diff --git a/bowtie.spec b/bowtie.spec new file mode 100644 index 0000000..32b9c47 --- /dev/null +++ b/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 - 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 - 0.12.5-3 +- really fix compilation flags + +* Wed Aug 25 2010 Adam Huffman - 0.12.5-2 +- fix compilation flags + +* Mon Aug 2 2010 Adam Huffman - 0.12.5-1 +- initial version + diff --git a/cufflinks.spec b/cufflinks.spec new file mode 100644 index 0000000..ca8056d --- /dev/null +++ b/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 - 0.9.3-1 +- initial version +- patch to fix bam.h header search and to link boost_thread-mt diff --git a/din.spec b/din.spec new file mode 100644 index 0000000..c42e3a2 --- /dev/null +++ b/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 - 1.5.8.0-3 +- official description + +* Fri Apr 29 2011 Adam Huffman - 1.5.8.0-2 +- BR for new subpackage libircclient-devel + +* Fri Apr 29 2011 Adam Huffman - 1.5.8.0-1 +- update patches for new version +- new upstream release +- add fftw and automake BR + +* Sun Feb 13 2011 Adam Huffman - 1.4.3-1 +- initial version +- look in Fedora location for Tcl headers +- store data in /usr/share, not /var diff --git a/libircclient.spec b/libircclient.spec new file mode 100644 index 0000000..6c8be00 --- /dev/null +++ b/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 - 1.3-6 +- better soname fix + +* Fri Apr 29 2011 Adam Huffman - 1.3-5 +- fix soname + +* Fri Apr 29 2011 Adam Huffman - 1.3-4 +- ignore provided makefiles +- devel subpackage + +* Fri Apr 29 2011 Adam Huffman - 1.3-3 +- remove static library + +* Sat Feb 12 2011 Adam Huffman - 1.3-2 +- fixes taken from Arch package to help with din +- build .so + +* Wed Jun 2 2010 Conrad Meyer - 1.3-1 +- First attempt at a package (crappy) diff --git a/mmseq.spec b/mmseq.spec new file mode 100644 index 0000000..362bd22 --- /dev/null +++ b/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 - 0.9.9-2 +- fix compilation flags for debuginfo +- include shell and Ruby scripts + +* Mon Apr 4 2011 Adam Huffman - 0.9.9-1 +- initial version + diff --git a/tabix.spec b/tabix.spec new file mode 100644 index 0000000..113ef48 --- /dev/null +++ b/tabix.spec @@ -0,0 +1,92 @@ +Name: tabix +Version: 0.2.4 +Release: 1%{?dist} +Summary: Generic indexer for TAB-delimited genome position files + +Group: Applications/Engineering +License: MIT +URL: http://samtools.sourceforge.net/tabix.shtml +Source0: http://download.sourceforge.net/samtools/%{name}-%{version}.tar.bz2 +BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) + +BuildRequires: zlib-devel +BuildRequires: perl(Exporter) +BuildRequires: perl(ExtUtils::MakeMaker) +BuildRequires: perl(Test::Simple) +Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version)) + +%{?perl_default_filter} + +%description +Tabix indexes a TAB-delimited genome position file in.tab.bgz and +creates an index file in.tab.bgz.tbi when region is absent from the +command-line. The input data file must be position sorted and +compressed by bgzip which has a gzip(1) like interface. After +indexing, tabix is able to quickly retrieve data lines overlapping +regions specified in the format "chr:beginPos-endPos". Fast data +retrieval also works over network if URI is given as a file name and +in this case the index file will be downloaded if it is not present +locally. + +%prep +%setup -q + + +%build +make %{?_smp_mflags} + +# Perl module not built by default - in separate subdir. +cd perl +%{__perl} Makefile.PL INSTALLDIRS=vendor OPTIMIZE="%{optflags}" +make %{?_smp_mflags} + + +%install +rm -rf %{buildroot} +mkdir -p %{buildroot}%{_bindir} +mkdir -p %{buildroot}%{_mandir}/man1 + +install -m 0755 bgzip %{buildroot}%{_bindir} +install -m 0755 tabix %{buildroot}%{_bindir} +install -m 0755 tabix.py %{buildroot}%{_bindir} +install -m 0644 tabix.1 %{buildroot}%{_mandir}/man1 + +cd perl +make pure_install DESTDIR=%{buildroot} +find %{buildroot} -type f -name .packlist -exec rm -f {} ';' +find %{buildroot} -depth -type d -exec rmdir {} 2>/dev/null ';' +%{_fixperms} %{buildroot}/* +rm %{buildroot}%{perl_vendorarch}/auto/Tabix/Tabix.bs + +%check +cd perl +make test + +%clean +rm -rf %{buildroot} + + +%files +%defattr(-,root,root,-) +%doc NEWS ChangeLog example.gtf.gz example.gtf.gz.tbi TabixReader.java + +%{_bindir}/bgzip +%{_bindir}/tabix +%{_bindir}/tabix.py + +%{_mandir}/man1/tabix.1* + +%{perl_vendorarch}/* +%exclude %dir %{perl_vendorarch}/auto/ + + +%changelog +* Tue Apr 19 2011 Adam Huffman - 0.2.4-1 +- new upstream release + +* Tue Mar 22 2011 Adam Huffman - 0.2.3-1 +- initial version +- include perl code not compiled by default +- remove static library +- remove Tabix.bs +- Java example in docs diff --git a/yoshimi.spec b/yoshimi.spec new file mode 100644 index 0000000..d063d9d --- /dev/null +++ b/yoshimi.spec @@ -0,0 +1,109 @@ +Name: yoshimi +Version: 0.060.10 +Release: 1%{?dist} +Summary: Rewrite of ZynAddSubFx aiming for better JACK support + +Group: Applications/Multimedia +License: GPLv2+ +URL: http://sourceforge.net/projects/yoshimi +Source0: http://downloads.sourceforge.net/%{name}/%{name}-%{version}.tar.bz2 +Source1: yoshimi.desktop +Source2: yoshimi.svg +BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) + +BuildRequires: jack-audio-connection-kit-devel +BuildRequires: cmake zlib-devel fontconfig-devel +BuildRequires: fltk-devel fltk-fluid fftw3-devel +BuildRequires: mxml-devel alsa-lib-devel libsndfile-devel +BuildRequires: desktop-file-utils boost-devel + +%description + +Yoshimi is a rewrite of ZynAddSubFx to improve its compatibility with +the Jack Audio Connection Kit. + +ZynAddSubFX is an open source software synthesizer capable of making a +countless number of instrument sounds. It is microtonal, and the instruments +made by it sounds like those from professional keyboards. The program has +effects like Reverb, Echo, Chorus, Phaser... + +%prep +%setup -q + + +%build +cd src +%cmake . +make VERBOSE=1 %{?_smp_mflags} + + +%install +rm -rf %{buildroot} +cd src +make install DESTDIR=%{buildroot} + + +mkdir -p %{buildroot}%{_datadir}/applications +desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1} + +mkdir -p %{buildroot}%{_datadir}/icons/hicolor/scalable/apps +install -m 644 %{SOURCE2} %{buildroot}%{_datadir}/icons/hicolor/scalable/apps/%{name}.svg + +# Fix directory permissions without affecting patch files +chmod 755 %{buildroot}%{_datadir}/%{name}/banks +chmod 755 %{buildroot}%{_datadir}/%{name}/banks/* +chmod 755 %{buildroot}%{_datadir}/%{name}/presets +chmod 755 %{buildroot}%{_datadir}/%{name}/presets/* + +%clean +rm -rf %{buildroot} + +%post +update-desktop-database -q +touch --no-create %{_datadir}/icons/hicolor/scalable/apps/ >&/dev/null || : + +%postun +update-desktop-database -q +if [ $1 -eq 0 ]; then + touch --no-create %{_datadir}/icons/hicolor/scalable/apps >&/dev/null || : + gtk-update-icon-cache %{_datadir}/icons/hicolor/scalable/apps >&/dev/null || : +fi + + +%files +%defattr(-,root,root,-) +%doc 0.060.10.notes COPYING +%{_bindir}/yoshimi +%{_datadir}/%{name}/banks/ +%{_datadir}/applications/%{name}.desktop +%{_datadir}/icons/hicolor/scalable/apps/%{name}.svg +%{_datadir}/%{name}/presets/ + +%changelog +* Sun Apr 17 2011 Adam Huffman - 0.060.10-1 +- new upstream release with further licensing clarification + +* Mon Apr 11 2011 Adam Huffman - 0.060.9-1 +- new upstream release with licence clarification + +* Sun Apr 10 2011 Adam Huffman - 0.060.8-2 +- add COPYING and notes to docs + +* Sat Apr 9 2011 Adam Huffman - 0.060.8-1 +- new upstream release 0.060.8 +- add boost-devel BR +- consistent use of macros +- fix directory permissions for banks/presets + +* Sun Jun 20 2010 Adam Huffman - 0.058-1 +- desktop file and icon added + +* Sun May 16 2010 Adam Huffman - 0.056-1 +- new upstream release, fixing PAD synth patch problems + +* Sun Mar 28 2010 Adam Huffman - 0.055.6-1 +- new upstream bugfilx release + +* Sat Mar 13 2010 Adam Huffman - 0.055.3-1 +- initial version +