Add initial ebuild for biskit, a structural bioinformatics framework.

3 files changed, 86 insertions, 0 deletions

diff --git a/sci-biology/biskit/Manifest b/sci-biology/biskit/Manifest
new file mode 100644
index 0000000..253fd50
--- /dev/null
+++ b/sci-biology/biskit/Manifest
@@ -0,0 +1,3 @@
+AUX 2.1.0_beta-fix-projectroot.patch 539 RMD160 95298e7235ecd4e04c5262f7a700db1d21249e1b SHA1 1b49b00ee4a349012f2adf43b379c0782d7546a8 SHA256 e8c6b93d6adf9b637037b00e8df6de0466483775db9e7cb6782fa746464b8157
+DIST biskit-2.1.0beta.tar.gz 6494771 RMD160 7cce1a79dbc13d4a6910be1b58267d101e0bc166 SHA1 ba399a8a7db029122366a4a6ca404f92e97a7af3 SHA256 936eba6df19a92cf80146a7ae88684d056a30aeeab89a7011fe57f429d5f5d98
+EBUILD biskit-2.1.0_beta.ebuild 1430 RMD160 17560421b04212e304b14e0b5ac484f01a280f93 SHA1 75dd2eaeb761eb2f4db7656e707804280eae2897 SHA256 1c7793939cff1bb4124a6e1f69a9fa567e817d0ec1ed967a3acd85d0eb7f7e92
diff --git a/sci-biology/biskit/biskit-2.1.0_beta.ebuild b/sci-biology/biskit/biskit-2.1.0_beta.ebuild
new file mode 100644
index 0000000..59bdb31
--- /dev/null
+++ b/sci-biology/biskit/biskit-2.1.0_beta.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils python portability
+
+MY_P=${P/_/}
+
+DESCRIPTION="This is a sample skeleton ebuild file"
+HOMEPAGE=""
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Core dependencies
+RDEPEND="dev-python/numpy
+	sci-libs/netcdf
+	dev-python/scientificpython"
+# Plotting
+RDEPEND="${RDEPEND}
+	media-libs/plotutils
+	sci-visualization/gnuplot
+	dev-python/python-biggles"
+# Homology modeling
+RDEPEND="${RDEPEND}
+	sci-biology/biopython"
+# Parallelization
+RDEPEND="${RDEPEND}
+	sys-cluster/pypvm"
+# Base package applications
+RDEPEND="${RDEPEND}
+	sci-biology/ncbi-tools
+	sci-biology/hmmer
+	sci-chemistry/pymol
+	sci-chemistry/dssp"
+# Biskit/Mod (homology modeling)
+RDEPEND="${RDEPEND}
+	sci-biology/t-coffee
+	sci-chemistry/modeller"
+DEPEND="${RDEPEND}"
+S=${WORKDIR}/${PN}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# Look for files in the right place
+	epatch "${FILESDIR}/${PV}-fix-projectroot.patch"
+}
+
+src_install() {
+	python_version
+	local py_root="/usr/$(get_libdir)/python${PYVER}/site-packages/"
+	dodir ${py_root} || die
+	treecopy Biskit "${D}${py_root}" || die
+
+	local biskit_root="/usr/share/biskit"
+	dodir ${biskit_root} || die
+	treecopy external "${D}${biskit_root}" || die
+	treecopy scripts "${D}${biskit_root}" || die
+
+	dodoc README.txt docs/* || die
+
+}
diff --git a/sci-biology/biskit/files/2.1.0_beta-fix-projectroot.patch b/sci-biology/biskit/files/2.1.0_beta-fix-projectroot.patch
new file mode 100644
index 0000000..c9bec1f
--- /dev/null
+++ b/sci-biology/biskit/files/2.1.0_beta-fix-projectroot.patch
@@ -0,0 +1,18 @@
+--- Biskit/tools.py.orig	2007-12-11 01:33:01.000000000 -0800
++++ Biskit/tools.py	2007-12-11 01:33:33.000000000 -0800
+@@ -559,13 +559,8 @@
+              i.e. '/home/Bis/raik/biskit'
+     @rtype: string
+     """
+-    ## import this module
+-    from Biskit import tools
+-    ## get location of this module
+-    f = absfile(tools.__file__)
+-    ## extract path and assume it is 'project_root/Biskit'
+-    f = osp.split( f )[0] + '/../'
+-    return absfile( f )
++	# Gentoo hardcoded default
++    return '/usr/share/biskit'
+ 
+ 
+ def testRoot():