Newer versions of SPIM are self-contained downloads
(and use Qt.)
Suggest that they be installed from the website:
http://spimsimulator.sourceforge.net/
This is an older text processing tool that is useful for doing alignment
of trailing characters (e.g., block of /* */ comments).
Signed-off-by: Adam Vandenberg <flangy@gmail.com>
* After seven years, libmikmod is back to active status.
* Change to the new Homepage.
* Upgrade to version 3.2.0b3 using the new tarball.
* Use the sha256 listed on the website.
* Remove all the autoreconf related commands and associated deps.
* Use the correct -Og or O2 for debug.
* Adjust the --with-debug option description to reflect that.
* Add the ENV.x11 rather than three configure flags for --with-x.
* Remove the --with-osx because it finds we are osx correctly.
* Remove the --with-debug=no, as it is the default.
* Keep the four inreplaces, as they are all still needed.
* All patches are merged upstream in HEAD. Noted in formula.
Signed-off-by: Adam Vandenberg <flangy@gmail.com>
GMAP/GSNAP is a widely used tool for alignment of high-throughput sequence data.
See details about GMAP/GSNAP here:
http://research-pub.gene.com/gmap
Here is the referencable peer-reviewed paper:
Thomas D. Wu and Colin K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21:1859-1875
PUBMED ID 15728110 full citation at http://www.ncbi.nlm.nih.gov/pubmed/15728110
Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Git can cache credentials used when accessing remotes over HTTP; this
helper provides integration with the OS X keychain.
Signed-off-by: Jack Nagel <jacknagel@gmail.com>
redis trunk doesn't propagate CC to the Lua build correctly, so just
pass it on the command-line because I'm lazy.
Signed-off-by: Jack Nagel <jacknagel@gmail.com>
- Fix discarded LDFLAGS so linking works as expected (required for
universal build).
ClosesHomebrew/homebrew#11178.
Signed-off-by: Jack Nagel <jacknagel@gmail.com>
jscoverage-0.5.1 has a file with hardcoded gcc and g++, named
configure.gnu. inreplace those with ENV.cc and ENV.cxx.
It also has three places in js/configure where the conftest uses
int main {
but also has two return commands. The first return command,
return;
does not return a value. The second one does `return 0;`.
This causes an error building with clang during configure
because `int main` should return a value. inline patch those
by removing the extra return command so that it does a `return 0;`
All four of these issues have been bug reported to their tracker,
and the formula comments include a link to the bug report. The
issues exist in HEAD. This now builds with all the compilers in
Lion and Snow Leopard, though no runtime tests were done as this
is unfamiliar software.
FixesHomebrew/homebrew#11600.
ClosesHomebrew/homebrew#11611.
Signed-off-by: Jack Nagel <jacknagel@gmail.com>
bash completion from scala-dist is still at 2.9.1 but changelog
doesn't mention any parameter changes to scala or scalac.
ClosesHomebrew/homebrew#11627.
Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Adam Vandenberg
kuperman
Anthony Ramine
Jannis Leidel
Jose Diaz-Gonzalez
nibbles 2bits
Sundar Raman
Justin Hileman
Angel Pizarro
Frank Celler
Fabian Zeindl
Will Ross
Julien Blanchard
jnothman
Jack Nagel
Mike McQuaid
Shawn Walker
Camillo Lugaresi
Michal Bendowski
Stian Eikeland
Jiyoon Jang
Doug Mayer
Ealden Esto E. Escanan
Anatol Pomozov
Xiyue Deng
Christian Köstlin
Nils Caspar
Berk D. Demir