README file for exonerate package.
FAQs
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General
=======
What does this package contain ?
------------------------------
This package contains exonerate and its libraries.
Exonerate is a general purpose tool for biological
sequence comparison. The libraries are provided with
the intention of providing general utility for development
of various sequence comparison programs.
This package was previously called ensembl-nci
to reflect the Nucleotide Comparison Interface
that was behind much of the code. This interface has now
being dropped, along with the name.
How do I get the latest version ?
-------------------------------
The latest version is in the exonerate CVS repository
available from http://www.ensembl.org/
To do this with anonymous CVS, you need to do:
(with bash)
export CVSROOT=":pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl"
(with tcsh)
setenv CVSROOT ":pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl"
Then:
cvs login # (password CVSUSER)
cvs co exonerate
This will checkout the CVS head which is unstable.
To get the latest stable version, use:
cvs co -r branch-0-9-0 exonerate
or download the latest tarball from:
http://www.ebi.ac.uk/~guy/exonerate/
How do I build exonerate ?
------------------------
If you have a version from CVS, it is a development version,
so you need a machine with the GNU autoconf/automake tools.
You need to do:
./maintain.sh ready
Then proceed as for a tarball releases.
For a tarball release, you just need to do:
./configure
make
Use "./configure --help" to see the configure options.
If you are using a stable (tarball) version,
then just use ./configure then make.
It is a good idea to also run "make check" to ensure
that everything is working OK on you machine.
How do I build exonerate for profiling with gprof ?
-------------------------------------------------
make clean
./configure --disable-assert --enable-gprof
make
What is glib ?
------------
glib is the C library which gtk is based upon.
It is highly portable, and provides useful data structures,
and convenient functions for handling things like dynamic
libraries.
glib needs to be installed with at least version 1.2.0
to use with exonerate. You can check this with the
command `glib-config --version`
glib is probably already installed on your system,
but is available from http://www.gtk.org/
Under which license is the code made available ?
----------------------------------------------
GPL, version 3. See: http://www.gnu.org/licenses/gpl.txt
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 GNU General Public License for more details.
(included in the file COPYING distributed with this package)
Which platforms will this run on ?
--------------------------------
The code has mostly been developed on GNU/Linux systems,
and is used mostly on Linux and alpha/OSF1 machines,
so it works well with those, but should be portable
to other architectures.
Is there a paper describing this ?
--------------------------------
See: BMC Bioinformatics 2005, 6:31
"Automated generation of heuristics for biological sequence comparison"
http://www.biomedcentral.com/1471-2105/6/31
More papers to follow.
How do I report a bug ?
---------------------
Run the supplied script buginfo.sh in the top level directory
to report info about the system on which you have found a bug.
You can also try running "make check" to ensure
that all the tests pass on your platform.
Please supply enough information to make the bug reproducible,
including a command line and sample sequences where appropriate.
Then send all this info to guy@ebi.ac.uk or ensembl-dev@ebi.ac.uk
How do I contribute to the project ?
----------------------------------
PLEASE DO NOT TRY TO CHECK CODE DIRECTLY INTO CVS.
If you have a fix for a bug, or would like to contribute
a new feature or optimisation to the package, then please
prepare a patch for review.
The code in the patch must be available under the LGPL.
Unified diff output with 5 lines of context is the preferred
format for patches. The easiest way to do this is to use CVS
to produce a diff against the version currently in the repository.
From the exonerate directory in the modified version, do:
cvs diff -u -5
What else is there in this package ?
----------------------------------
This code base also include the program iPCRess
(In-silico PCR Experiment Simulation System),
and also some utilities for manipulation of large fasta files.
These are not installed by default, but can be found
in the src/util directory.
I hope the names are fairly self explanatory.
Use ./fasta<whatever> -h for more info.
The utilities are:
esd2esi fasta2esd fastaannotatecdna fastachecksum
fastaclean fastaclip fastacomposition fastadiff fastaexplode
fastafetch fastahardmask fastaindex fastalength fastanrdb
fastaoverlap fastareformat fastaremove fastarevcomp fastasoftmask
fastasort fastasplit fastasubseq fastatranslate fastavalidcds
How can I get more help ?
-----------------------
Using any of the programs with -h or --help will
give you more information about the options available.
There are man pages available for exonerate, exonerate-server and ipcress.
If they have not yet been installed, you can view them
from the source distribution using:
nroff -man doc/man/man1/exonerate.1 | less
nroff -man doc/man/man1/exonerate-server.1 | less
nroff -man doc/man/man1/ipcress.1 | less
Failing that, you can email me: guy@ebi.ac.uk
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Exonerate specific questions
============================
How do I make exonerate run faster ?
----------------------------------
Checklist:
o Did you ./configure --disable-assert ?
o Are the sequences being read from local disk ?
o Are the sequences repeat masked with RepeatMasker and dust ?
o Are you using the default parameters ?
o Are you multiplexing the query and using the -M flag ?
Quick and dirty searching parameters:
-w 16 -t 80 -H 80 -D 5 -a 1000 -m 1024
Why is it taking ages to build ?
------------------------------
Exonerate uses the C4 dynamic programming library,
which optimises the viterbi algorithm by using code
generation. About 1,000,000 of code is generated
by default for efficient viterbi calculations
of the various models.
All the generated code for this is written into
the codegen directory.
The environment variables $C4_CC, $C4_LD, $C4_CCFLAGS
and $C4_LDFLAGS can be used to change the behaviour
during the code generation. The linking can be modified
by using $C4_AR, $C4_AR_INIT and $C4_AR_APPEND
(see examples below).
If you only want to use exonerate for a couple of
models, you can speed up the compilation (and reduce
the executable size) by specifying which models to
generate code for by using $C4_COMPILED_MODELS.
eg. export C4_COMPILED_MODELS="est2genome protein2genome"
If you try to run exonerate on a model for which it does
not have code generation, a warning is issued, and the
viterbi algorithm will run much more slowly.
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--
Farm Notes:
----------
Linux:
# For Intel CC:
# setenv PATH /opt/intel_cc_80/bin/:${PATH}
# setenv LD_LIBRARY_PATH /opt/intel_cc_80/lib
# setenv CC "icc"
# setenv CFLAGS "-O3 -axWK"
# setenv C4_CC $CC
# setenv C4_CFLAGS "$CFLAGS"
./maintain.sh ready
make clean
rm config.cache
rm -rf codegen
./configure --enable-largefile
--prefix=/acari/work2/gs2/gs2/local/archive/Linux/1.0.0
make
make install-strip
TRU64:
rm -f config.cache
make clean
# setenv C4_AR "/bin/ar"
# setenv C4_AR_INIT "czr"
# setenv C4_AR_APPEND "zr"
# setenv CC "cc"
# setenv CFLAGS "-O3 -arch ev6 -fast"
# setenv CFLAGS "-O3 -arch ev67 -fast"
setenv C4_CC $CC
setenv C4_CFLAGS "$CFLAGS"
./configure \
--prefix=/acari/work2/gs2/gs2/local/archive/OSF1/1.0.0
make
make install-strip
Darwin:
# export C4_AR_INIT="csq"
# export C4_AR_APPEND="sq"
./configure --enable-largefile --prefix=/wherever/
make
make install-strip
ia64:
./configure --enable-largefile
--prefix=/acari/work2/gs2/gs2/local/archive/ia64/1.0.0
Making .deb
dh_make -e guy@ebi.ac.uk -f ../exonerate-1.0.0.tar.gz
vi debian/control
Section: science
Build-Depends: libglib1.2-dev
as root: dpkg-buildpackage
--