[gentoo-commits] proj/sci:master commit in: sci-biology/amos/

[Martin Mokrejs]

commit:     4a386700427979e83e4338695563aec7a1b1cfe9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 23 19:09:23 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 23 19:09:23 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a386700

sci-biology/amos: document 'Could not open file  
LIBGUESTFS_PATH=/usr/share/guestfs/appliance' error to be solved; add support 
for a system-wide config file via AMOSCONF env variable

Package-Manager: portage-2.2.26

 sci-biology/amos/amos-3.1.0-r2.ebuild |  9 ++++++++-
 sci-biology/amos/amos-9999.ebuild     | 10 +++++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild 
b/sci-biology/amos/amos-3.1.0-r2.ebuild
index bbf768f..ff04169 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -10,7 +10,7 @@ inherit eutils python-r1
 PERL_EXPORT_PHASE_FUNCTIONS=no
 inherit perl-module eutils toolchain-funcs
 
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple 
assemblies"
 HOMEPAGE="http://amos.sourceforge.net/";
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 
@@ -38,6 +38,9 @@ src_prepare() {
        epatch \
                "${FILESDIR}"/${P}-gcc-4.7.patch \
                "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+       # $ gap-links
+       # ERROR:  Could not open file  
LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+       # $
 }
 
 #  --with-jellyfish        location of Jellyfish headers
@@ -57,4 +60,8 @@ src_install() {
        # zap the mis-placed files ('make install' is at fault)
        rm -f "${D}"/usr/lib64/AMOS/*.pm
        rm -rf "${D}"/usr/lib64/TIGR
+       echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+       mkdir -p "${ED}"/etc || die
+       touch "${ED}"/etc/amos.acf || die
+       doenvd "${S}/99amos"
 }

diff --git a/sci-biology/amos/amos-9999.ebuild 
b/sci-biology/amos/amos-9999.ebuild
index 07a140a..fca8f2e 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -10,7 +10,7 @@ inherit perl-module eutils toolchain-funcs
 AUTOTOOLS_AUTORECONF=true
 inherit autotools-utils git-r3
 
-DESCRIPTION="Genome assembly package live cvs sources"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple 
assemblies"
 HOMEPAGE="http://sourceforge.net/projects/amos";
 SRC_URI=""
 EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
@@ -34,6 +34,10 @@ RDEPEND="${DEPEND}
 
 #  --with-jellyfish        location of Jellyfish headers
 
+# $ gap-links
+# ERROR:  Could not open file  LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+# $
+
 src_install() {
        default
        python_replicate_script "${ED}"/usr/bin/goBambus2
@@ -49,4 +53,8 @@ src_install() {
        # zap the mis-placed files ('make install' is at fault)
        rm -f "${D}"/usr/lib64/AMOS/*.pm
        rm -rf "${D}"/usr/lib64/TIGR
+       echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+       mkdir -p "${ED}"/etc || die
+       touch "${ED}"/etc/amos.acf || die
+       doenvd "${S}/99amos"
 }