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

[Martin Mokrejs]

commit:     d174cca6d660563e4d1ac95875628d8b4ec94867
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 28 21:46:20 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 28 21:46:20 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d174cca6

sci-biology/maker: some progress with the ebuild, empty KEYWORDS

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../{maker-2.31.8.ebuild => maker-2.31.10.ebuild}  | 32 ++++++++++++++++++----
 ...ker-2.31.8.ebuild => maker-3.01.02_beta.ebuild} | 16 +++++++----
 2 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.10.ebuild
similarity index 80%
copy from sci-biology/maker/maker-2.31.8.ebuild
copy to sci-biology/maker/maker-2.31.10.ebuild
index e5c791ab2..b7dc780a9 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -21,6 +21,10 @@ IUSE="mpi"
 
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm             # bug #566360
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+#
+# MAKER does not work with MVAPICH2.
+# It can work with Intel MPI and OpenMPI with some command line modification.
+# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.
 DEPEND="
 	mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
 	dev-perl/DBI
@@ -104,12 +108,14 @@ pkg_nofetch() {
 src_compile(){
 	perl Build.PL || die
 	./Build install || die
+	./Build installdeps || die
 }
 
-# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data,
-# …/maker/lib, and …/maker/perl directories. You should really either add the location of
-# …/maker/bin to you PATH environmental variable or at most soft link the executables somewhere
-# else using the ‘ln -s’ command.
+# If you move it, then the executables won't able to locate dependencies
+# in the /maker/data, /maker/lib, /maker/perl directories. You should
+# really either add the location of /maker/bin to you PATH environmental
+# variable or at most soft link the executables somewhere
+# else using the 'ln -s' command.
 src_install(){
 	cd "${WORKDIR}"/maker || die
 	rm -f bin/fasta_tool # is part of sci-biology/GAL
@@ -121,11 +127,25 @@ src_install(){
 	insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
 	doins perl/lib/MAKER/*.pm
 	doman perl/man/*.3pm
+	#
+	# FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
+	# You do not have write access to install missing Modules.
+	# I can try and install these locally (i.e. only for MAKER)
+	# in the .../maker/perl/lib directory, or you can run
+	# './Build installdeps' as root or using sudo and try again.
+	# Do want MAKER to try and build a local installation? [N ]N 
+	# 
+	# 
+	# WARNING: You do not appear to have write access to install missing
+	# Modules. Please run './Build installdeps' as root or using sudo.
+	# 
+	# Do you want to continue anyway? [N ]N 
+	# 
+	doins -r lib/*
 	insinto "${VENDOR_LIB}"/Parallel/Application
 	doins perl/lib/Parallel/Application/*.pm
 	insinto /usr/share/"${PN}"/data
 	doins data/*
-	# FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
 	dodoc README INSTALL
 	insinto /usr/share/"${PN}"/GMOD/Apollo
 	doins GMOD/Apollo/gff3.tiers

diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
similarity index 87%
rename from sci-biology/maker/maker-2.31.8.ebuild
rename to sci-biology/maker/maker-3.01.02_beta.ebuild
index e5c791ab2..d6ad845d1 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -21,6 +21,10 @@ IUSE="mpi"
 
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm             # bug #566360
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+#
+# MAKER does not work with MVAPICH2.
+# It can work with Intel MPI and OpenMPI with some command line modification.
+# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.
 DEPEND="
 	mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
 	dev-perl/DBI
@@ -93,6 +97,7 @@ S="${WORKDIR}"/maker/src
 pkg_nofetch() {
 	einfo "Please visit ${HOMEPAGE} and obtain the file"
 	einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
+	einfo "If it is '-beta' rename it to '_beta'"
 	einfo "You must also install sci-biology/repeatmasker otherwise"
 	einfo "MAKER install process will stop."
 	einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
@@ -106,10 +111,11 @@ src_compile(){
 	./Build install || die
 }
 
-# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data,
-# …/maker/lib, and …/maker/perl directories. You should really either add the location of
-# …/maker/bin to you PATH environmental variable or at most soft link the executables somewhere
-# else using the ‘ln -s’ command.
+# If you move it, then the executables won't able to locate dependencies
+# in the /maker/data, /maker/lib, /maker/perl directories. You should
+# really either add the location of /maker/bin to you PATH environmental
+# variable or at most soft link the executables somewhere
+# else using the 'ln -s' command.
 src_install(){
 	cd "${WORKDIR}"/maker || die
 	rm -f bin/fasta_tool # is part of sci-biology/GAL