[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: d635c86902bb7d00ae05c542f2ec3be0a32a76cd Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Dec 13 12:26:55 2021 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Dec 13 12:26:55 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d635c869 sci-biology/bowtie: remove duplicate Signed-off-by: Andrew Ammerlaan gentoo.org> .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 81 -- sci-biology/bowtie/bowtie-1.3.0.ebuild | 63 - sci-biology/bowtie/bowtie-2.4.2.ebuild | 62 - .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 - .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 - .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 -- .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 - sci-biology/bowtie/metadata.xml| 16 - 9 files changed, 323 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild deleted file mode 100644 index 857bc9cd1..0 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic toolchain-funcs git-r3 - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; -EGIT_BRANCH="bug_fixes" -COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" -# sci-biology/seqan:1.4" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -#PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) -# not needed -# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b -# -# still to be considered -#PATCHES=( -# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" -# "${FILESDIR}/${P}-unbundle-seqan.patch" -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled library of headers, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild deleted file mode 100644 index 118cc1303..0 --- a/sci-biology/bowtie/bowtie-1.3.0.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" -# sci-biology/seqan:1.4" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - default - - # remove bundled library of headers, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d Author: Andrew Ammerlaan riseup net> AuthorDate: Wed Mar 17 10:37:01 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Wed Mar 17 10:37:01 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a54a4d sci-biology/bowtie: add version 1.3.0 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/bowtie/bowtie-1.3.0.ebuild | 63 ++ 1 file changed, 63 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild new file mode 100644 index 0..118cc1303 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.3.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_prepare() { + default + + # remove bundled library of headers, use system seqan 1.4 + # rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 841b73539cdc92799497752d37b764c16793582b Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Mar 16 18:11:02 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Tue Mar 16 18:11:02 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=841b7353 Revert "sci-biology/bowtie: drop old" This reverts commit 718c86792641e4203877c23d69e9d4dcb0274388. Signed-off-by: Andrew Ammerlaan riseup.net> .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 81 ++ .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 + .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 + .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++ .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 + 6 files changed, 182 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild new file mode 100644 index 0..f7a1b92d4 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs git-r3 + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; +EGIT_BRANCH="bug_fixes" +COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) +# not needed +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b +# +# still to be considered +#PATCHES=( +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" +# "${FILESDIR}/${P}-unbundle-seqan.patch" +# "${FILESDIR}/${P}-fix-setBegin-call.patch" +# "${FILESDIR}/${P}-seqan-popcount.patch" +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" +# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" +# "${FILESDIR}/${P}-spelling.patch" +# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" +#) + +src_prepare() { + default + + # remove bundled library of headers, use system seqan 1.4 + # rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch new file mode 100644 index 0..4bcd61ba3 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch @@ -0,0 +1,17 @@ +Description: Change class name of _Context_LSS + New version 1.4 of SeQan uses a different name of the class. +Forwarded: no +Author: Gert Wollny +Last-Update: 2014-100-06 + +--- bowtie-1.2.2/diff_sample.h 2017-11-03 01:25:56.0 +0100 bowtie-1.2.2/diff_sample.h 2019-02-18 12:50:37.894674282 +0100 +@@ -979,7 +979,7 @@ + { + Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); + VMSG_NL(" Invoking Larsson-Sadakane on ranks"); +- _Context_LSS c; ++ ContextLss_ c; + c.suffixsort( + (TIndexOff*)begin(_isaPrime, Standard()), + (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch new file mode 100644 index 0..75942efb5 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch @@ -0,0 +1,32 @@ +fix compilation errors with Intel compilers: +error: no operator "=" matches these operands +author: Ward Poelmans +--- bowtie-1.2.2/hit.h 2018-01-24 12:57:47.135575442 +0100 +
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: ecf85a996b942336d7f2e23c11e3acd723914e36 Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Mar 16 18:15:31 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Tue Mar 16 18:15:31 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecf85a99 sci-biology/bowtie: EAPI bump bowtie-1 patch does not apply (anymore) Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild index f7a1b92d4..857bc9cd1 100644 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit flag-o-matic toolchain-funcs git-r3 @@ -25,7 +25,7 @@ DEPEND="${RDEPEND} DOCS=( AUTHORS NEWS TUTORIAL doc/README ) HTML_DOCS=( doc/{manual.html,style.css} ) -PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) +#PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) # not needed # "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b #
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 718c86792641e4203877c23d69e9d4dcb0274388 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 10:02:43 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 10:02:43 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=718c8679 sci-biology/bowtie: drop old Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 81 -- .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 - .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 - .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 -- .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 - 6 files changed, 182 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild deleted file mode 100644 index f7a1b92d4..0 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs git-r3 - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; -EGIT_BRANCH="bug_fixes" -COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" -# sci-biology/seqan:1.4" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) -# not needed -# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b -# -# still to be considered -#PATCHES=( -# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" -# "${FILESDIR}/${P}-unbundle-seqan.patch" -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled library of headers, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch deleted file mode 100644 index 4bcd61ba3..0 --- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Change class name of _Context_LSS - New version 1.4 of SeQan uses a different name of the class. -Forwarded: no -Author: Gert Wollny -Last-Update: 2014-100-06 - bowtie-1.2.2/diff_sample.h 2017-11-03 01:25:56.0 +0100 -+++ bowtie-1.2.2/diff_sample.h 2019-02-18 12:50:37.894674282 +0100 -@@ -979,7 +979,7 @@ - { - Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); - VMSG_NL(" Invoking Larsson-Sadakane on ranks"); -- _Context_LSS c; -+ ContextLss_ c; - c.suffixsort( - (TIndexOff*)begin(_isaPrime, Standard()), - (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch deleted file mode 100644 index 75942efb5..0 --- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch +++ /dev/null @@ -1,32 +0,0 @@ -fix compilation errors with Intel compilers: -error: no operator "=" matches these operands -author: Ward Poelmans bowtie-1.2.2/hit.h 2018-01-24 12:57:47.135575442 +0100 -+++ bowtie-1.2
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 3b6fcb10881cdda5486994a4b3e6a6c1476f6946 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 10:02:19 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 10:02:19 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b6fcb10 sci-biology/bowtie: EAPI bump Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/bowtie/bowtie-2.4.2.ebuild | 9 ++--- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/sci-biology/bowtie/bowtie-2.4.2.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild index 3cd8c2cdc..03cf3f8a9 100644 --- a/sci-biology/bowtie/bowtie-2.4.2.ebuild +++ b/sci-biology/bowtie/bowtie-2.4.2.ebuild @@ -1,13 +1,12 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs DESCRIPTION="Popular short read aligner for Next-generation sequencing data" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" @@ -61,7 +60,3 @@ src_install() { doins -r example fi } - -src_test(){ - emake test -}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 7653e736bbdbd6d7373e8015b0b79e1855032f83 Author: Martin Mokrejs gmail com> AuthorDate: Wed Dec 30 22:52:06 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Dec 30 22:52:26 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7653e736 sci-biology/bowtie: version bump the sci-biology/sra_sdk is not complete in Gentoo so bowtie cannot use this optional dependency (yet) Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/bowtie/{bowtie-2.4.1.ebuild => bowtie-2.4.2.ebuild} | 9 - 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/sci-biology/bowtie/bowtie-2.4.1.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild similarity index 86% rename from sci-biology/bowtie/bowtie-2.4.1.ebuild rename to sci-biology/bowtie/bowtie-2.4.2.ebuild index a4d6837ba..3cd8c2cdc 100644 --- a/sci-biology/bowtie/bowtie-2.4.1.ebuild +++ b/sci-biology/bowtie/bowtie-2.4.2.ebuild @@ -14,13 +14,15 @@ LICENSE="GPL-3" SLOT="2" KEYWORDS="~amd64 ~x86" -IUSE="examples cpu_flags_x86_sse2 +tbb" +IUSE="examples cpu_flags_x86_sse2 +tbb" # sra +# IUSE=sra Use sra-toolkit to download input datasets on the fly. RDEPEND="dev-lang/perl tbb? ( dev-cpp/tbb )" DEPEND="${RDEPEND} app-arch/unzip sys-libs/readline" +# sra? ( sci-biology/sra_sdk )" S="${WORKDIR}/${PN}2-${PV}" @@ -42,6 +44,7 @@ src_compile() { EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" \ WITH_TBB="$(usex tbb 1 0)" + # USE_SRA="$(usex sra 1 0)" } src_install() { @@ -58,3 +61,7 @@ src_install() { doins -r example fi } + +src_test(){ + emake test +}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 1f6479da30739c1e62b5df19384df7e5c2674e14 Author: Martin Mokrejs gmail com> AuthorDate: Fri Feb 28 23:06:48 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Feb 28 23:07:25 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f6479da sci-biology/bowtie: version bump (bugfix release) Package-Manager: Portage-2.3.87, Repoman-2.3.20 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/bowtie/{bowtie-2.4.0.ebuild => bowtie-2.4.1.ebuild} | 0 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/sci-biology/bowtie/bowtie-2.4.0.ebuild b/sci-biology/bowtie/bowtie-2.4.1.ebuild similarity index 100% rename from sci-biology/bowtie/bowtie-2.4.0.ebuild rename to sci-biology/bowtie/bowtie-2.4.1.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 731ea47715109fabdd7cc3944b6c522509619f56 Author: Martin Mokrejs gmail com> AuthorDate: Wed Feb 26 08:48:45 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Feb 26 08:49:28 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=731ea477 sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5 Package-Manager: Portage-2.3.87, Repoman-2.3.20 Signed-off-by: Martin Mokrejs gmail.com> .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 2 +- sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 63 -- .../{bowtie-2.3.5.1.ebuild => bowtie-2.4.0.ebuild} | 2 +- 3 files changed, 2 insertions(+), 65 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild index fcf0b4516..f7a1b92d4 100644 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild deleted file mode 100644 index 2a6fc04eb..0 --- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" -SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip"; - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl - tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip - sys-libs/readline" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) -#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update -PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch - "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.4.0.ebuild similarity index 97% rename from sci-biology/bowtie/bowtie-2.3.5.1.ebuild rename to sci-biology/bowtie/bowtie-2.4.0.ebuild index c2fef8667..a4d6837ba 100644 --- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild +++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 37d6c90ece12854ac4ae220e0d95bc88ec3af1b9 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Dec 23 15:38:01 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Dec 23 15:38:01 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=37d6c90e sci-biology/bowtie: version bump Package-Manager: Portage-2.3.75, Repoman-2.3.17 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-2.3.5.1.ebuild | 60 ++ .../bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 -- .../files/bowtie-2.3.5-fix-interleaved.patch | 15 -- 3 files changed, 60 insertions(+), 30 deletions(-) diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild new file mode 100644 index 0..c2fef8667 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" +SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip + sys-libs/readline" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +} diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch deleted file mode 100644 index 136bb1e69..0 --- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch +++ /dev/null @@ -1,15 +0,0 @@ -https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4 - -diff --git a/pat.cpp b/pat.cpp -index 453ba69..6d862f8 100644 a/pat.cpp -+++ b/pat.cpp -@@ -494,7 +494,7 @@ void CFilePatternSource::open() { - - is_fifo = S_ISFIFO(st.st_mode) != 0; - #endif -- if (pp_.format != BAM || is_fifo || is_gzipped_file(fd)) { -+ if (pp_.format != BAM && (is_fifo || is_gzipped_file(fd))) { - zfp_ = gzdopen(fd, "r"); - compressed_ = true; - } else { diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch deleted file mode 100644 index 45d6a0f96..0 --- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch +++ /dev/null @@ -1,15 +0,0 @@ -https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e - -diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp -index 1d53741..c59e39c 100644 bowtie-2.3.5/bt2_search.cpp -+++ bowtie-2.3.5/bt2_search.cpp -@@ -1673,7 +1673,7 @@ static void parseOptions(int argc, const char **argv) { -<< "sequences must be specified with -1 and -2." << endl; - throw 1; - } -- if(interleaved && (format != FASTA || format != FASTQ)) { -+ if(interleaved && (format != FASTA && format != FASTQ)) { - cerr << "Error: --interleaved only works in combination with FASTA (-f) and FASTQ (-q) formats." << endl; - throw 1; - }
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Fri Mar 29 23:28:32 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Mar 29 23:28:32 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f sci-biology/bowtie: add another upstream patch Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 3 ++- sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 +++ .../bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 2 ++ 3 files changed, 19 insertions(+), 1 deletion(-) diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild index f79dcb9cb..2a6fc04eb 100644 --- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild +++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild @@ -27,7 +27,8 @@ S="${WORKDIR}/${PN}2-${PV}" DOCS=( AUTHORS NEWS TUTORIAL ) HTML_DOCS=( doc/{manual.html,style.css} ) #PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update -PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch ) +PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch + "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) pkg_pretend() { if ! use cpu_flags_x86_sse2 ; then diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch new file mode 100644 index 0..136bb1e69 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch @@ -0,0 +1,15 @@ +https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4 + +diff --git a/pat.cpp b/pat.cpp +index 453ba69..6d862f8 100644 +--- a/pat.cpp b/pat.cpp +@@ -494,7 +494,7 @@ void CFilePatternSource::open() { + + is_fifo = S_ISFIFO(st.st_mode) != 0; + #endif +- if (pp_.format != BAM || is_fifo || is_gzipped_file(fd)) { ++ if (pp_.format != BAM && (is_fifo || is_gzipped_file(fd))) { + zfp_ = gzdopen(fd, "r"); + compressed_ = true; + } else { diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch index b2f24a7fa..45d6a0f96 100644 --- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch +++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch @@ -1,3 +1,5 @@ +https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e + diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp index 1d53741..c59e39c 100644 --- bowtie-2.3.5/bt2_search.cpp
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 2b44f30b60c65d2485250cb71e7dabe10a2694a6 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Wed Mar 27 22:45:47 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Mar 27 22:45:47 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b44f30b sci-biology/bowtie: patch --interleaved, add KEYWORDS Do not unset contents of CFLAGS and CXXFLAGS. Thanks to ch4rr0 at https://github.com/BenLangmead/bowtie2/issues/239 Add deemed patch from https://github.com/BenLangmead/bowtie2/issues/240 Added KEYWORDS. Closes: https://bugs.gentoo.org/649824 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> .../bowtie/{bowtie-2.3.5.ebuild => bowtie-2.3.5-r1.ebuild} | 5 ++--- sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 13 + 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/sci-biology/bowtie/bowtie-2.3.5.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild similarity index 94% rename from sci-biology/bowtie/bowtie-2.3.5.ebuild rename to sci-biology/bowtie/bowtie-2.3.5-r1.ebuild index dd4d8be66..f79dcb9cb 100644 --- a/sci-biology/bowtie/bowtie-2.3.5.ebuild +++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild @@ -12,7 +12,7 @@ SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-$ LICENSE="GPL-3" SLOT="2" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" IUSE="examples cpu_flags_x86_sse2 +tbb" @@ -27,6 +27,7 @@ S="${WORKDIR}/${PN}2-${PV}" DOCS=( AUTHORS NEWS TUTORIAL ) HTML_DOCS=( doc/{manual.html,style.css} ) #PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update +PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch ) pkg_pretend() { if ! use cpu_flags_x86_sse2 ; then @@ -40,8 +41,6 @@ src_compile() { CC="$(tc-getCC)" \ CPP="$(tc-getCXX)" \ CXX="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" \ WITH_TBB="$(usex tbb 1 0)" diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch new file mode 100644 index 0..b2f24a7fa --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch @@ -0,0 +1,13 @@ +diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp +index 1d53741..c59e39c 100644 +--- bowtie-2.3.5/bt2_search.cpp bowtie-2.3.5/bt2_search.cpp +@@ -1673,7 +1673,7 @@ static void parseOptions(int argc, const char **argv) { +<< "sequences must be specified with -1 and -2." << endl; + throw 1; + } +- if(interleaved && (format != FASTA || format != FASTQ)) { ++ if(interleaved && (format != FASTA && format != FASTQ)) { + cerr << "Error: --interleaved only works in combination with FASTA (-f) and FASTQ (-q) formats." << endl; + throw 1; + }
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 922b05adcf80432d8e8212128b90b456b8ad3fc5 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Mar 25 11:20:55 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 25 11:20:55 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=922b05ad sci-biology/bowtie: update SRC_URI and hash for 2.3.5 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/{bowtie-2.3.4.3.ebuild => bowtie-2.3.5.ebuild} | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild b/sci-biology/bowtie/bowtie-2.3.5.ebuild similarity index 93% rename from sci-biology/bowtie/bowtie-2.3.4.3.ebuild rename to sci-biology/bowtie/bowtie-2.3.5.ebuild index eea3059cf..dd4d8be66 100644 --- a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild +++ b/sci-biology/bowtie/bowtie-2.3.5.ebuild @@ -8,6 +8,7 @@ inherit toolchain-funcs DESCRIPTION="Popular short read aligner for Next-generation sequencing data" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" +SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip"; LICENSE="GPL-3" SLOT="2"
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: b6846dd42e04e42c0103983272b6db0db248f75a Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Feb 19 11:26:14 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 19 11:26:14 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6846dd4 sci-biology/bowtie: removing not working -1.2.2 ebuild Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 -- 1 file changed, 77 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild deleted file mode 100644 index cae085bff..0 --- a/sci-biology/bowtie/bowtie-1.2.2.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - sci-biology/seqan:1.4 - app-arch/unzip" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( - "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" - "${FILESDIR}/${P}-fix-Intel-compilation.patch" - "${FILESDIR}/${P}-unbundle-seqan.patch" -) -# other patches to be still considered -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled libraries, use system seqan 1.4 - rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 51f9e3636c1422b40200dcc11c4122f356cfe4de Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Feb 19 11:24:18 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 19 11:24:18 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=51f9e363 sci-biology/bowtie: removing - ebuild Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-.ebuild | 81 --- 1 file changed, 81 deletions(-) diff --git a/sci-biology/bowtie/bowtie-.ebuild b/sci-biology/bowtie/bowtie-.ebuild deleted file mode 100644 index d54d0a544..0 --- a/sci-biology/bowtie/bowtie-.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs git-r3 - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; -EGIT_BRANCH="bug_fixes" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - sci-biology/seqan:1.4 - app-arch/unzip" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( "${FILESDIR}/bowtie--fix-isa-return-type.patch" ) -# not needed -# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b -#PATCHES=( -# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" -# "${FILESDIR}/${P}-fix-Intel-compilation.patch" -# "${FILESDIR}/${P}-unbundle-seqan.patch" -#) -# other patches to be still considered -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled libraries, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 85794dc2e25580c628e007d4a528ffc2e24d4239 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Feb 19 11:20:51 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 19 11:20:51 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2 sci-biology/bowtie: working 1.2.2 snapshot This ebuild keeps the bundled SeqAn-1.1 sources (a library of headers) and does not insist on system-wide installed SeqAn-1.4 (for which too many patches are needed and I am unable to evaluate/apply them all). Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 81 ++ sci-biology/bowtie/bowtie-.ebuild | 81 ++ .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++ 3 files changed, 184 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild new file mode 100644 index 0..fcf0b4516 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs git-r3 + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; +EGIT_BRANCH="bug_fixes" +COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) +# not needed +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b +# +# still to be considered +#PATCHES=( +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" +# "${FILESDIR}/${P}-unbundle-seqan.patch" +# "${FILESDIR}/${P}-fix-setBegin-call.patch" +# "${FILESDIR}/${P}-seqan-popcount.patch" +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" +# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" +# "${FILESDIR}/${P}-spelling.patch" +# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" +#) + +src_prepare() { + default + + # remove bundled library of headers, use system seqan 1.4 + # rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/bowtie-.ebuild b/sci-biology/bowtie/bowtie-.ebuild new file mode 100644 index 0..d54d0a544 --- /dev/null +++ b/sci-biology/bowtie/bowtie-.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs git-r3 + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; +EGIT_BRANCH="bug_fixes" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4 + app-arch/unzip" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( "${FILESDIR}/bowtie--fix-isa-return-type.patch" ) +# not needed +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b +#PATCHES=( +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" +# "${FILESDIR}/${P}-fix-Intel-compilation.patch" +# "${FILESDIR}/${P}-unbundle-seqan.patch" +#) +# other patches to be still considered +# "${FILESDIR}/${P}-fix-setBegin-call.patch" +# "${FILESDIR}/${P}-seqan-popcount.patch" +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 3c65e999c45f956a48f434581ed74f27732c9c2a Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Feb 18 13:44:27 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Feb 18 13:44:27 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c65e999 sci-biology/bowtie: add some compile patches from Debian Seems both bowtie1 and bowtie2 are bound too much to SeqAn-1.1 and need more patches for SeqAn-1.4. Per reports on github it seems one should be able to compile bowtie-1.2.2 using -std=c++03 (but not me). Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 ++ sci-biology/bowtie/bowtie-2.3.4.3.ebuild | 62 + .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 + .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 + .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 + sci-biology/bowtie/metadata.xml| 16 + 7 files changed, 234 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild new file mode 100644 index 0..cae085bff --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.2.2.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4 + app-arch/unzip" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( + "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" + "${FILESDIR}/${P}-fix-Intel-compilation.patch" + "${FILESDIR}/${P}-unbundle-seqan.patch" +) +# other patches to be still considered +# "${FILESDIR}/${P}-fix-setBegin-call.patch" +# "${FILESDIR}/${P}-seqan-popcount.patch" +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" +# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" +# "${FILESDIR}/${P}-spelling.patch" +# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" +#) + +src_prepare() { + default + + # remove bundled libraries, use system seqan 1.4 + rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild new file mode 100644 index 0..eea3059cf --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip + sys-libs/readline" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) +#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WI
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 525b717f7cebfc901579e10b1c45622bddf68eb6 Author: Justin Lecher gentoo org> AuthorDate: Thu Oct 15 17:12:19 2015 + Commit: Justin Lecher gentoo org> CommitDate: Thu Oct 15 17:12:19 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=525b717f Moved to tree Signed-off-by: Justin Lecher gentoo.org> sci-biology/bowtie/ChangeLog | 37 -- sci-biology/bowtie/bowtie-1.1.1.ebuild | 53 sci-biology/bowtie/bowtie-1.1.2.ebuild | 58 -- sci-biology/bowtie/bowtie-2.2.3.ebuild | 52 --- sci-biology/bowtie/bowtie-2.2.5.ebuild | 52 --- sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 -- sci-biology/bowtie/metadata.xml| 13 - 8 files changed, 333 deletions(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog deleted file mode 100644 index 6530be0..000 --- a/sci-biology/bowtie/ChangeLog +++ /dev/null @@ -1,37 +0,0 @@ -# ChangeLog for sci-biology/bowtie -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*bowtie-2.2.6 (10 Oct 2015) - - 10 Oct 2015; Ted Tanberry +bowtie-2.2.6.ebuild: - sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with - USE flag. - -*bowtie-1.1.2 (10 Oct 2015) - - 10 Oct 2015; Ted Tanberry +bowtie-1.1.2.ebuild, - +files/bowtie-1.1.2-tbb-tinythread-missing.patch, metadata.xml: - sci-biology/bowtie: Version bump to 1.1.2, support dev-cpp/tbb with - USE flag. - - 08 Jun 2015; Justin Lecher metadata.xml: - sci-biology/bowtie: Updating remote-id in metadata.xml - - 01 May 2015; Martin Mokrejs bowtie-1.1.1.ebuild, - bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild: - sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) - -*bowtie-2.2.3 (27 Apr 2015) -*bowtie-2.2.5 (27 Apr 2015) - - 27 Apr 2015; Martin Mokrejs - +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild: - sci-biology/bowtie: version bump - - 06 Feb 2015; Ted Tanberry bowtie-1.1.1.ebuild, - bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build - system bugs - - 28 Sep 2013; Justin Lecher bowtie-2.1.0.ebuild: - Exchange common variables, fix SRC_URI diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild deleted file mode 100644 index 387e06c..000 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples" - -DEPEND="app-arch/unzip" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # Suppress useless -Wall pollution - sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild deleted file mode 100644 index 1988f6b..000 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples tbb" - -DEPEND="app-arch/unzip - tbb? ( dev-cpp/tbb )" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # Suppress useless -Wall pollution - sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die - - # always include tinythread.cpp - epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-g
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 87642b198308aa88ce351b935b79a58a08cf164b Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 17:48:48 2015 + Commit: Marius Brehler linux sungazer de> CommitDate: Sat Oct 10 17:48:48 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=87642b19 sci-biology/bowtie: Version bump to 2.2.6 dev-cpp/tbb is now supported with 'tbb' USE flag. sci-biology/bowtie/ChangeLog | 6 sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++ 2 files changed, 60 insertions(+) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 42bdbdf..6530be0 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*bowtie-2.2.6 (10 Oct 2015) + + 10 Oct 2015; Ted Tanberry +bowtie-2.2.6.ebuild: + sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with + USE flag. + *bowtie-1.1.2 (10 Oct 2015) 10 Oct 2015; Ted Tanberry +bowtie-1.1.2.ebuild, diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild new file mode 100644 index 000..fce2985 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2 tbb" +REQUIRED_USE="cpu_flags_x86_sse2" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND} + app-arch/unzip + tbb? ( dev-cpp/tbb )" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 05f13955c6ce57de4194483c2e1e15744d02cf5d Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 17:50:43 2015 + Commit: Marius Brehler linux sungazer de> CommitDate: Sat Oct 10 17:50:43 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=05f13955 sci-biology/bowtie: Use 'usex' instead of defining TBB variable. sci-biology/bowtie/bowtie-1.1.2.ebuild | 8 +--- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild index e443686..1988f6b 100644 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -32,12 +32,6 @@ src_prepare() { } src_compile() { - if use tbb ; then - TBB="1" - else - TBB="0" - fi - emake \ CC="$(tc-getCC)" \ CPP="$(tc-getCXX)" \ @@ -45,7 +39,7 @@ src_compile() { CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="${TBB}" + WITH_TBB="$(usex tbb 1 0)" } src_install() {
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 72ec06023243088ee31dacc6a9189c986c011561 Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 17:21:59 2015 + Commit: Marius Brehler linux sungazer de> CommitDate: Sat Oct 10 17:21:59 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=72ec0602 sci-biology/bowtie: Version bump to 1.1.2 dev-cpp/tbb is now supported with 'tbb' USE flag. sci-biology/bowtie/ChangeLog | 7 +++ sci-biology/bowtie/bowtie-1.1.2.ebuild | 64 ++ .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 + sci-biology/bowtie/metadata.xml| 5 ++ 4 files changed, 90 insertions(+) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index e05b4dc..42bdbdf 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*bowtie-1.1.2 (10 Oct 2015) + + 10 Oct 2015; Ted Tanberry +bowtie-1.1.2.ebuild, + +files/bowtie-1.1.2-tbb-tinythread-missing.patch, metadata.xml: + sci-biology/bowtie: Version bump to 1.1.2, support dev-cpp/tbb with + USE flag. + 08 Jun 2015; Justin Lecher metadata.xml: sci-biology/bowtie: Updating remote-id in metadata.xml diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild new file mode 100644 index 000..e443686 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +IUSE="examples tbb" + +DEPEND="app-arch/unzip + tbb? ( dev-cpp/tbb )" +RDEPEND="" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_prepare() { + # Suppress useless -Wall pollution + sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die + + # always include tinythread.cpp + epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" +} + +src_compile() { + if use tbb ; then + TBB="1" + else + TBB="0" + fi + + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="${TBB}" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch new file mode 100644 index 000..2a081ff --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch @@ -0,0 +1,14 @@ +--- bowtie-1.1.2/Makefile bowtie-1.1.2/Makefile +@@ -106,10 +106,7 @@ + endif + + OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ +- edit.cpp ebwt.cpp +-ifneq (1,$(WITH_TBB)) +- OTHER_CPPS += tinythread.cpp +-endif ++ edit.cpp ebwt.cpp tinythread.cpp + + SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \ + log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \ diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index e493417..1aef690 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -5,4 +5,9 @@ bowtie-bio + +Enables building bowtie with the Intel + Threading Building Blocks from dev-cpp/tbb. This + flag is recommended. +
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: a6949bfe7f087ab37f5ebf875ecc154dda9d8593 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri May 1 20:37:44 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri May 1 20:37:44 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6949bfe sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) Package-Manager: portage-2.2.18 sci-biology/bowtie/ChangeLog | 4 sci-biology/bowtie/bowtie-1.1.1.ebuild | 2 +- sci-biology/bowtie/bowtie-2.2.3.ebuild | 2 +- sci-biology/bowtie/bowtie-2.2.5.ebuild | 2 +- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 0bc0afa..4be1ee3 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 01 May 2015; Martin Mokrejs bowtie-1.1.1.ebuild, + bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild: + sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) + *bowtie-2.2.3 (27 Apr 2015) *bowtie-2.2.5 (27 Apr 2015) diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index 536e9d8..e6e5c3a 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="An ultrafast memory-efficient short read aligner" +DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" HOMEPAGE="http://bowtie-bio.sourceforge.net/"; SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" diff --git a/sci-biology/bowtie/bowtie-2.2.3.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild index d8059fc..e987cdb 100644 --- a/sci-biology/bowtie/bowtie-2.2.3.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.3.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="An ultrafast memory-efficient short read aligner" +DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" diff --git a/sci-biology/bowtie/bowtie-2.2.5.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild index d8059fc..e987cdb 100644 --- a/sci-biology/bowtie/bowtie-2.2.5.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.5.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="An ultrafast memory-efficient short read aligner" +DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 56eef21f8af41d10246dc582ce51ec09cd514c3e Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Apr 27 11:00:54 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Apr 27 11:00:54 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=56eef21f sci-biology/bowtie: version bump Package-Manager: portage-2.2.18 sci-biology/bowtie/ChangeLog| 8 +++- sci-biology/bowtie/{bowtie-2.2.4.ebuild => bowtie-2.2.3.ebuild} | 0 sci-biology/bowtie/{bowtie-2.2.4.ebuild => bowtie-2.2.5.ebuild} | 0 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index f3d98e2..0bc0afa 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,10 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*bowtie-2.2.3 (27 Apr 2015) +*bowtie-2.2.5 (27 Apr 2015) + + 27 Apr 2015; Martin Mokrejs + +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild: + sci-biology/bowtie: version bump + 06 Feb 2015; Ted Tanberry bowtie-1.1.1.ebuild, bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build system bugs 28 Sep 2013; Justin Lecher bowtie-2.1.0.ebuild: Exchange common variables, fix SRC_URI - diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild similarity index 100% copy from sci-biology/bowtie/bowtie-2.2.4.ebuild copy to sci-biology/bowtie/bowtie-2.2.3.ebuild diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild similarity index 100% rename from sci-biology/bowtie/bowtie-2.2.4.ebuild rename to sci-biology/bowtie/bowtie-2.2.5.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 60ba53b88755c62f589c3787765bd6f39da78eef Author: Ted Tanberry gmail com> AuthorDate: Fri Feb 6 08:52:03 2015 + Commit: Christoph Junghans gentoo org> CommitDate: Fri Feb 6 20:24:01 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60ba53b8 Updated bowtie:{1,2} ebuilds to match current ebuild policy. --- sci-biology/bowtie/bowtie-1.1.1.ebuild | 29 +++-- sci-biology/bowtie/bowtie-2.2.4.ebuild | 23 --- 2 files changed, 31 insertions(+), 21 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index ad20591..f152518 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -4,22 +4,27 @@ EAPI=5 -inherit base eutils toolchain-funcs +inherit eutils toolchain-funcs DESCRIPTION="An ultrafast memory-efficient short read aligner" HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" LICENSE="Artistic" SLOT="1" -IUSE="" KEYWORDS="~amd64 ~x86 ~x64-macos" +IUSE="examples" + DEPEND="app-arch/unzip" RDEPEND="" PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) +src_prepare() { + epatch ${PATCHES[@]} +} + src_compile() { unset CFLAGS emake \ @@ -29,14 +34,18 @@ src_compile() { } src_install() { - dobin bowtie bowtie-* - exeinto /usr/share/${PN}/scripts - doexe scripts/* + dobin ${PN} ${PN}-* - insinto /usr/share/${PN} - doins -r genomes indexes + exeinto /usr/libexec/${PN} + doexe scripts/* - newman MANUAL bowtie.1 + newman MANUAL ${PN} dodoc AUTHORS NEWS TUTORIAL doc/README - dohtml doc/{manual.html,style.css} + docinto html + dodoc doc/{manual.html,style.css} + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi } diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild index 19e0bca..4b518ca 100644 --- a/sci-biology/bowtie/bowtie-2.2.4.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit base eutils toolchain-funcs +inherit eutils toolchain-funcs DESCRIPTION="An ultrafast memory-efficient short read aligner" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; @@ -12,9 +12,11 @@ SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source LICENSE="GPL-3" SLOT="2" -IUSE="examples" KEYWORDS="~amd64 ~x86" +IUSE="examples cpu_flags_x86_sse2" +REQUIRED_USE="cpu_flags_x86_sse2" + RDEPEND="dev-lang/perl" DEPEND="${RDEPEND} app-arch/unzip" @@ -23,16 +25,13 @@ S="${WORKDIR}/${PN}2-${PV}" PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) -pkg_pretend() { - grep "sse2" /proc/cpuinfo > /dev/null - if [[ $? -ne 0 ]] ; then - ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine." - fi +src_prepare() { + epatch ${PATCHES[@]} } src_compile() { + unset CFLAGS emake \ - CC="$(tc-getCC)" \ CXX="$(tc-getCXX)" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" @@ -40,12 +39,14 @@ src_compile() { src_install() { dobin ${PN}2 ${PN}2-* - exeinto /usr/share/${PN}2/scripts + + exeinto /usr/libexec/${PN}2 doexe scripts/* - newman MANUAL ${PN}2.1 + newman MANUAL ${PN}2.2 dodoc AUTHORS NEWS TUTORIAL - dohtml doc/manual.html doc/style.css + docinto html + dodoc doc/{manual.html,style.css} if use examples; then insinto /usr/share/${PN}2
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: d9b4902dd52631d0ff4cbf2d92a1448c722989fd Author: Ted Tanberry gmail com> AuthorDate: Sat Feb 7 13:03:26 2015 + Commit: Christoph Junghans gentoo org> CommitDate: Sat Feb 7 13:03:26 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d9b4902d Added die to sed command for bowtie-1.1.1.ebuild --- sci-biology/bowtie/bowtie-1.1.1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index bc6d514..536e9d8 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -24,7 +24,7 @@ HTML_DOCS=( doc/{manual.html,style.css} ) src_prepare() { # Suppress useless -Wall pollution - sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile + sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die } src_compile() {
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 59c62dccda24a226ceb535dee59e081c4f1002eb Author: Ted Tanberry gmail com> AuthorDate: Thu Feb 5 21:54:51 2015 + Commit: Christoph Junghans gentoo org> CommitDate: Fri Feb 6 20:24:01 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=59c62dcc Updated sci-biology/bowtie. Bowtie1 is now properly slotted in SLOT=1. Additional build system fixes. --- sci-biology/bowtie/bowtie-1.1.1.ebuild | 42 ++ .../{bowtie-2.1.0.ebuild => bowtie-2.2.4.ebuild} | 14 .../bowtie/files/bowtie-1.1.1-buildsystem.patch| 37 +++ ...system.patch => bowtie-2.2.4-buildsystem.patch} | 21 ++- 4 files changed, 97 insertions(+), 17 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild new file mode 100644 index 000..ad20591 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit base eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip" + +LICENSE="Artistic" +SLOT="1" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) + +src_compile() { + unset CFLAGS + emake \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + + insinto /usr/share/${PN} + doins -r genomes indexes + + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL doc/README + dohtml doc/{manual.html,style.css} +} diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild similarity index 82% rename from sci-biology/bowtie/bowtie-2.1.0.ebuild rename to sci-biology/bowtie/bowtie-2.2.4.ebuild index aedf017..19e0bca 100644 --- a/sci-biology/bowtie/bowtie-2.1.0.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild @@ -1,13 +1,13 @@ -# 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 toolchain-funcs +inherit base eutils toolchain-funcs DESCRIPTION="An ultrafast memory-efficient short read aligner" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" LICENSE="GPL-3" @@ -21,6 +21,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}/${PN}2-${PV}" +PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) + pkg_pretend() { grep "sse2" /proc/cpuinfo > /dev/null if [[ $? -ne 0 ]] ; then @@ -28,14 +30,10 @@ pkg_pretend() { fi } -src_prepare() { - epatch "${FILESDIR}/${P}-buildsystem.patch" -} - src_compile() { emake \ CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" } diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch new file mode 100644 index 000..9563a33 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch @@ -0,0 +1,37 @@ +--- Makefile Makefile +@@ -5,16 +5,11 @@ + SEQAN_DIR = SeqAn-1.1 + SEQAN_INC = -I $(SEQAN_DIR) + INC = $(SEQAN_INC) -I third_party +-CPP = g++ +-CXX = $(CPP) +-CC = gcc + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 + BOWTIE_SHARED_MEM = 1 + EXTRA_FLAGS = +-EXTRA_CFLAGS = + EXTRA_CXXFLAGS = +-CFLAGS += $(EXTRA_CFLAGS) + CXXFLAGS += $(EXTRA_CXXFLAGS) + + # Detect Cygwin or MinGW +@@ -127,7 +122,7 @@ + endif + + DEBUG_FLAGS = -O0 -g3 -m64 +-RELEASE_FLAGS = -O3 -m64 ++RELEASE_FLAGS = $(CXXFLAGS) + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE + +@@ -198,7 +193,7 @@ + $(MM_DEF) \ + $(SHMEM_DEF) + +-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) ++ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS) + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" + diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch similarity index 55% rename from sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch rename to sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch index 97300b1..8b9218b 100644 --- a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch +++ b/sci-biolo
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 9944df7ebb74c77f354dba013b5ac9d4bdab0c8f Author: Ted Tanberry gmail com> AuthorDate: Fri Feb 6 21:15:40 2015 + Commit: Christoph Junghans gentoo org> CommitDate: Fri Feb 6 21:15:40 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9944df7e Removed all patches, setting CXXFLAGS and such via emake now. Fixed the wrong manpage categories. --- sci-biology/bowtie/ChangeLog | 6 +++- sci-biology/bowtie/bowtie-1.1.1.ebuild | 18 ++- sci-biology/bowtie/bowtie-2.2.4.ebuild | 19 +-- .../bowtie/files/bowtie-1.1.1-buildsystem.patch| 37 -- .../bowtie/files/bowtie-2.2.4-buildsystem.patch| 23 -- 5 files changed, 23 insertions(+), 80 deletions(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 1a636c5..f3d98e2 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/bowtie -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Feb 2015; Ted Tanberry bowtie-1.1.1.ebuild, + bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build + system bugs + 28 Sep 2013; Justin Lecher bowtie-2.1.0.ebuild: Exchange common variables, fix SRC_URI diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index f152518..bc6d514 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -19,16 +19,20 @@ IUSE="examples" DEPEND="app-arch/unzip" RDEPEND="" -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) src_prepare() { - epatch ${PATCHES[@]} + # Suppress useless -Wall pollution + sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile } src_compile() { - unset CFLAGS emake \ - CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS}" } @@ -39,10 +43,8 @@ src_install() { exeinto /usr/libexec/${PN} doexe scripts/* - newman MANUAL ${PN} - dodoc AUTHORS NEWS TUTORIAL doc/README - docinto html - dodoc doc/{manual.html,style.css} + newman MANUAL ${PN}.1 + einstalldocs if use examples; then insinto /usr/share/${PN} diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild index 4b518ca..d8059fc 100644 --- a/sci-biology/bowtie/bowtie-2.2.4.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild @@ -23,16 +23,15 @@ DEPEND="${RDEPEND} S="${WORKDIR}/${PN}2-${PV}" -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) - -src_prepare() { - epatch ${PATCHES[@]} -} +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) src_compile() { - unset CFLAGS emake \ - CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" } @@ -43,10 +42,8 @@ src_install() { exeinto /usr/libexec/${PN}2 doexe scripts/* - newman MANUAL ${PN}2.2 - dodoc AUTHORS NEWS TUTORIAL - docinto html - dodoc doc/{manual.html,style.css} + newman MANUAL ${PN}2.1 + einstalldocs if use examples; then insinto /usr/share/${PN}2 diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch deleted file mode 100644 index 9563a33..000 --- a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch +++ /dev/null @@ -1,37 +0,0 @@ Makefile -+++ Makefile -@@ -5,16 +5,11 @@ - SEQAN_DIR = SeqAn-1.1 - SEQAN_INC = -I $(SEQAN_DIR) - INC = $(SEQAN_INC) -I third_party --CPP = g++ --CXX = $(CPP) --CC = gcc - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 1 - EXTRA_FLAGS = --EXTRA_CFLAGS = - EXTRA_CXXFLAGS = --CFLAGS += $(EXTRA_CFLAGS) - CXXFLAGS += $(EXTRA_CXXFLAGS) - - # Detect Cygwin or MinGW -@@ -127,7 +122,7 @@ - endif - - DEBUG_FLAGS = -O0 -g3 -m64 --RELEASE_FLAGS = -O3 -m64 -+RELEASE_FLAGS = $(CXXFLAGS) - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE - -@@ -198,7 +193,7 @@ - $(MM_DEF) \ - $(SHMEM_DEF) - --ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) -+ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS) - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" - diff --g