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

[Andrew Ammerlaan]

commit:     67b756ceafdc4378861efdbf82f83844a31ccf20
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb  4 05:23:24 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb  4 05:23:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=67b756ce

sci-biology/sambamba: version bump, EAPI bump

does not compile, seems to require some other compiler
that is not packaged in ::gentoo at the moment

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/sambamba/sambamba-0.6.5.ebuild | 27 ----------------------
 sci-biology/sambamba/sambamba-0.8.0.ebuild | 36 ++++++++++++++++++++++++++++++
 sci-biology/sambamba/sambamba-9999.ebuild  | 10 ++++-----
 3 files changed, 41 insertions(+), 32 deletions(-)

diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild
deleted file mode 100644
index ab2fb990e..000000000
--- a/sci-biology/sambamba/sambamba-0.6.5.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_compile(){
-	if use debug ; then
-		emake sambamba-ldmd2-debug
-	else
-		emake sambamba-ldmd2-64
-	fi
-}

diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
new file mode 100644
index 000000000..d6da97806
--- /dev/null
+++ b/sci-biology/sambamba/sambamba-0.8.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
+
+DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
+HOMEPAGE="https://lomereiter.github.io/sambamba/"
+SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug"
+
+# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
+#
+# contains bundled htslib
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+	default
+	rm -r "${S}/lz4" || die
+	mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die
+}
+
+src_compile(){
+	if use debug ; then
+		emake debug all
+	else
+		emake all
+	fi
+}

diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
index 8cd4c3ba2..e655b10b0 100644
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ b/sci-biology/sambamba/sambamba-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3
 
 DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
+HOMEPAGE="https://lomereiter.github.io/sambamba/"
 EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
 
 LICENSE="GPL-2+"
@@ -21,8 +21,8 @@ RDEPEND="${DEPEND}"
 
 src_compile(){
 	if use debug ; then
-		emake sambamba-ldmd2-debug
+		emake debug all
 	else
-		emake sambamba-ldmd2-64
+		emake all
 	fi
 }