive if and only if the number of transcripts covering
this region is equal to the number of known transcripts for this gene.
Any other exon is subject to a splicing event.
* modify as/RegionChunk.cpp to correctly merge a set of transcript exon
locations.
All previous changes are stored in the release-notes.txt file.
-----
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited, and others. All rights reserved.
Copying and distribution of this file, with or without
modification, are permitted provided the copyright notice and this
notice are preserved.
Installation:
------------
This package uses GNU autoconf generated configure scripts, see the
file INSTALL.configure for generic configure documentation.
Pre-requisites:
--------------
You'll need to install 2 extra libraries that are used by the toolkit:
* The Boost C++ libraries or boost for short (http://www.boost.org)
which provides free portable libraries compatible with standard
libraries.
We currently rely on boost version 1.37.0.
This version can be downloaded at:
http://sourceforge.net/projects/boost/files/
* Log for C++ library or Log4cpp for short.
Log4cpp is a library of C++ classes for flexible logging to files,
syslog, IDSA and other destinations.
See the page of the project on SourceForge:
http://log4cpp.sourceforge.net/
AltSplicingToolkit:
------------------
Once Boost and Log4cpp are installed, simply type:
./configure --prefix=<altsplicingtoolkit installation path> \
--with-boost-include=<boost installation path>/include/boost-1_37 \
--with-boost-lib=<boost installation path>/lib \
--with-log4cpp=<log4cpp installation path>
make
and (as root)
make install
Installation Instructions
*************************
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
2006, 2007, 2008 Free Software Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
Basic Installation
==================
Briefly, the shell commands `./configure; make; make install' should
configure, build, and install this package. The following
more-detailed instructions are generic; see the `README' file for
instructions specific to this package.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions. Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').
It can also use an optional file (typically called `config.cache'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring. Caching is
disabled by default to prevent problems with accidental use of stale
cache files.
If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release. If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.
The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'. You need `configure.ac' if
you want to change it or regenerate `configure' using a newer version
of `autoconf'.
The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system.
Running `configure' might take a while. While running, it prints
some messages telling which features it is checking for.
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
the package.
4. Type `make install' to install the programs and any data files and
documentation.
5. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.
6. Often, you can also type `make uninstall' to remove the installed
files again.
Compilers and Options
=====================
Some systems require unusual options for compilation or linking that
the `configure' script does not know about. Run `./configure --help'
for details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
./configure CC=c99 CFLAGS=-g LIBS=-lposix
*Note Defining Variables::, for more details.
Compiling For Multiple Architectures
====================================
You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory. To do this, you can use GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.
With a non-GNU `make', it is safer to compile the package for one
architecture at a time in the source code directory. After you have
installed the package for one architecture, use `make distclean' before
reconfiguring for another architecture.
On MacOS X 10.5 and later systems, you can create libraries and
executables that work on multiple system types--known as "fat" or
"universal" binaries--by specifying multiple `-arch' options to the
compiler but only a single `-arch' option to the preprocessor. Like
this:
./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CPP="gcc -E" CXXCPP="g++ -E"
This is not guaranteed to produce working output in all cases, you
may have to build one architecture at a time and combine the results
using the `lipo' tool if you have problems.
Installation Names
==================
By default, `make install' installs the package's commands under
`/usr/local/bin', include files under `/usr/local/include', etc. You
can specify an installation prefix other than `/usr/local' by giving
`configure' the option `--prefix=PREFIX'.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
pass the option `--exec-prefix=PREFIX' to `configure', the package uses
PREFIX as the prefix for installing programs and libraries.
Documentation and other data files still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=DIR' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
you can set and what kinds of files go in them.
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
Optional Features
=================
Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.
For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
Particular systems
==================
On HP-UX, the default C compiler is not ANSI C compatible. If GNU
CC is not installed, it is recommended to use the following options in
order to use an ANSI C compiler:
./configure CC="cc -Ae"
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
parse its `<wchar.h>' header file. The option `-nodtk' can be used as
a workaround. If GNU CC is not installed, it is therefore recommended
to try
./configure CC="cc"
and if that doesn't work, try
./configure CC="cc -nodtk"
Specifying the System Type
==========================
There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of machine the package
will run on. Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
CPU-COMPANY-SYSTEM
where SYSTEM can have one of these forms:
OS KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the option `--target=TYPE' to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the