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| author |   Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-02-04 06:23:24 +0100 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-02-04 06:23:24 +0100 |
| commit | 67b756ceafdc4378861efdbf82f83844a31ccf20 (patch) | |
| tree | c87ccbb0b42eae601b23a56e004995126b45e17b | |
| parent | sci-biology/sailfish: fix configure phase (diff) | |
| download | sci-67b756ceafdc4378861efdbf82f83844a31ccf20.tar.gz sci-67b756ceafdc4378861efdbf82f83844a31ccf20.tar.bz2 sci-67b756ceafdc4378861efdbf82f83844a31ccf20.zip | |
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@riseup.net>
| -rw-r--r-- | sci-biology/sambamba/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/sambamba/sambamba-0.6.5.ebuild | 27 | ||||
| -rw-r--r-- | sci-biology/sambamba/sambamba-0.8.0.ebuild | 36 | ||||
| -rw-r--r-- | sci-biology/sambamba/sambamba-9999.ebuild | 10 |
4 files changed, 43 insertions, 33 deletions
diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest index c8fbec14b..3e3052479 100644 --- a/sci-biology/sambamba/Manifest +++ b/sci-biology/sambamba/Manifest @@ -1 +1,2 @@ -DIST sambamba-0.6.5.tar.gz 249275 BLAKE2B a01b2863053838c1fe7151e7baf3041c1396ad547ec962d495b8c486cc6f0cdfcbd1cc5c6963795017dfd77e27a605462aa11fb7043dcf2f6ad666e64ad8bbef SHA512 a0353523bb921a32e4f7601d9c5552b2103567cfa23fb622b213170028122f49cb6929942e9a630890ddd93b7ebf00f048344edb75d5f2d10b1c86bae018497c +DIST b3692db46d2b23a7c0af2d5e69988c94f126e10a.tar.gz 320972 BLAKE2B e9af776d3a867f551e20c2a3c234f2c9a27e729b972a0b40e25eee830f1c2a2975fe939de68459fda6d56a1b3a63e26937cfbf77fcbb2b711ecdbc9385069d91 SHA512 f51c5332fdc5a74bcd4f9597b187721cc2f33bc535c374c0ff47f438f79f6bec382e20462bb90d8be5f6bdf02ff5d7b4f5bf358bba55e03211ee566035ef3fbd +DIST sambamba-0.8.0.tar.gz 630637 BLAKE2B ea51a86bb546de3792e6d8bc0494aa2afe525d3914d1cc15ad8d52ca1acd2d109f726154273e98ef0e6144266fc34048f8c5008fe5c50be093b4082fb3fac1b5 SHA512 2d74c5ca3188fe0628b4873891eebecb1f514474bb1a2a8aca4ca3f40275acfb0fda0de5e11097754d317cac39b982b6ae45c5dde457cd83d6f684596ca5a5ac 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 } |