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Commit b60f6802 authored by Gautier Koscielny's avatar Gautier Koscielny
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First official release of the Alternative Splicing Toolkit as part of Ensembl 

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misc-scripts/alternative_splicing/AltSplicingToolkit/AUTHORS 0 → 100644
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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>.
misc-scripts/alternative_splicing/AltSplicingToolkit/BUGS 0 → 100644
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-*- 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.
misc-scripts/alternative_splicing/AltSplicingToolkit/COPYING 0 → 100644
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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.
misc-scripts/alternative_splicing/AltSplicingToolkit/ChangeLog 0 → 100644
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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.
misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL 0 → 100644
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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
misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL.configure 0 → 100644
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Installation Instructions
*************************
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
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This file is free documentation; the Free Software Foundation gives
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Basic Installation
==================
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misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.am 0 → 100644
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#
# Author: Gautier Koscielny <koscieln@ebi.ac.uk> 2008 - 2010
#
# Master Makefile for alternative splicing toolkit.
SUBDIRS = src
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