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

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

[Martin Mokrejs]

commit:     9ce7d7d02ffa5ea884d926a61506108d5db723a5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:14:56 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:14:56 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ce7d7d0

sci-biology/sga: new package; forces its own optimization flags but works fine

---
 sci-biology/sga/ChangeLog       | 10 +++++++++
 sci-biology/sga/metadata.xml    |  9 ++++++++
 sci-biology/sga/sga-9999.ebuild | 47 +++++++++++++++++++++++++++++++++++++++++
 3 files changed, 66 insertions(+)

diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog
new file mode 100644
index 0000000..0f7e181
--- /dev/null
+++ b/sci-biology/sga/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/sga
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*sga-9999 (24 Mar 2014)
+
+  24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild,
+  +metadata.xml:
+  new package; forces its own optimization flags but works fine
+

diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/sga/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>

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
new file mode 100644
index 0000000..5393f87
--- /dev/null
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="String Graph Assembler for short-read assemblies"
+HOMEPAGE="https://github.com/jts/sga"
+EGIT_REPO_URI="git://github.com/jts/sga"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE="jemalloc python"
+
+DEPEND="dev-cpp/sparsehash
+	sci-biology/bamtools
+	sys-libs/zlib
+	jemalloc? ( dev-libs/jemalloc )
+	python? ( sci-biology/pysam
+			sci-biology/ruffus )"
+RDEPEND="${DEPEND}"
+
+src_configure(){
+	cd src || die
+	./autogen.sh
+	econf --with-bamtools=/usr
+}
+
+src_compile(){
+	cd src || die
+	emake
+}
+
+src_install(){
+	cd src || die
+	dodoc README
+	emake install DESTDIR="${D}"
+	insinto /usr/share/sga/examples
+	doins examples/*
+	cd .. ||
+	dodoc README.md
+}

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

[Jauhien Piatlicki]

commit:     2e6bdb2872ef38eadf82d56d0728871d7da3dad9
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  5 11:49:31 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Fri Sep  5 11:49:31 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e6bdb28

sci-biology/sga: silence repoman

---
 sci-biology/sga/metadata.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml
index 2bc8930..4e873d8 100644
--- a/sci-biology/sga/metadata.xml
+++ b/sci-biology/sga/metadata.xml
@@ -6,4 +6,7 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
+<use>
+  <flag name='jemalloc'>Use <pkg>dev-libs/jemalloc</pkg></flag>
+</use>
 </pkgmetadata>

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

[Justin Lecher]

commit:     3a9a8985f4975eca4af6be847be3c0955beaa344
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Feb  9 09:06:46 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb  9 09:08:53 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3a9a8985

sci-biology/sga-9999: Switch from git-2 to git-r3; Cleanup; Add missing die

---
 sci-biology/sga/ChangeLog       | 5 ++++-
 sci-biology/sga/sga-9999.ebuild | 8 +++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog
index 0f7e181..1408f94 100644
--- a/sci-biology/sga/ChangeLog
+++ b/sci-biology/sga/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/sga
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sga-9999.ebuild:
+  Switch from git-2 to git-r3; Cleanup; Add missing die
+
 *sga-9999 (24 Mar 2014)
 
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild,

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 5393f87..5f43969 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -1,12 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=5
 
-inherit eutils
-
-[ "$PV" == "9999" ] && inherit git-2
+inherit eutils git-r3
 
 DESCRIPTION="String Graph Assembler for short-read assemblies"
 HOMEPAGE="https://github.com/jts/sga"
@@ -27,7 +25,7 @@ RDEPEND="${DEPEND}"
 
 src_configure(){
 	cd src || die
-	./autogen.sh
+	./autogen.sh || die
 	econf --with-bamtools=/usr
 }
 

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

[Justin Lecher]

commit:     39e5299cb3cf0ff5a74be740057581675e9b10a8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun  5 11:13:14 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun  5 11:13:14 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=39e5299c

sci-biology/sga: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/sga/ChangeLog    | 4 +++-
 sci-biology/sga/metadata.xml | 9 ++++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog
index 1408f94..af67163 100644
--- a/sci-biology/sga/ChangeLog
+++ b/sci-biology/sga/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-biology/sga: Add github to remote-id in metadata.xml
+
   09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sga-9999.ebuild:
   Switch from git-2 to git-r3; Cleanup; Add missing die
 
@@ -10,4 +13,3 @@
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild,
   +metadata.xml:
   new package; forces its own optimization flags but works fine
-

diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml
index 4e873d8..5ac32df 100644
--- a/sci-biology/sga/metadata.xml
+++ b/sci-biology/sga/metadata.xml
@@ -6,7 +6,10 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
-<use>
-  <flag name='jemalloc'>Use <pkg>dev-libs/jemalloc</pkg></flag>
-</use>
+  <use>
+    <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg></flag>
+  </use>
+  <upstream>
+    <remote-id type="github">jts/sga</remote-id>
+  </upstream>
 </pkgmetadata>

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

[Martin Mokrejs]

commit:     293cc646066232a16190180c93e6e52b569924aa
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr  8 19:10:06 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr  8 19:10:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=293cc646

sci-biology/sga: improve package description

Package-Manager: portage-2.2.28

 sci-biology/sga/sga-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index a2d4897..5f245db 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.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
 # $Id$
 
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit eutils git-r3
 
-DESCRIPTION="String Graph Assembler for short-read assemblies"
+DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)"
 HOMEPAGE="https://github.com/jts/sga"
 EGIT_REPO_URI="git://github.com/jts/sga"
 

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

[Martin Mokrejs]

commit:     be0a658cc1a5ece410424fb184174399f9ff1a3e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 09:55:24 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 09:55:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=be0a658c

sci-biology/sga: move optional runtime deps to RDEPEND

Package-Manager: portage-2.2.28

 sci-biology/sga/sga-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 5f245db..0d35212 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -18,10 +18,10 @@ IUSE="jemalloc python"
 DEPEND="dev-cpp/sparsehash
 	sci-biology/bamtools
 	sys-libs/zlib
-	jemalloc? ( dev-libs/jemalloc )
+	jemalloc? ( dev-libs/jemalloc )"
+RDEPEND="${DEPEND}
 	python? ( sci-biology/pysam
 			sci-biology/ruffus )"
-RDEPEND="${DEPEND}"
 
 src_configure(){
 	cd src || die

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

[Martin Mokrejs]

commit:     a84e4aa7f75897685dd1aa844aca28c80eb2a642
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 11:27:58 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 11:27:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a84e4aa7

sci-biology/sga: compilation against bamtools does not work, see link

Package-Manager: portage-2.2.28

 sci-biology/sga/sga-9999.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 0d35212..e21c072 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -23,6 +23,7 @@ RDEPEND="${DEPEND}
 	python? ( sci-biology/pysam
 			sci-biology/ruffus )"
 
+# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm
 src_configure(){
 	cd src || die
 	./autogen.sh || die

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

[Martin Mokrejs]

commit:     ddee33dd856818debfc6c27809e224753bc8a494
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 10 14:56:09 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 10 14:56:09 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ddee33dd

sci-biology/sga: also install needed *.preqc files

These files are typically needed for preqc analysis.
See https://github.com/jts/sga/wiki/preqc for a typical
use case.

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/sga/sga-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index aa27979f0..6a8dd665b 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -39,7 +39,7 @@ src_install(){
 	dodoc README
 	emake install DESTDIR="${D}"
 	insinto /usr/share/sga/examples
-	doins examples/*
+	doins -r examples/*
 	cd .. ||
 	dodoc README.md
 }

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

[Martin Mokrejs]

commit:     e55632f5cb0b064a02cdf3d5e5189de03b540927
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 10 15:47:00 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 10 15:47:00 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e55632f5

sci-biology/sga: respect EPREFIX

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/sga/sga-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 6a8dd665b..a9d46d697 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -26,7 +26,7 @@ RDEPEND="${DEPEND}
 src_configure(){
 	cd src || die
 	./autogen.sh || die
-	econf --with-bamtools=/usr
+	econf --with-bamtools="${EPREFIX}"/usr
 }
 
 src_compile(){

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

[Martin Mokrejs]

commit:     1c723baf788de9babc310c1988d63347f4429f43
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:36:54 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:36:54 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c723baf

sci-biology/sga: convert git:// to https://

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/sga/sga-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index a9d46d697..38212a3e2 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -7,7 +7,7 @@ inherit eutils git-r3
 
 DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)"
 HOMEPAGE="https://github.com/jts/sga"
-EGIT_REPO_URI="git://github.com/jts/sga"
+EGIT_REPO_URI="https://github.com/jts/sga"
 
 LICENSE="GPL-3"
 SLOT="0"

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

[Martin Mokrejs]

commit:     2a587647f03490b80841358dfed7deb62cfe3097
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 25 19:52:27 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 25 19:52:27 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a587647

sci-biology/sga: add missing RDEPEND, more comments

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/sga/sga-9999.ebuild | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 38212a3e2..8ec029f94 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -19,6 +19,7 @@ DEPEND="dev-cpp/sparsehash
 	sys-libs/zlib
 	jemalloc? ( dev-libs/jemalloc )"
 RDEPEND="${DEPEND}
+	sci-biology/abyss
 	python? ( sci-biology/pysam
 			sci-biology/ruffus )"
 
@@ -30,7 +31,14 @@ src_configure(){
 }
 
 src_compile(){
-	cd src || die
+	# https://github.com/AlgoLab/FastStringGraph/issues/1#issuecomment-345999596
+	# https://github.com/jts/sga/issues/106
+	# https://github.com/jts/sga/pull/110
+	# https://github.com/jts/sga/issues/108
+	#
+	# other unreviewed patches:
+	# https://github.com/jts/sga/issues/96
+	cd src || die "Try -atd=g++-98, try gcc-5 or -std=c++03"
 	default
 }
 

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

[Martin Mokrejs]

commit:     8171b99830c37a7ceb1fed36d3cf8f2eb70d6d98
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Jan 10 16:12:25 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 10 16:12:42 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8171b998

sci-biology/sga: fix typo

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/sga/sga-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 8ec029f94..52f7bb69c 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -38,7 +38,7 @@ src_compile(){
 	#
 	# other unreviewed patches:
 	# https://github.com/jts/sga/issues/96
-	cd src || die "Try -atd=g++-98, try gcc-5 or -std=c++03"
+	cd src || die "Try -std=g++-98, try gcc-5 or -std=c++03"
 	default
 }
 

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

[Andrew Ammerlaan]

commit:     14b1dbd3fe67cddaf19c0502199733077cbd776b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 14:25:07 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 14:25:07 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=14b1dbd3

sci-biology/sga: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/sga/sga-9999.ebuild | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 52f7bb69c..7519b3e2a 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils git-r3
+inherit git-r3 autotools
 
 DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)"
 HOMEPAGE="https://github.com/jts/sga"
@@ -14,20 +14,27 @@ SLOT="0"
 KEYWORDS=""
 IUSE="jemalloc python"
 
-DEPEND="dev-cpp/sparsehash
+DEPEND="
+	dev-cpp/sparsehash
 	sci-biology/bamtools
 	sys-libs/zlib
-	jemalloc? ( dev-libs/jemalloc )"
+	jemalloc? ( dev-libs/jemalloc )
+"
 RDEPEND="${DEPEND}
 	sci-biology/abyss
 	python? ( sci-biology/pysam
 			sci-biology/ruffus )"
 
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
 # http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm
 src_configure(){
-	cd src || die
-	./autogen.sh || die
-	econf --with-bamtools="${EPREFIX}"/usr
+	econf --with-bamtools="${EPREFIX}"/usr --with-sparsehash="${EPREFIX}"/usr
 }
 
 src_compile(){
@@ -38,12 +45,10 @@ src_compile(){
 	#
 	# other unreviewed patches:
 	# https://github.com/jts/sga/issues/96
-	cd src || die "Try -std=g++-98, try gcc-5 or -std=c++03"
 	default
 }
 
 src_install(){
-	cd src || die
 	dodoc README
 	emake install DESTDIR="${D}"
 	insinto /usr/share/sga/examples