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File glimmer.spec of Package Glimmer

# spec file for package Glimmer
#
# Copyright (c) 2012 Scott R. Santos (santos@auburn.edu), Auburn University
# This file and all modifications and additions to the pristine
# package are under the same license as the package itself.
#
# Please submit bugfixes or comments via
# <halocaridina@gmail.com>
##

Summary:			Glimmer is a system for finding genes in microbial DNA
Name:				glimmer
Version:			302
Release:			1
License:			OSI Certified Open Source Software
Group:				Other
URL:				http://cbcb.umd.edu/software/glimmer/
Source0:			%{name}%{version}.tar.gz
BuildRoot:			%{_tmppath}/%{name}%{version}-build
BuildRequires:  		gcc-c++
Patch0:				glimmer.patch

%description
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, 
archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov 
models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, 
described in our Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0 , 
uses a combination of Markov models from 1st through 8th-order, weighting each model according to its 
predictive power. Glimmer uses 3-periodic nonhomogenous Markov models in its IMMs. 

Glimmer was the primary microbial gene finder used at The Institute for Genomic Research (TIGR), where it was 
first developed, and has been used to annotate the complete genomes of over 100 bacterial species from TIGR 
and other labs. Glimmer3 predictions are available for all NCBI RefSeq bacterial genomes at their ftp site.

Compiled with the patch from here:

http://seqanswers.com/forums/showthread.php?t=2790

%package        scripts
Summary:        Scripts for use with Glimmer
Group:          Other

%description    scripts
Scripts for use with Glimmer.

%prep
%setup -q -n glimmer3.02
%patch0 -p1

%build
cd src/ && %__make && cd ..

%install
test "%{buildroot}" != "/" && %__rm -rf %{buildroot}

%__mkdir_p %{buildroot}/%{_bindir}
%__cp bin/anomaly %{buildroot}%{_bindir}
%__cp bin/build-fixed %{buildroot}%{_bindir}
%__cp bin/build-icm %{buildroot}%{_bindir}
%__cp bin/entropy-profile %{buildroot}%{_bindir}
%__cp bin/entropy-score %{buildroot}%{_bindir}
%__cp bin/extract %{buildroot}%{_bindir}
%__cp bin/glimmer3 %{buildroot}%{_bindir}
%__cp bin/long-orfs %{buildroot}%{_bindir}
%__cp bin/multi-extract %{buildroot}%{_bindir}
%__cp bin/score-fixed %{buildroot}%{_bindir}
%__cp bin/start-codon-distrib %{buildroot}%{_bindir}
%__cp bin/test %{buildroot}%{_bindir}
%__cp bin/uncovered %{buildroot}%{_bindir}
%__cp bin/window-acgt %{buildroot}%{_bindir}

%__cp scripts/g3-from-scratch.csh %{buildroot}%{_bindir}
%__cp scripts/g3-from-training.csh %{buildroot}%{_bindir}
%__cp scripts/g3-iterated.csh %{buildroot}%{_bindir}
%__cp scripts/get-motif-counts.awk %{buildroot}%{_bindir}
%__cp scripts/glim-diff.awk %{buildroot}%{_bindir}
%__cp scripts/match-list-col.awk %{buildroot}%{_bindir}
%__cp scripts/not-acgt.awk %{buildroot}%{_bindir}
%__cp scripts/upstream-coords.awk %{buildroot}%{_bindir}

%clean
test "%{buildroot}" != "/" && %__rm -rf %{buildroot}

%files
%defattr(-,root,root)
%doc glim302notes.pdf LICENSE
%{_bindir}/anomaly
%{_bindir}/build-fixed
%{_bindir}/build-icm
%{_bindir}/entropy-profile
%{_bindir}/entropy-score
%{_bindir}/extract
%{_bindir}/glimmer3
%{_bindir}/long-orfs
%{_bindir}/multi-extract
%{_bindir}/score-fixed
%{_bindir}/start-codon-distrib
%{_bindir}/test
%{_bindir}/uncovered
%{_bindir}/window-acgt

%files scripts
%{_bindir}/g3-from-scratch.csh
%{_bindir}/g3-from-training.csh
%{_bindir}/g3-iterated.csh
%{_bindir}/get-motif-counts.awk
%{_bindir}/glim-diff.awk
%{_bindir}/match-list-col.awk
%{_bindir}/not-acgt.awk
%{_bindir}/upstream-coords.awk

%changelog
* Fri Dec 07 2012 Scott Santos <santos@auburn.edu> - 302-2
- move supplemental scripts to own package - 302-2

* Sun Nov 25 2012 Scott Santos <santos@auburn.edu> - 302-1
- initial release - 302-1