* [gentoo-commits] proj/sci:master commit in: sci-biology/MAKER/
@ 2015-03-30 19:50 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-03-30 19:50 UTC (permalink / raw
To: gentoo-commits
commit: 4e5f247e6640ad89353ec2f10e9453e6ee280491
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 19:50:10 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 19:50:10 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e5f247e
renamed to maker
sci-biology/MAKER/ChangeLog | 12 ------------
sci-biology/MAKER/MAKER-9999.ebuild | 21 ---------------------
sci-biology/MAKER/metadata.xml | 9 ---------
3 files changed, 42 deletions(-)
diff --git a/sci-biology/MAKER/ChangeLog b/sci-biology/MAKER/ChangeLog
deleted file mode 100644
index d954ed6..0000000
--- a/sci-biology/MAKER/ChangeLog
+++ /dev/null
@@ -1,12 +0,0 @@
-# ChangeLog for sci-biology/MAKER
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild:
- added license
-
-*MAKER-9999 (23 Mar 2014)
-
- 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild,
- +metadata.xml:
- a skeleton for a new package
diff --git a/sci-biology/MAKER/MAKER-9999.ebuild b/sci-biology/MAKER/MAKER-9999.ebuild
deleted file mode 100644
index fa4733e..0000000
--- a/sci-biology/MAKER/MAKER-9999.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI=""
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/MAKER/metadata.xml b/sci-biology/MAKER/metadata.xml
deleted file mode 100644
index 2bc8930..0000000
--- a/sci-biology/MAKER/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2021-08-31 9:24 Andrew Ammerlaan
0 siblings, 0 replies; 25+ messages in thread
From: Andrew Ammerlaan @ 2021-08-31 9:24 UTC (permalink / raw
To: gentoo-commits
commit: 9aab83a69bedd08a4acf16d01347b3851ab73da4
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:22:41 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:22:41 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9aab83a6
sci-biology/maker: remove last-rited pack
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/maker/maker-3.01.02_beta.ebuild | 135 ----------------------------
sci-biology/maker/metadata.xml | 12 ---
2 files changed, 147 deletions(-)
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
deleted file mode 100644
index 975a83c14..000000000
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI="maker-"${PV}".tgz"
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-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
- dev-perl/DBD-SQLite
- dev-perl/File-Which
- dev-perl/Bit-Vector
- dev-perl/Inline-C
- dev-perl/IO-All
- dev-perl/libwww-perl
- dev-perl/DBD-Pg
- dev-perl/Module-Build
- dev-perl/Want
- dev-perl/IO-Prompt
- dev-perl/Perl-Unsafe-Signals
- dev-perl/forks
- >=sci-biology/GAL-0.2.1
- >=sci-biology/bioperl-1.6
- sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
- sci-biology/snap
- sci-biology/exonerate
- >=sci-biology/augustus-2.0
- sci-biology/repeatmasker"
- #sci-biology/GeneMark_ES-bin
- #sci-biology/GeneMark_S-bin
- #>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
-RDEPEND="${DEPEND}"
-# dev-perl/forks-shared ?
-
-# ==============================================================================
-# STATUS MAKER v2.31.8
-# ==============================================================================
-# PERL Dependencies: MISSING
-# ! Perl::Unsafe::Signals
-# ! Want
-# ! forks
-# ! forks::shared
-#
-# External Programs: MISSING
-# ! RepeatMasker
-#
-# External C Libraries: VERIFIED
-# MPI SUPPORT: DISABLED
-# MWAS Web Interface: DISABLED
-# MAKER PACKAGE: MISSING PREREQUISITES
-#
-#
-# Important Commands:
-# ./Build installdeps #installs missing PERL dependencies
-# ./Build installexes #installs all missing external programs
-# ./Build install #installs MAKER
-# ./Build status #Shows this status menu
-#
-# Other Commands:
-# ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
-# ./Build blast #installs BLAST (NCBI BLAST+)
-# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
-# ./Build snap #installs SNAP
-# ./Build augustus #installs Augustus
-# ./Build apollo #installs Apollo
-# ./Build gbrowse #installs GBrowse (must be root)
-# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
-# ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
-# ./Build mpich2 #installs MPICH2 (but manual install recommended)
-# Building MAKER
-#
-# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
-
-S="${WORKDIR}"/maker/src
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "maker-"${PV}".tgz and place it into your DISTDIR folder"
- 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"
- einfo "to obtain sci-biology/repeatmasker-libraries data file"
- einfo "For execution through openmpi or mpich please read INSTALL file"
- einfo "Customization typically go into maker_opts.ctl file"
-}
-
-src_compile(){
- perl Build.PL || die
- ./Build install || die
-}
-
-# 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 "${WORKDIR}"/maker || die
- rm -f bin/fasta_tool # is part of sci-biology/GAL
- mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
- dobin bin/*
- perl_set_version
- perl_domodule perl/lib/MAKER/*.pm
- doman perl/man/*.3pm
- perl_domodule perl/lib/Parallel/Application/*.pm
- insinto /usr/share/"${PN}"/data
- doins data/*
- # FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
- dodoc README INSTALL
- insinto /usr/share/"${PN}"/GMOD/Apollo
- doins GMOD/Apollo/gff3.tiers
- insinto /usr/share/"${PN}"/GMOD/JBrowse
- doins GMOD/JBrowse/maker.css
-}
diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/maker/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2021-03-19 11:08 Andrew Ammerlaan
0 siblings, 0 replies; 25+ messages in thread
From: Andrew Ammerlaan @ 2021-03-19 11:08 UTC (permalink / raw
To: gentoo-commits
commit: 57da578241ce149fbcdc2ab052b26eb27247e86a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar 19 10:57:43 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar 19 10:57:43 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57da5782
sci-biology/maker: fix MisplacedVariable
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/maker/maker-3.01.02_beta.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
index 81c71dbac..975a83c14 100644
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -95,7 +95,7 @@ S="${WORKDIR}"/maker/src
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
+ einfo "maker-"${PV}".tgz and place it into your DISTDIR folder"
einfo "If it is '-beta' rename it to '_beta'"
einfo "You must also install sci-biology/repeatmasker otherwise"
einfo "MAKER install process will stop."
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 25+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: e42e7f6f3b60e1e77ee2e18296c66d8c359bdab6
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:49:33 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:49:33 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e42e7f6f
sci-biology/maker: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/maker/maker-3.01.02_beta.ebuild | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
index afad7ce1e..81c71dbac 100644
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -121,11 +121,9 @@ src_install(){
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
perl_set_version
- insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
- doins perl/lib/MAKER/*.pm
+ perl_domodule perl/lib/MAKER/*.pm
doman perl/man/*.3pm
- insinto "${VENDOR_LIB}"/Parallel/Application
- doins perl/lib/Parallel/Application/*.pm
+ perl_domodule perl/lib/Parallel/Application/*.pm
insinto /usr/share/"${PN}"/data
doins data/*
# FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2021-03-06 12:17 Andrew Ammerlaan
0 siblings, 0 replies; 25+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 12:17 UTC (permalink / raw
To: gentoo-commits
commit: e68c2d0d6e6b5aec1afea78e17593cf89c69ae26
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 12:12:52 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 12:12:52 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e68c2d0d
sci-biology/maker: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/maker/maker-3.01.02_beta.ebuild | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
index dd8b088ac..afad7ce1e 100644
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module
+inherit perl-functions
DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 25+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 92e50f54acd3921fced262210c878f1fdc8bf99a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:22:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:22:20 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=92e50f54
sci-biology/maker: drop old
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/maker/maker-2.31.10.ebuild | 154 ---------------------------------
1 file changed, 154 deletions(-)
diff --git a/sci-biology/maker/maker-2.31.10.ebuild b/sci-biology/maker/maker-2.31.10.ebuild
deleted file mode 100644
index b7dc780a9..000000000
--- a/sci-biology/maker/maker-2.31.10.ebuild
+++ /dev/null
@@ -1,154 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI="maker-"${PV}".tgz"
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug #566360
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
-#
-# MAKER does not work with MVAPICH2.
-# It can work with Intel MPI and OpenMPI with some command line modification.
-# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.
-DEPEND="
- mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
- dev-perl/DBI
- dev-perl/DBD-SQLite
- dev-perl/File-Which
- dev-perl/Bit-Vector
- dev-perl/Inline-C
- dev-perl/IO-All
- dev-perl/libwww-perl
- dev-perl/DBD-Pg
- dev-perl/Module-Build
- dev-perl/Want
- dev-perl/IO-Prompt
- dev-perl/Perl-Unsafe-Signals
- dev-perl/forks
- >=sci-biology/GAL-0.2.1
- >=sci-biology/bioperl-1.6
- sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
- sci-biology/snap
- sci-biology/exonerate
- >=sci-biology/augustus-2.0
- sci-biology/repeatmasker"
- #sci-biology/GeneMark_ES-bin
- #sci-biology/GeneMark_S-bin
- #>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
-RDEPEND="${DEPEND}"
-# dev-perl/forks-shared ?
-
-# ==============================================================================
-# STATUS MAKER v2.31.8
-# ==============================================================================
-# PERL Dependencies: MISSING
-# ! Perl::Unsafe::Signals
-# ! Want
-# ! forks
-# ! forks::shared
-#
-# External Programs: MISSING
-# ! RepeatMasker
-#
-# External C Libraries: VERIFIED
-# MPI SUPPORT: DISABLED
-# MWAS Web Interface: DISABLED
-# MAKER PACKAGE: MISSING PREREQUISITES
-#
-#
-# Important Commands:
-# ./Build installdeps #installs missing PERL dependencies
-# ./Build installexes #installs all missing external programs
-# ./Build install #installs MAKER
-# ./Build status #Shows this status menu
-#
-# Other Commands:
-# ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
-# ./Build blast #installs BLAST (NCBI BLAST+)
-# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
-# ./Build snap #installs SNAP
-# ./Build augustus #installs Augustus
-# ./Build apollo #installs Apollo
-# ./Build gbrowse #installs GBrowse (must be root)
-# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
-# ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
-# ./Build mpich2 #installs MPICH2 (but manual install recommended)
-# Building MAKER
-#
-# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
-
-S="${WORKDIR}"/maker/src
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
- einfo "You must also install sci-biology/repeatmasker otherwise"
- einfo "MAKER install process will stop."
- einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
- einfo "to obtain sci-biology/repeatmasker-libraries data file"
- einfo "For execution through openmpi or mpich please read INSTALL file"
- einfo "Customization typically go into maker_opts.ctl file"
-}
-
-src_compile(){
- perl Build.PL || die
- ./Build install || die
- ./Build installdeps || die
-}
-
-# If you move it, then the executables won't able to locate dependencies
-# in the /maker/data, /maker/lib, /maker/perl directories. You should
-# really either add the location of /maker/bin to you PATH environmental
-# variable or at most soft link the executables somewhere
-# else using the 'ln -s' command.
-src_install(){
- cd "${WORKDIR}"/maker || die
- rm -f bin/fasta_tool # is part of sci-biology/GAL
- # drop development related accessory script requiring Parallel/MPIcar.pm
- find . -name mpi_evaluator | xargs rm || die
- mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
- dobin bin/*
- perl_set_version
- 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/*
- dodoc README INSTALL
- insinto /usr/share/"${PN}"/GMOD/Apollo
- doins GMOD/Apollo/gff3.tiers
- insinto /usr/share/"${PN}"/GMOD/JBrowse
- doins GMOD/JBrowse/maker.css
-}
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2019-07-01 8:15 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2019-07-01 8:15 UTC (permalink / raw
To: gentoo-commits
commit: 69bf257d740cc8fa15a30afdcfb3b22ed1a7db08
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 1 08:15:27 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 1 08:15:27 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=69bf257d
sci-biology/maker-3.01.02_beta: mpi_evaluator is already gone
The mpi_evaluator is not anymore in the distribution
tarball. When rm is called with no arguments it obviously
breaks. Drop the commands altogether.
Package-Manager: Portage-2.3.67, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/maker/maker-3.01.02_beta.ebuild | 2 --
1 file changed, 2 deletions(-)
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
index d6ad845d1..dd8b088ac 100644
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -119,8 +119,6 @@ src_compile(){
src_install(){
cd "${WORKDIR}"/maker || die
rm -f bin/fasta_tool # is part of sci-biology/GAL
- # drop development related accessory script requiring Parallel/MPIcar.pm
- find . -name mpi_evaluator | xargs rm || die
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
perl_set_version
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2019-03-28 21:46 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2019-03-28 21:46 UTC (permalink / raw
To: gentoo-commits
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
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2016-12-03 18:47 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2016-12-03 18:47 UTC (permalink / raw
To: gentoo-commits
commit: 00c696ea8f4123f5992f4e674db071c4cde8a136
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Dec 3 18:47:36 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Dec 3 18:47:36 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=00c696ea
sci-biology/maker: record required augustus version actually
Package-Manager: portage-2.3.2
sci-biology/maker/maker-2.31.8.ebuild | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 17661aa..58b30cf 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -42,8 +42,11 @@ DEPEND="
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
sci-biology/exonerate
- sci-biology/augustus
+ >=sci-biology/augustus-2.0
sci-biology/repeatmasker"
+ #sci-biology/GeneMark_ES-bin
+ #sci-biology/GeneMark_S-bin
+ #>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
RDEPEND="${DEPEND}"
# dev-perl/forks-shared ?
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2016-08-02 15:21 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2016-08-02 15:21 UTC (permalink / raw
To: gentoo-commits
commit: c8acacd097c01e3fcdf254a41d17a6a25e1d648b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Aug 2 15:21:43 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Aug 2 15:21:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c8acacd0
sci-biology/maker: roughly install correctly the main part
Package-Manager: portage-2.3.0
sci-biology/maker/maker-2.31.8.ebuild | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 21734c2..17661aa 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -4,6 +4,7 @@
EAPI=5
+PERL_EXPORT_PHASE_FUNCTIONS=no
inherit eutils perl-module
DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
@@ -36,7 +37,6 @@ DEPEND="
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
dev-perl/forks
- dev-perl/forks-shared
>=sci-biology/GAL-0.2.1
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
@@ -45,6 +45,7 @@ DEPEND="
sci-biology/augustus
sci-biology/repeatmasker"
RDEPEND="${DEPEND}"
+# dev-perl/forks-shared ?
# ==============================================================================
# STATUS MAKER v2.31.8
@@ -114,9 +115,18 @@ src_install(){
find . -name mpi_evaluator | xargs rm || die
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
+ perl_set_version
+ insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
+ doins perl/lib/MAKER/*.pm
+ doman perl/man/*.3pm
+ 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
+ insinto /usr/share/"${PN}"/GMOD/Apollo
doins GMOD/Apollo/gff3.tiers
- insinto /usr/share/"{PN}"/GMOD/JBrowse
+ insinto /usr/share/"${PN}"/GMOD/JBrowse
doins GMOD/JBrowse/maker.css
}
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2016-08-02 14:50 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2016-08-02 14:50 UTC (permalink / raw
To: gentoo-commits
commit: 3d453585d191dca9ce0577865db62270bbcb1842
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Aug 2 14:49:41 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Aug 2 14:49:41 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d453585
sci-biology/maker: add some comments to the ebuild
Package-Manager: portage-2.3.0
sci-biology/maker/maker-2.31.8.ebuild | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 60abb3a..21734c2 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -95,6 +95,7 @@ pkg_nofetch() {
einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
einfo "to obtain sci-biology/repeatmasker-libraries data file"
einfo "For execution through openmpi or mpich please read INSTALL file"
+ einfo "Customization typically go into maker_opts.ctl file"
}
src_compile(){
@@ -102,9 +103,15 @@ 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.
src_install(){
cd "${WORKDIR}"/maker || die
rm -f bin/fasta_tool # is part of sci-biology/GAL
+ # drop development related accessory script requiring Parallel/MPIcar.pm
+ find . -name mpi_evaluator | xargs rm || die
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
dodoc README INSTALL
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-31 21:26 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-31 21:26 UTC (permalink / raw
To: gentoo-commits
commit: cc20c5c57f35f32361e627442c3550207c04e4b0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 31 21:25:08 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 31 21:25:08 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc20c5c5
sci-biology/maker: DEPEND on external sci-biology/GAL package; rename 'compare' binary as agreed with upstream
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 4 ++++
sci-biology/maker/maker-2.31.8.ebuild | 3 +++
2 files changed, 7 insertions(+)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 16cf654..c06e483 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: DEPEND on external sci-biology/GAL package; rename
+ 'compare' binary as agreed with upstream
+
30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: do install from a top-level directory; there is a file
collision with /usr/bin/compare from media-gfx/imagemagick and with
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index bb0dba6..60abb3a 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -37,6 +37,7 @@ DEPEND="
dev-perl/Perl-Unsafe-Signals
dev-perl/forks
dev-perl/forks-shared
+ >=sci-biology/GAL-0.2.1
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
@@ -103,6 +104,8 @@ src_compile(){
src_install(){
cd "${WORKDIR}"/maker || die
+ rm -f bin/fasta_tool # is part of sci-biology/GAL
+ mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
dodoc README INSTALL
insinto /usr/share/"{PN}"/GMOD/Apollo
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-30 19:16 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-30 19:16 UTC (permalink / raw
To: gentoo-commits
commit: 389c7dcdd5a39c1bb6748d52d49bb61981258dfd
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 30 19:15:05 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 30 19:15:05 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=389c7dcd
sci-biology/maker: do install from a top-level directory; there is a file collision with /usr/bin/compare from media-gfx/imagemagick and with /usr/bin/fasta_tool from sci-biology/trinityrnaseq
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 5 +++++
sci-biology/maker/maker-2.31.8.ebuild | 1 +
2 files changed, 6 insertions(+)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 2befe1a..16cf654 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -3,6 +3,11 @@
# $Id$
30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: do install from a top-level directory; there is a file
+ collision with /usr/bin/compare from media-gfx/imagemagick and with
+ /usr/bin/fasta_tool from sci-biology/trinityrnaseq
+
+ 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: added openmpi as dependency; define our own src_install();
add einfo message; added dev-perl/forks-shared dependency
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index b631293..bb0dba6 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -102,6 +102,7 @@ src_compile(){
}
src_install(){
+ cd "${WORKDIR}"/maker || die
dobin bin/*
dodoc README INSTALL
insinto /usr/share/"{PN}"/GMOD/Apollo
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-30 18:17 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-30 18:17 UTC (permalink / raw
To: gentoo-commits
commit: c5c8232d407b040a96110c2a04ca4049e6e7d86f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 30 18:16:19 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 30 18:16:19 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5c8232d
sci-biology/maker: added openmpi as dependency; define our own src_install(); add einfo message; added dev-perl/forks-shared dependency
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 4 ++++
sci-biology/maker/maker-2.31.8.ebuild | 13 ++++++++++++-
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 254d082..2befe1a 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -3,6 +3,10 @@
# $Id$
30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: added openmpi as dependency; define our own src_install();
+ add einfo message; added dev-perl/forks-shared dependency
+
+ 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: added dependency on dev-perl/forks
18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 37e8755..b631293 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -22,7 +22,7 @@ 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
DEPEND="
- mpi? ( sys-cluster/mpich2 )
+ mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
dev-perl/DBI
dev-perl/DBD-SQLite
dev-perl/File-Which
@@ -36,6 +36,7 @@ DEPEND="
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
dev-perl/forks
+ dev-perl/forks-shared
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
@@ -92,9 +93,19 @@ pkg_nofetch() {
einfo "MAKER install process will stop."
einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
einfo "to obtain sci-biology/repeatmasker-libraries data file"
+ einfo "For execution through openmpi or mpich please read INSTALL file"
}
src_compile(){
perl Build.PL || die
./Build install || die
}
+
+src_install(){
+ dobin bin/*
+ dodoc README INSTALL
+ insinto /usr/share/"{PN}"/GMOD/Apollo
+ doins GMOD/Apollo/gff3.tiers
+ insinto /usr/share/"{PN}"/GMOD/JBrowse
+ doins GMOD/JBrowse/maker.css
+}
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-30 17:43 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-30 17:43 UTC (permalink / raw
To: gentoo-commits
commit: 60b0b1d0c3b1f14e04787ef48c5418ba0f288636
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 30 17:39:30 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 30 17:39:30 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=60b0b1d0
sci-biology/maker: added dependency on dev-perl/forks
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 3 +++
sci-biology/maker/maker-2.31.8.ebuild | 1 +
2 files changed, 4 insertions(+)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 352afd8..254d082 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: added dependency on dev-perl/forks
+
18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: drop duplicated Module-Build requirement
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 23eb6fb..37e8755 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -35,6 +35,7 @@ DEPEND="
dev-perl/Want
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
+ dev-perl/forks
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-18 14:16 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-18 14:16 UTC (permalink / raw
To: gentoo-commits
commit: 87fb66148724534387833ffdeac9472e680b692f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 18 14:15:13 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 18 14:15:13 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87fb6614
sci-biology/maker: drop duplicated Module-Build requirement
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 3 +++
sci-biology/maker/maker-2.31.8.ebuild | 1 -
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index fbb7786..352afd8 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -3,6 +3,9 @@
# $Id$
18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: drop duplicated Module-Build requirement
+
+ 18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: fix Module-Build dependency
01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 38f7860..23eb6fb 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -35,7 +35,6 @@ DEPEND="
dev-perl/Want
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
- dev-perl/Module-Build
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-18 13:51 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-18 13:51 UTC (permalink / raw
To: gentoo-commits
commit: 7f421a68a042c7c6ab77cd6e0bf74909edc84041
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 18 13:50:57 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 18 13:50:57 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f421a68
sci-biology/maker: fix Module-Build dependency
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 3 +++
sci-biology/maker/maker-2.31.8.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index d54951b..fbb7786 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: fix Module-Build dependency
+
01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: add DEPENDency on dev-perl/Module-Build
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 5c531af..38f7860 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -35,7 +35,7 @@ DEPEND="
dev-perl/Want
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
- virtual/perl-Module-Build
+ dev-perl/Module-Build
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-12-01 12:01 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-12-01 12:01 UTC (permalink / raw
To: gentoo-commits
commit: a4c85442ddf6391aaeffbc996c3d899c439a11eb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec 1 12:00:36 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec 1 12:00:36 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4c85442
sci-biology/maker: add DEPENDency on dev-perl/Module-Build
Package-Manager: portage-2.2.26
sci-biology/maker/ChangeLog | 3 +++
sci-biology/maker/maker-2.31.8.ebuild | 1 +
2 files changed, 4 insertions(+)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 114f18d..d54951b 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: add DEPENDency on dev-perl/Module-Build
+
20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: document opened Gentoo bugzilla tickets
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 9ab0eed..5c531af 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -31,6 +31,7 @@ DEPEND="
dev-perl/IO-All
dev-perl/libwww-perl
dev-perl/DBD-Pg
+ dev-perl/Module-Build
dev-perl/Want
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-11-24 17:06 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-11-24 17:06 UTC (permalink / raw
To: gentoo-commits
commit: 86239003790adfcc24b9ec2bebc0a065fc81e036
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 24 17:06:18 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 24 17:06:18 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=86239003
sci-biology/maker: added DEPENDencies on two new dev-perl/ packages added by Andreas K. Hüttel to the main portage tree
sci-biology/maker/maker-2.31.8.ebuild | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 7f422b9..9ab0eed 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -19,10 +19,8 @@ SLOT="0"
KEYWORDS=""
IUSE="mpi"
-# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ # bug #566358
# 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
-# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm # bug #566362
DEPEND="
mpi? ( sys-cluster/mpich2 )
dev-perl/DBI
@@ -34,6 +32,8 @@ DEPEND="
dev-perl/libwww-perl
dev-perl/DBD-Pg
dev-perl/Want
+ dev-perl/IO-Prompt
+ dev-perl/Perl-Unsafe-Signals
virtual/perl-Module-Build
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
@@ -88,9 +88,9 @@ pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
einfo "You must also install sci-biology/repeatmasker otherwise"
- einfo "MAKER install will stop."
+ einfo "MAKER install process will stop."
einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
- einfo "to obtain for sci-biology/repeatmasker-libraries"
+ einfo "to obtain sci-biology/repeatmasker-libraries data file"
}
src_compile(){
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-11-20 21:38 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-11-20 21:38 UTC (permalink / raw
To: gentoo-commits
commit: 7028de3e8e30208ab7bde0da4a84a0572cb9da02
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 20 21:36:56 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 20 21:36:56 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7028de3e
sci-biology/maker: document opened Gentoo bugzilla tickets
Package-Manager: portage-2.2.18
sci-biology/maker/ChangeLog | 3 +++
sci-biology/maker/maker-2.31.8.ebuild | 6 +++---
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index bf295cf..114f18d 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -3,6 +3,9 @@
# $Id$
20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: document opened Gentoo bugzilla tickets
+
+ 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on
repeatmasker because install process does not continue without it, document
additional perl modules not available in portage
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 00a88da..7f422b9 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -19,10 +19,10 @@ SLOT="0"
KEYWORDS=""
IUSE="mpi"
-# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm
+# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ # bug #566358
+# 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
-# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm
+# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm # bug #566362
DEPEND="
mpi? ( sys-cluster/mpich2 )
dev-perl/DBI
^ permalink raw reply related [flat|nested] 25+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-11-20 21:28 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-11-20 21:28 UTC (permalink / raw
To: gentoo-commits
commit: e32ec5ec672fcded9199d4943aaa12cf9f1b9224
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 20 21:26:51 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 20 21:26:51 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e32ec5ec
sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on repeatmasker because install process does not continue without it, document additional perl modules not available in portage
Package-Manager: portage-2.2.18
sci-biology/maker/ChangeLog | 5 ++++
sci-biology/maker/maker-2.31.8.ebuild | 56 +++++++++++++++++++++++++++++------
2 files changed, 52 insertions(+), 9 deletions(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 62f6717..bf295cf 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -3,6 +3,11 @@
# $Id$
20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on
+ repeatmasker because install process does not continue without it, document
+ additional perl modules not available in portage
+
+ 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
sci-biology/maker: respect USE=mpi, remove hard DEPENDency on repeatmasker-
libraries which are fetch restricted
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index d005e19..00a88da 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -24,7 +24,7 @@ IUSE="mpi"
# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm
DEPEND="
- mpi? ( virtual/mpi )
+ mpi? ( sys-cluster/mpich2 )
dev-perl/DBI
dev-perl/DBD-SQLite
dev-perl/File-Which
@@ -33,29 +33,67 @@ DEPEND="
dev-perl/IO-All
dev-perl/libwww-perl
dev-perl/DBD-Pg
+ dev-perl/Want
virtual/perl-Module-Build
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
sci-biology/exonerate
- sci-biology/augustus"
+ sci-biology/augustus
+ sci-biology/repeatmasker"
RDEPEND="${DEPEND}"
+# ==============================================================================
+# STATUS MAKER v2.31.8
+# ==============================================================================
+# PERL Dependencies: MISSING
+# ! Perl::Unsafe::Signals
+# ! Want
+# ! forks
+# ! forks::shared
+#
+# External Programs: MISSING
+# ! RepeatMasker
+#
+# External C Libraries: VERIFIED
+# MPI SUPPORT: DISABLED
+# MWAS Web Interface: DISABLED
+# MAKER PACKAGE: MISSING PREREQUISITES
+#
+#
+# Important Commands:
+# ./Build installdeps #installs missing PERL dependencies
+# ./Build installexes #installs all missing external programs
+# ./Build install #installs MAKER
+# ./Build status #Shows this status menu
+#
+# Other Commands:
+# ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
+# ./Build blast #installs BLAST (NCBI BLAST+)
+# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
+# ./Build snap #installs SNAP
+# ./Build augustus #installs Augustus
+# ./Build apollo #installs Apollo
+# ./Build gbrowse #installs GBrowse (must be root)
+# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
+# ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
+# ./Build mpich2 #installs MPICH2 (but manual install recommended)
+# Building MAKER
+#
+# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
+
S="${WORKDIR}"/maker/src
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
- einfo "It is also advisable to install sci-biology/repeatmasker"
- einfo "and in turn register for sci-biology/repeatmasker-libraries"
+ einfo "You must also install sci-biology/repeatmasker otherwise"
+ einfo "MAKER install will stop."
+ einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
+ einfo "to obtain for sci-biology/repeatmasker-libraries"
}
src_compile(){
perl Build.PL || die
./Build install || die
}
-
-pkg_postinst(){
- einfo "It is also advisable to install sci-biology/repeatmasker"
- einfo "and in turn register for sci-biology/repeatmasker-libraries"
-}
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-11-20 21:09 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-11-20 21:09 UTC (permalink / raw
To: gentoo-commits
commit: a51248c80ee344d420c305b219c6272aae937030
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 20 21:08:24 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 20 21:08:24 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a51248c8
sci-biology/maker: respect USE=mpi, remove hard DEPENDency on repeatmasker-libraries which are fetch restricted
Package-Manager: portage-2.2.18
sci-biology/maker/ChangeLog | 8 ++++++--
sci-biology/maker/maker-2.31.8.ebuild | 13 ++++++++++---
2 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
index 9ad3002..62f6717 100644
--- a/sci-biology/maker/ChangeLog
+++ b/sci-biology/maker/ChangeLog
@@ -1,7 +1,11 @@
-# ChangeLog for sci-biology/MAKER
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# ChangeLog for sci-biology/maker
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild:
+ sci-biology/maker: respect USE=mpi, remove hard DEPENDency on repeatmasker-
+ libraries which are fetch restricted
+
16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild:
added license
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 9ec94fe..d005e19 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -17,13 +17,14 @@ RESTRICT="fetch"
LICENSE="|| ( GPL-2 Artistic-2 )"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="mpi"
# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/
# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm
# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm
-DEPEND="virtual/mpi
+DEPEND="
+ mpi? ( virtual/mpi )
dev-perl/DBI
dev-perl/DBD-SQLite
dev-perl/File-Which
@@ -36,7 +37,6 @@ DEPEND="virtual/mpi
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
- sci-biology/repeatmasker
sci-biology/exonerate
sci-biology/augustus"
RDEPEND="${DEPEND}"
@@ -46,9 +46,16 @@ S="${WORKDIR}"/maker/src
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
+ einfo "It is also advisable to install sci-biology/repeatmasker"
+ einfo "and in turn register for sci-biology/repeatmasker-libraries"
}
src_compile(){
perl Build.PL || die
./Build install || die
}
+
+pkg_postinst(){
+ einfo "It is also advisable to install sci-biology/repeatmasker"
+ einfo "and in turn register for sci-biology/repeatmasker-libraries"
+}
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/maker/
@ 2015-03-30 18:25 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2015-03-30 18:25 UTC (permalink / raw
To: gentoo-commits
commit: 024e8b388e709b7340cfcb8c620d057fc6bcdef4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 18:25:09 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 18:25:09 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=024e8b38
sci-biology/maker: improving the ebuild, needs some perl packages to be first introduced into portage tree; needs proper install and to avoid bundled 3rd-party binaries, not sure if the perl modules are a copy of bioperl or not
Package-Manager: portage-2.2.18
sci-biology/maker/ChangeLog | 12 ++++++++
sci-biology/maker/maker-2.31.8.ebuild | 54 +++++++++++++++++++++++++++++++++++
sci-biology/maker/metadata.xml | 9 ++++++
3 files changed, 75 insertions(+)
diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
new file mode 100644
index 0000000..d954ed6
--- /dev/null
+++ b/sci-biology/maker/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/MAKER
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild:
+ added license
+
+*MAKER-9999 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild,
+ +metadata.xml:
+ a skeleton for a new package
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
new file mode 100644
index 0000000..6bc8ff5
--- /dev/null
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils perl-module
+
+DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
+HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
+SRC_URI="maker-"${PV}".tgz"
+
+RESTRICT="fetch"
+
+# for academia: GPL-v2 or Artistic-2
+# for commercial: ask
+LICENSE="|| ( GPL-2 Artistic-2 )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/
+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm
+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm
+DEPEND="virtual/mpi
+ dev-perl/DBI
+ dev-perl/DBD-SQLite
+ dev-perl/File-Which
+ dev-perl/Bit-Vector
+ dev-perl/Inline-C
+ dev-perl/IO-All
+ dev-perl/libwww-perl
+ dev-perl/DBD-Pg
+ virtual/perl-Module-Build
+ >=sci-biology/bioperl-1.6
+ sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
+ sci-biology/snap
+ sci-biology/repeatmasker
+ sci-biology/exonerate
+ sci-biology/augustus"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/maker/src
+
+pkg_nofetch() {
+ einfo "Please visit ${HOMEPAGE} and obtain the file"
+ einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
+}
+
+src_compile(){
+ perl Build.PL || die
+ ./Build install || die
+}
diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/maker/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/MAKER/
@ 2014-09-16 4:07 Christoph Junghans
0 siblings, 0 replies; 25+ messages in thread
From: Christoph Junghans @ 2014-09-16 4:07 UTC (permalink / raw
To: gentoo-commits
commit: ace31469f95bef383c8036c0787889091fcf1722
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 02:38:39 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 02:38:39 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ace31469
added license
Package-Manager: portage-2.2.8-r1
---
sci-biology/MAKER/ChangeLog | 4 +++-
sci-biology/MAKER/MAKER-9999.ebuild | 5 ++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/MAKER/ChangeLog b/sci-biology/MAKER/ChangeLog
index c281aca..d954ed6 100644
--- a/sci-biology/MAKER/ChangeLog
+++ b/sci-biology/MAKER/ChangeLog
@@ -2,9 +2,11 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild:
+ added license
+
*MAKER-9999 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild,
+metadata.xml:
a skeleton for a new package
-
diff --git a/sci-biology/MAKER/MAKER-9999.ebuild b/sci-biology/MAKER/MAKER-9999.ebuild
index c55e791..fa4733e 100644
--- a/sci-biology/MAKER/MAKER-9999.ebuild
+++ b/sci-biology/MAKER/MAKER-9999.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
@@ -12,11 +12,10 @@ RESTRICT="fetch"
# for academia: GPL-v2 or Artistic-2
# for commercial: ask
-LICENSE=""
+LICENSE="|| ( GPL-2 Artistic-2 )"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}"
-
^ permalink raw reply related [flat|nested] 25+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/MAKER/
@ 2014-03-23 21:06 Martin Mokrejs
0 siblings, 0 replies; 25+ messages in thread
From: Martin Mokrejs @ 2014-03-23 21:06 UTC (permalink / raw
To: gentoo-commits
commit: 5078f9d30089083b440dae87ed9b8d91f47c4c50
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 21:05:03 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 21:05:03 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5078f9d3
sci-biology/MAKER: a skeleton for a new package
---
sci-biology/MAKER/ChangeLog | 10 ++++++++++
sci-biology/MAKER/MAKER-9999.ebuild | 22 ++++++++++++++++++++++
sci-biology/MAKER/metadata.xml | 9 +++++++++
3 files changed, 41 insertions(+)
diff --git a/sci-biology/MAKER/ChangeLog b/sci-biology/MAKER/ChangeLog
new file mode 100644
index 0000000..c281aca
--- /dev/null
+++ b/sci-biology/MAKER/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/MAKER
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*MAKER-9999 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild,
+ +metadata.xml:
+ a skeleton for a new package
+
diff --git a/sci-biology/MAKER/MAKER-9999.ebuild b/sci-biology/MAKER/MAKER-9999.ebuild
new file mode 100644
index 0000000..c55e791
--- /dev/null
+++ b/sci-biology/MAKER/MAKER-9999.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
+HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
+SRC_URI=""
+
+RESTRICT="fetch"
+
+# for academia: GPL-v2 or Artistic-2
+# for commercial: ask
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
diff --git a/sci-biology/MAKER/metadata.xml b/sci-biology/MAKER/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/MAKER/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 25+ messages in thread
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