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

[Justin Lecher]

commit:     97598a49ff923b98b8fc93be497373ef754cccf3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 29 00:14:51 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 29 00:14:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=97598a49

sci-biology/amos: Move to tree

Package-Manager: portage-2.2.7

---
 sci-biology/amos/ChangeLog                         |  6 +++
 sci-biology/amos/amos-3.1.0-r1.ebuild              | 30 -------------
 sci-biology/amos/amos-9999.ebuild                  |  8 ++--
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    | 15 -------
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 -----------
 sci-biology/amos/files/amos.m4.patch               | 49 ----------------------
 6 files changed, 9 insertions(+), 124 deletions(-)

diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 22c5625..7d1df6d 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Dec 2013; Justin Lecher <jlec@g.o> -amos-3.1.0-r1.ebuild,
+  amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch,
+  -files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch,
+  -files/amos.m4.patch:
+  Move to tree
+
 *amos-3.1.0-r1 (11 Sep 2013)
 
   11 Sep 2013; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>

diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild
deleted file mode 100644
index f1e0470..0000000
--- a/sci-biology/amos/amos-3.1.0-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0.ebuild,v 1.8 2013/03/19 07:41:20 jlec Exp $
-
-EAPI=4
-
-inherit eutils
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="qt4"
-
-DEPEND="qt4? ( dev-qt/qtcore:4 )"
-RDEPEND="${DEPEND}
-	dev-perl/DBI
-	dev-perl/Statistics-Descriptive
-	sci-biology/mummer"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-gcc-4.7.patch \
-		"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
-}

diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 67180f8..29ae041 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -4,11 +4,9 @@
 
 EAPI=5
 
-[ "$PV" == "9999" ] && VCS=git-2
-
 AUTOTOOLS_AUTORECONF=true
 
-inherit autotools-utils ${VCS}
+inherit autotools-utils git-r3
 
 DESCRIPTION="Genome assembly package live cvs sources"
 HOMEPAGE="http://sourceforge.net/projects/amos"
@@ -24,5 +22,5 @@ DEPEND="
 	dev-libs/boost
 	dev-qt/qtcore:4"
 RDEPEND="${DEPEND}
-		dev-perl/DBI
-		sci-biology/mummer"
+	dev-perl/DBI
+	sci-biology/mummer"

diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
deleted file mode 100644
index de2a411..0000000
--- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/Align/find-tandem.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
-index ddf1cab..a29e21e 100644
---- a/src/Align/find-tandem.cc
-+++ b/src/Align/find-tandem.cc
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <ctime>
- #include <sys/time.h>
-+#include <unistd.h>
- using namespace std;
- 
- const int OFFSET_TABLE_SIZE = 100;

diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
deleted file mode 100644
index 97a8f59..0000000
--- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- amos-3.1.0/src/Pipeline/goBambus2.py.orig	2013-09-11 01:05:29.850090457 +0200
-+++ amos-3.1.0/src/Pipeline/goBambus2.py	2013-09-11 01:07:03.250090701 +0200
-@@ -1,7 +1,7 @@
- #pipeline script for assembly + Bambus 2
- #contributed by Todd J Treangen
- 
--import string, sys, os, subprocess#, spincursor
-+import sys, os, subprocess#, spincursor
- 
- RED =    "\033[0;31m"
- GREEN =  "\033[0;32m"
-@@ -360,7 +360,7 @@
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
- 
--       p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-+        p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
- 
-         if xopt_dict["verbose"] == 1:
-             print "10) running OutputResults"
-@@ -388,4 +388,3 @@
-             else:
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
--)

diff --git a/sci-biology/amos/files/amos.m4.patch b/sci-biology/amos/files/amos.m4.patch
deleted file mode 100644
index 3c811b3..0000000
--- a/sci-biology/amos/files/amos.m4.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- config/amos.m4.ori	2010-12-05 17:33:13.000000000 +0100
-+++ config/amos.m4	2010-12-05 17:46:26.000000000 +0100
-@@ -219,7 +219,7 @@
-        ); then
- 
-       if test x"$amos_qt_dir" = x; then
--        amos_qt_dir="$amos_qt_bin_dir"
-+        amos_qt_dir=
-       fi
-       if test x"$amos_qt_include_dir" = x; then
-         amos_qt_include_dir="$amos_qt_dir/include"
-@@ -279,16 +279,6 @@
-     QT_LIBS="$amos_qt_LIBS"
-     # If amos_qt_dir is defined, utilities are expected to be in the
-     # bin subdirectory
--    if test x"$amos_qt_dir" != x; then
--        if test -x "$amos_qt_dir/bin/uic"; then
--          QT_UIC="$amos_qt_dir/bin/uic"
--        else
--          # Old versions of Qt don't have uic
--          QT_UIC=
--        fi
--      QT_MOC="$amos_qt_dir/bin/moc"
--    else
--      # Or maybe we are told where to look for the utilities
-       if test x"$amos_qt_bin_dir" != x; then
-         if test -x "$amos_qt_bin_dir/uic"; then
-           QT_UIC="$amos_qt_bin_dir/uic"
-@@ -297,11 +287,19 @@
-           QT_UIC=
-         fi
-         QT_MOC="$amos_qt_bin_dir/moc"
--      else
-+      if test x"$QT_MOC" = "x/moc"; then
-       # Last possibility is that they are in $PATH
-         QT_UIC="`which uic`"
-         QT_MOC="`which moc`"
-       fi
-+    elif test x"$amos_qt_dir" != x; then
-+        if test -x "$amos_qt_dir/bin/uic"; then
-+          QT_UIC="$amos_qt_dir/bin/uic"
-+        else
-+          # Old versions of Qt don't have uic
-+          QT_UIC=
-+        fi
-+      QT_MOC="$amos_qt_dir/bin/moc"
-     fi
-     # All variables are defined, report the result
-     AC_MSG_RESULT([$have_qt])