reinit the tree, so we can have metadata

4 files changed, 107 insertions, 0 deletions

diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
new file mode 100644
index 000000000000..d364d949bf1d
--- /dev/null
+++ b/sci-biology/vcftools/Manifest
@@ -0,0 +1,6 @@
+AUX vcftools-0.1.14-buildsystem.patch 1159 SHA256 acb5156489d73a0b87785ad6717a781178844f3c063ba3c2b0b1a95fdc9cad7c SHA512 838cade29bbeeee090ea52f546c37b68eee868f3329ceccb710da0dbcf0f14e1b18dcc7b05ceefdbf72d400f450374389649f56fc6981bd86f6e176469b054ea WHIRLPOOL fa996b5909985075d00ae766bf070dbf15a214515aba56a0ac9f24a4f2116d94c6ae9b820d7f812bc6c75bf809f6b346276f04a49bc1ce0742e97db1889e8bdd
+DIST vcftools-0.1.14.tar.gz 342369 SHA256 76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 WHIRLPOOL 6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8
+EBUILD vcftools-0.1.14.ebuild 870 SHA256 fdaa68736705d831d6b6db0bf8dec04a19275d1d76911ed60171d437bf7292d8 SHA512 9b31b758a2fc70507b8060ca2aac6207e0fb3833426ba3f8bca63bff81952828f36c94b4a2e4b4476f8d9c8c0663b2b8ae437a7b50178c94e80b3d8a8b53b42c WHIRLPOOL 7cbc04995801a2fefc772eb8047fa4ebd156c78bceca82d965824953efd4dc6ca7cc784dcf97a0e5c7b0b121aabf76afa44431b7e349e3bee97b42eb7c8e633b
+MISC ChangeLog 3285 SHA256 5dd2ff0b88fedb21fbcfe90795fe27f8eb3a03515fd3db6168b75f4d6cce20ee SHA512 5777485e6ecc739b2fe4cdc4240846b4af7391c9840f3a8ff417df62355eb45859388bd1d55225535fc09a5f3fe2a1d007d9f8f1fd217f7f26259c0f6813901a WHIRLPOOL 0ef204f5aa99e80ba880d1ed9fd499af546a981339b424e1fd5702e28617b1e38d417a878bc1b93d7cf1ed5f85cd40da4b16c84d15bc26afc731715d60be6a75
+MISC ChangeLog-2015 1487 SHA256 c87f01e46cefe44f2a84676c7e48130dc2ed8065437bb9a66b47336a9881c976 SHA512 f6bbb15623533764f13192f55fad78dcd41fdbb9eab73d4b089022471e0a001728285677d12a889443b83b370b768f617d84b4ca692105abdcc23ac9cb8e40de WHIRLPOOL e300a50ed4949b7051479e0a0b744b57e5cef5c3bf2c624d05a473c29749c394f1b3f8d9e50370dbb8143eb616fb4c1b9227a48c77aba0b0e68a6fd7d6e7b3d2
+MISC metadata.xml 408 SHA256 ac1e7a9c967f31f40fa6140b78c58360a82fda8735cdca29189804b77ea37c99 SHA512 637b53b7fc140cfde69bd0e39ee1e942a86a3fb77934946e942e12ca65cf01a8c3559d606ab3131ffc762aa3508fb3ab60148b4aaee28b60bc6d97cb8dd00f3e WHIRLPOOL 6a75268fb966ab0cc6e963a6cae542483372df05a1ff61726717655bff52ccdcf401c702f58b773608c40adeffe685c24189e80802aa8a818c8f9eca81a5ac8f
diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
new file mode 100644
index 000000000000..126a709385db
--- /dev/null
+++ b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
@@ -0,0 +1,50 @@
+* Add prefix in Makefiles, not the configure script
+* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB,
+  as it is more flexible and helps us with LAPACK
+* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -34,7 +34,7 @@
+       [--with-pmdir=DIR],
+       [install Perl modules in DIR]),
+     [PMDIR=${withval}],
+-    [PMDIR='${prefix}'/"$pmdir_relative_path"])
++    [PMDIR="$pmdir_relative_path"])
+ 
+ AC_SUBST([PMDIR])
+ 
+@@ -73,9 +73,9 @@
+               [pca=${enableval}],
+               [pca=no])
+ 
+-if test "x${pca}" = "xyes" ; then
+-  AC_CHECK_LIB(lapack, dgeev_)
+-fi
++AS_IF([test "x${pca}" = "xyes"],[
++  AC_SEARCH_LIBS([dgeev_], [lapack])
++])
+ 
+ # Generate output.
+ AC_CONFIG_FILES([Makefile
+--- a/src/cpp/Makefile.am
++++ b/src/cpp/Makefile.am
+@@ -1,6 +1,6 @@
+ bin_PROGRAMS = vcftools
+ 
+-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
++vcftools_CPPFLAGS = $(ZLIB_CFLAGS)
+ vcftools_LDADD = $(ZLIB_LIBS)
+ 
+ vcftools_SOURCES = \
+--- a/src/perl/Makefile.am
++++ b/src/perl/Makefile.am
+@@ -24,7 +24,7 @@
+ 	vcf-tstv \
+ 	vcf-validator
+ 
+-pmdir = $(PMDIR)
++pmdir = $(exec_prefix)/$(PMDIR)
+ 
+ dist_pm_DATA = \
+ 	FaSlice.pm \
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
new file mode 100644
index 000000000000..6c22d19200ae
--- /dev/null
+++ b/sci-biology/vcftools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">vcftools</remote-id>
+    <remote-id type="github">vcftools/vcftools</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild
new file mode 100644
index 000000000000..baa5f7c32ea5
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools flag-o-matic perl-functions toolchain-funcs
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="sys-libs/zlib
+	dev-lang/perl:=
+	lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" )
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	perl_set_version
+
+	append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
+	append-libs $($(tc-getPKG_CONFIG) --libs lapack)
+
+	econf \
+		$(use_enable lapack pca) \
+		--with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
+}