3 files changed, 29 insertions, 26 deletions

diff --git a/biology/crux/Makefile b/biology/crux/Makefile
index 8223812249a2..f483a50b21ef 100644
--- a/biology/crux/Makefile
+++ b/biology/crux/Makefile
@@ -6,8 +6,8 @@
 #
 
 PORTNAME=      crux
-PORTVERSION=   1.1.0
-PORTREVISION=	1
+PORTVERSION=   1.2.0
+PORTREVISION=  1
 CATEGORIES=    biology python
 MASTER_SITES=  http://www.canonware.com/download/Crux/
 
diff --git a/biology/crux/distinfo b/biology/crux/distinfo
index e7efa757dd20..1d83b0201d63 100644
--- a/biology/crux/distinfo
+++ b/biology/crux/distinfo
@@ -1,3 +1,3 @@
-MD5 (crux-1.1.0.tar.bz2) = ffafa44e7b3886d2a86168da23cf63a5
-SHA256 (crux-1.1.0.tar.bz2) = 0f3be31d426a2c94c30213371aa1320a1c711a2870b78bace6f5eba8b01a93da
-SIZE (crux-1.1.0.tar.bz2) = 1188496
+MD5 (crux-1.2.0.tar.bz2) = 07e3a38e82f17d7ae5caea1be622bb14
+SHA256 (crux-1.2.0.tar.bz2) = 11f677e8bf62db69e75271670ea50fb5a23c8a2c526fa9d16ccf2e736e5212c5
+SIZE (crux-1.2.0.tar.bz2) = 1187274
diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
index 146a86412c1c..f95c872254d3 100644
--- a/biology/crux/pkg-plist
+++ b/biology/crux/pkg-plist
@@ -2,60 +2,63 @@
 bin/crux
 bin/redpoint
 bin/MrRogers
-%%PYTHON_SITELIBDIR%%/Crux/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
 %%PYTHON_SITELIBDIR%%/Crux/Character.so
 %%PYTHON_SITELIBDIR%%/Crux/Config.py
 %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
 %%PYTHON_SITELIBDIR%%/Crux/Copying.py
 %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
-%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
+%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/Fasta.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Newick.so
 %%PYTHON_SITELIBDIR%%/Crux/Taxa.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Cx.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMath.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMat.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxNewickLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxRi.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/CxDistMatrixLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMath.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMat.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxNewickLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxRi.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Cx.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree/CxLik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/CxLik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
+%%PYTHON_SITELIBDIR%%/Crux/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Parsing.so
 share/Crux/lib/libCx.so
 share/Crux/parsers/Fasta.log
 share/Crux/parsers/Fasta.pickle
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT