commit: 1f18e25a472d14585102cdf0fc2819fdf8090bc0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 4 07:56:01 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 4 08:05:57 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1f18e25a
Rename eclass to compensate API changes
* Require at least EAPI=5
* Clean tiny bits
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
eclass/{emboss.eclass => emboss-r1.eclass} | 28 ++++++++++--------------
sci-biology/emboss/emboss-6.6.0.ebuild | 25 +++++++++-------------
sci-biology/emboss/files/README.gentoo | 34 ++++++++++++++++++++++++++++++
3 files changed, 55 insertions(+), 32 deletions(-)
diff --git a/eclass/emboss.eclass b/eclass/emboss-r1.eclass
similarity index 85%
rename from eclass/emboss.eclass
rename to eclass/emboss-r1.eclass
index 3ba65bb..b185802 100644
--- a/eclass/emboss.eclass
+++ b/eclass/emboss-r1.eclass
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-# @ECLASS: emboss.eclass
+# @ECLASS: emboss-r1.eclass
# @MAINTAINER:
# [email protected]
# [email protected]
@@ -13,14 +13,13 @@
# Next gen author: Ted Tanberry <[email protected]>
# @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS
add-ons).
# @DESCRIPTION:
-# The inheriting ebuild must set at least EAPI=4 and provide EBO_DESCRIPTION
before the inherit line.
+# The inheriting ebuild must set at least EAPI=5 and provide EBO_DESCRIPTION
before the inherit line.
# KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard
# ebuild variables can be extended (FOO+=" bar").
-# Default installation of following DOCS=()
#
# Example:
#
-# EAPI="4"
+# EAPI="5"
#
# EBO_DESCRIPTION="applications from the CBS group"
#
@@ -42,8 +41,8 @@
# Extra config options passed to econf, similar to EXTRA_ECONF.
case ${EAPI:-0} in
- 4|5) ;;
- *) die "this eclass doesn't support < EAPI 4" ;;
+ 5) ;;
+ *) die "this eclass doesn't support < EAPI 5" ;;
esac
if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
@@ -85,26 +84,23 @@ if [[ ${PN} == embassy-* ]]; then
S="${WORKDIR}"/${EF}
fi
-DOCS=()
-
# @FUNCTION: emboss_src_prepare
# @DESCRIPTION:
# Does the following things
#
# 1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present,
# and eventually runs eautoreconf in autotools-utils
-# 2. Patches with "${WORKDIR}"/${P}-upstream-r1.patch, if ${EBO_PATCH} is set
-# 3. Patches with "${FILESDIR}"/${PF}.patch, if present
+# 2. Patches with "${FILESDIR}"/${PF}.patch, if present
+# 3. Applies ${PATCHES[@]} via autotools-utils.eclass
#
-emboss_src_prepare() {
+emboss-r1_src_prepare() {
if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
mv configure.{in,ac} || die
epatch "${FILESDIR}"/${P}_fix-build-system.patch
fi
- [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream-r1.patch
- [[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
+ [[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
autotools-utils_src_prepare
}
@@ -125,14 +121,13 @@ emboss_src_prepare() {
# --docdir="${EPREFIX}/usr/share/doc/${PF}"
# ${EBO_EXTRA_ECONF}
-emboss_src_configure() {
+emboss-r1_src_configure() {
local myeconfargs=(
$(use_with X x)
$(use_with png pngdriver "${EPREFIX}/usr")
$(use_with pdf hpdf "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config")
$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config")
- $(use_enable static-libs static)
--enable-large
--without-java
--enable-systemlibs
@@ -140,9 +135,8 @@ emboss_src_configure() {
${EBO_EXTRA_ECONF}
)
- if [[ ${EMBASSY_PACKAGE} == yes ]]; then
+ [[ ${EMBASSY_PACKAGE} == yes ]] && \
append-cppflags "-I${EPREFIX}/usr/include/emboss"
- fi
autotools-utils_src_configure
}
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild
b/sci-biology/emboss/emboss-6.6.0.ebuild
index 7ac75b6..59285d7 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -4,10 +4,7 @@
EAPI=5
-inherit autotools-utils emboss eutils
-
-EBO_PATCH=""
-EBOV=${PV}
+inherit autotools-utils emboss-r1 eutils readme.gentoo
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence
analysis package"
SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz";
@@ -25,38 +22,36 @@ PDEPEND+="
sci-biology/rebase
)"
-S="${WORKDIR}"/EMBOSS-${EBOV}
-
-EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
+S="${WORKDIR}"/EMBOSS-${PV}
DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )
+
PATCHES=(
- "${FILESDIR}/${P}_FORTIFY_SOURCE-fix.patch"
- "${FILESDIR}/${P}_plplot-declarations.patch"
- "${FILESDIR}/${P}_qa-implicit-declarations.patch"
+ "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+ "${FILESDIR}"/${P}_plplot-declarations.patch
+ "${FILESDIR}"/${P}_qa-implicit-declarations.patch
)
src_install() {
# Use autotools-utils_* to remove useless *.la files
autotools-utils_src_install
- sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 >
README.Gentoo && \
- dodoc README.Gentoo
+ readme.gentoo_create_doc
# Install env file for setting libplplot and acd files path.
- cat <<- EOF > 22emboss
+ cat > 22emboss <<- EOF
# ACD files location
EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
EOF
doenvd 22emboss
- # Remove useless dummy files from the image.
+ # Remove useless dummy files
find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to
remove dummy files."
# Move the provided codon files to a different directory. This will
avoid
# user confusion and file collisions on case-insensitive file systems
(see
- # bug #115446). This change is documented in "README.Gentoo".
+ # bug #115446). This change is documented in "README.gentoo".
mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
die "Failed to move CODON directory."
}
diff --git a/sci-biology/emboss/files/README.gentoo
b/sci-biology/emboss/files/README.gentoo
new file mode 100644
index 0000000..d1879bd
--- /dev/null
+++ b/sci-biology/emboss/files/README.gentoo
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion
between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+ # cd ${EPREFIX}/usr/share/EMBOSS/data
+ # ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+ # cd ${EPREFIX}/usr/share/EMBOSS/data
+ # ln -s embossre.equ.orig embossre.equ
