Add other spec files for in-progress reviews

bowtie.spec

@@ -0,0 +1,74 @@
+Name:           bowtie
+Version:        0.12.7
+Release:        1%{?dist}
+Summary:        An ultrafast, memory-efficient short read aligner
+
+Group:          Applications/Engineering
+License:        Artistic 2.0
+URL:            http://bowtie-bio.sourceforge.net/index.shtml
+Source0:        http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip
+BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+
+%description
+
+Bowtie, an ultrafast, memory-efficient short read aligner for short
+DNA sequences (reads) from next-gen sequencers. Please cite: Langmead
+B, et al. Ultrafast and memory-efficient alignment of short DNA
+sequences to the human genome. Genome Biol 10:R25.
+
+%prep
+%setup -q
+
+
+%build
+make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}"
+
+
+%install
+rm -rf %{buildroot}
+
+mkdir -p %{buildroot}/%{_bindir}
+mkdir -p %{buildroot}/%{_datadir}/bowtie
+
+
+install -m 0755 bowtie %{buildroot}/%{_bindir}
+install -m 0755 bowtie-build %{buildroot}/%{_bindir}
+install -m 0755 bowtie-inspect %{buildroot}/%{_bindir}
+
+cp -a reads %{buildroot}/%{_datadir}/bowtie/
+cp -a indexes %{buildroot}/%{_datadir}/bowtie/
+cp -a genomes %{buildroot}/%{_datadir}/bowtie/
+cp -a scripts %{buildroot}/%{_datadir}/bowtie/
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc MANUAL NEWS VERSION AUTHORS TUTORIAL
+%dir %{_datadir}/bowtie
+%{_bindir}/bowtie
+%{_bindir}/bowtie-build
+%{_bindir}/bowtie-inspect
+%{_datadir}/bowtie/genomes
+%{_datadir}/bowtie/indexes
+%{_datadir}/bowtie/reads
+%{_datadir}/bowtie/scripts
+
+%changelog
+* Mon Sep 13 2010 Adam Huffman <[email protected]> - 0.12.7-1
+- new upstream release 0.12.7
+- changelog at http://bowtie-bio.sourceforge.net/index.shtml
+
+* Tue Aug 31 2010 Adam Huffman <[email protected]> - 0.12.5-3
+- really fix compilation flags
+
+* Wed Aug 25 2010 Adam Huffman <[email protected]> - 0.12.5-2
+- fix compilation flags
+
+* Mon Aug  2 2010 Adam Huffman <[email protected]> - 0.12.5-1
+- initial version
+

cufflinks.spec

@@ -0,0 +1,59 @@
+Name:		cufflinks
+Version:	0.9.3
+Release:	1%{?dist}
+Summary:	RNA-Seq transcript assembly, differential expression/regulation
+
+Group:		Applications/Engineering
+License:	Boost
+URL:		http://cufflinks.cbcb.umd.edu/
+Source0:	http://cufflinks.cbcb.umd.edu/downloads/%{name}-%{version}.tar.gz
+Patch0:		%{name}-bam-header.patch
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	boost-devel samtools-devel zlib-devel
+BuildRequires:	autoconf automake
+
+
+%description 
+Cufflinks assembles transcripts, estimates their abundances, and tests
+for differential expression and regulation in RNA-Seq samples. It
+accepts aligned RNA-Seq reads and assembles the alignments into a
+parsimonious set of transcripts. Cufflinks then estimates the relative
+abundances of these transcripts based on how many reads support each
+one.
+
+Cufflinks is a collaborative effort between the Laboratory for
+Mathematical and Computational Biology, led by Lior Pachter at UC
+Berkeley, Steven Salzberg's group at the University of Maryland Center
+for Bioinformatics and Computational Biology, and Barbara Wold's lab
+at Caltech.
+
+%prep
+%setup -q
+%patch0 -p1
+
+%build
+autoreconf
+%configure
+make %{?_smp_mflags}
+
+
+%install
+rm -rf %{buildroot}
+make install DESTDIR=%{buildroot}
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc README AUTHORS LICENSE
+%{_bindir}/*
+
+
+%changelog
+* Mon Apr  4 2011 Adam Huffman <[email protected]> - 0.9.3-1
+- initial version
+- patch to fix bam.h header search and to link boost_thread-mt

din.spec

@@ -0,0 +1,77 @@
+Name:		din
+Version:	1.5.8.0
+Release:	3%{?dist}
+Summary:	A musical instrument using multiple Bezier curves
+
+Group:		Applications/Multimedia
+License:	GPLv2
+URL:		http://www.dinisnoise.org
+Source0:	http://din.googlecode.com/files/din-%{version}.tar.gz
+Patch0:		din-build.patch
+Patch1:		din-libs.patch
+Patch2:		din-include.patch
+Patch3:		din-data.patch
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	tcl-devel libircclient-devel SDL-devel liblo-devel
+BuildRequires:	jack-audio-connection-kit-devel mesa-libGL-devel
+BuildRequires:	automake fftw-devel
+
+%description
+
+din is a software musical instrument and audio synthesizer. Bezier
+curves are used to draw and sculpt waveforms, create gating and
+modulation (FM and AM) patterns, and create delay feedback and volume
+patterns. You can also create an unlimited number of drones and sculpt
+their waveforms. It uses JACK to output audio, and supports MIDI, OSC
+and IRC bot for input. din can be extended and customized with Tcl/Tk
+scripts.
+
+
+%prep
+%setup -q
+%patch0 -p1
+%patch1 -p1
+%patch2 -p1 
+%patch3 -p1
+
+%build
+autoreconf
+%configure --localstatedir=/usr/share
+make %{?_smp_mflags}
+
+
+%install
+rm -rf %{buildroot}
+make install DESTDIR=%{buildroot}
+
+chmod 0755 %{buildroot}/%{_datadir}/%{name}/m00
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc README TODO CHANGELOG AUTHORS COPYING BUGS
+%{_bindir}/din
+%{_bindir}/checkdotdin
+%dir %{_datadir}/%{name}
+%{_datadir}/%{name}/*
+
+%changelog
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.5.8.0-3
+- official description
+
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.5.8.0-2
+- BR for new subpackage libircclient-devel
+
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.5.8.0-1
+- update patches for new version
+- new upstream release
+- add fftw and automake BR
+
+* Sun Feb 13 2011 Adam Huffman <[email protected]> - 1.4.3-1
+- initial version
+- look in Fedora location for Tcl headers
+- store data in /usr/share, not /var

libircclient.spec

@@ -0,0 +1,116 @@
+Name:		libircclient
+Version:	1.3
+Release:	6%{?dist}
+Summary:	Library implementing client-server IRC protocol
+Group:		System Environment/Libraries
+License:	LGPLv2+
+URL:		http://libircclient.sourceforge.net/
+Source0:	http://downloads.sourceforge.net/project/libircclient/libircclient/%{version}/libircclient-%{version}.tar.gz
+Patch0:		libircclient-makefile.patch
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	automake
+
+%description
+It is designed to be small, fast, portable and compatible to RFC standards,
+and most IRC clients. libircclient features include:
+  * Full multi-threading support.
+  * Single threads handles all the IRC processing.
+  * Support for single-threaded applications, and socket-based
+    applications, which use select()
+  * Synchronous and asynchronous interfaces.
+  * CTCP support with optional build-in reply code.
+  * Flexible DCC support, including both DCC chat, and DCC file transfer.
+  * Can both initiate and react to initiated DCC.
+  * Can accept or decline DCC sessions asynchronously.
+  * Plain C interface and implementation (possible to use from C++ code,
+    obviously)
+  * Compatible with RFC 1459 and most IRC clients.
+  * Free, licensed under LGPL license.
+  * Good documentation and examples available.
+
+%package devel
+Summary: Header files and libraries for compiling against %{name}
+Group:	 Development/System
+Requires: %name = %version-%release
+
+%description devel
+
+Header files for compiling against %{name}
+
+%prep
+%setup -q
+%patch0
+
+%build
+autoreconf
+%configure --enable-ipv6
+
+cd src
+gcc %{optflags} -fPIC -I../include -c libircclient.c
+ar rc libircclient-%{version}.a libircclient.o
+gcc -shared -Wl,-soname,libircclient.so.1 libircclient.o -o libircclient.so.1
+
+%install
+rm -rf %{buildroot}
+mkdir -p %{buildroot}%{_libdir}
+mkdir -p %{buildroot}%{_includedir}
+mkdir -p %{buildroot}%{_mandir}/man3
+cd src
+
+install -m 0755 libircclient.so.1 %{buildroot}%{_libdir}/
+cd %{buildroot}%{_libdir}
+ln -s libircclient.so.1 libircclient.so
+
+cd -
+cd ../include
+for hdr in libirc*.h ; do
+    install -m 644 "$hdr" %{buildroot}%{_includedir}/
+done
+cd ../doc
+for mp in man/man3/*.3 ; do
+    install -m 644 "$mp" %{buildroot}%{_mandir}/man3/
+done
+
+
+
+%clean
+rm -rf %{buildroot}
+
+%post -p /sbin/ldconfig
+
+%postun -p /sbin/ldconfig
+
+%files
+%defattr(-,root,root,-)
+%doc Changelog LICENSE README THANKS 
+%{_libdir}/libircclient.so.*
+%{_mandir}/man3/*
+
+%files devel
+%defattr(-,root,root,-)
+%doc doc/html examples
+%{_includedir}/*
+%{_libdir}/libircclient.so
+
+
+%changelog
+* Mon May  2 2011 Adam Huffman <[email protected]> - 1.3-6
+- better soname fix
+
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.3-5
+- fix soname
+
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.3-4
+- ignore provided makefiles
+- devel subpackage
+
+* Fri Apr 29 2011 Adam Huffman <[email protected]> - 1.3-3
+- remove static library
+
+* Sat Feb 12 2011 Adam Huffman <[email protected]> - 1.3-2
+- fixes taken from Arch package to help with din
+- build .so
+
+* Wed Jun 2 2010 Conrad Meyer <[email protected]> - 1.3-1
+- First attempt at a package (crappy)

mmseq.spec

@@ -0,0 +1,60 @@
+Name:		mmseq
+Version:	0.9.9
+Release:	2%{?dist}
+Summary:	Haplotype and isoform specific expression estimation for RNA-seq
+
+Group:		Applications/Engineering
+License:	GPLv2+
+URL:		http://www.bgx.org.uk/software/mmseq.html
+Source0:	http://www.bgx.org.uk/software/%{name}_%{version}.zip
+Patch0:		mmseq-sam-header.patch
+Patch1:		mmseq-flags.patch
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	boost-devel samtools-devel gsl-devel zlib-devel
+
+Requires:	ruby
+
+%description
+Software and instructions for fast, scalable isoform expression
+estimation using multi-mapping RNA-seq reads.
+
+%prep
+%setup -q -n %{name}_%{version}
+%patch0 -p1
+%patch1 -p1
+
+%build
+make %{?_smp_mflags} CXXFLAGS="%{optflags}"
+
+
+%install
+rm -rf %{buildroot}
+
+mkdir -p %{buildroot}%{_bindir}
+install -m 0755 bam2hits %{buildroot}%{_bindir}
+install -m 0755 mmseq %{buildroot}%{_bindir}
+install -m 0755 *.sh %{buildroot}%{_bindir}
+install -m 0755 *.rb %{buildroot}%{_bindir}
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc AUTHORS VERSION
+%{_bindir}/bam2hits
+%{_bindir}/mmseq
+%{_bindir}/*.sh
+%{_bindir}/*.rb
+
+%changelog
+* Sat Apr  9 2011 Adam Huffman <[email protected]> - 0.9.9-2
+- fix compilation flags for debuginfo
+- include shell and Ruby scripts
+
+* Mon Apr  4 2011 Adam Huffman <[email protected]> - 0.9.9-1
+- initial version
+