AvocadoDB 0.3.9

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
GMAP/GSNAP 2012-04-10

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>
Install `mongod.conf` if one isn't present.

Reduce the amount of mindless copy/paste required by one.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
git-encrypt 0.3.3

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
libmikmod 3.2.0b3

* 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>
Grok 0.9.2

Closes #11409.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
GDAL: Reset ARCHFLAGS in case they've been set outside

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
libcaca 0.99.beta18

The formula now properly depends on imlib2 to enable support of other
formats than BMP.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
tal 1.9

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>
Remove libsgml

Formula download was removed.
Nothing in Homebrew depends on this (Io used to, but now vends
its own version.)

Closes #11244.
uWSGI 1.1.2
Remove SPIM.

Newer versions of SPIM are self-contained downloads
(and use Qt.)

Suggest that they be installed from the website:
http://spimsimulator.sourceforge.net/
Remove shen.

The Shen 3.1 source tarball has frequent in-place changes, which causes
the formula checksum to break.

Would accept this as a head-only formula in Homebrew-ALT, or if upstream
stops doing these sorts of non-versioned updates.
tests: setup and teardown cleanups

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
tests: replace tests script with rake-based runner

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
fbida 2.09

Added a makefile patch to fbida-2.09

The patch has also been submitted upstream to the author.

Fixes #10801.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
tests: silence test_detect_failed_configure

The standard `nostdout` method doesn't work here because Formula#system
does some redirection of its own; both stdout and stderr have to be of
the same type, so just do it manually here.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
gbdfed 1.6

gbdfed is a font editor for bitmap fonts: http://sofia.nmsu.edu/~mleisher/Software/gbdfed/

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
tests: silence `zip` output in test_bucket

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
GHC: Refuse to install on Leopard

The binary releases of the GHC compiler are no longer compatible with OS X
10.5.

Fixes #11671.