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 }
