[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/

2021-12-13 Thread Andrew Ammerlaan 
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/

2021-03-17 Thread Andrew Ammerlaan 
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/

2021-03-16 Thread Andrew Ammerlaan 
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/

2021-03-16 Thread Andrew Ammerlaan 
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/

2021-03-06 Thread Andrew Ammerlaan 
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
-+++

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

2021-03-06 Thread Andrew Ammerlaan 
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/

2020-12-30 Thread Martin Mokrejs 
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/

2020-02-28 Thread Martin Mokrejs 
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/

2020-02-26 Thread Martin Mokrejs 
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/

2019-12-23 Thread Martin Mokrejs 
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/

2019-03-29 Thread Martin Mokrejs 
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/

2019-03-27 Thread Martin Mokrejs 
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/

2019-03-25 Thread Martin Mokrejs 
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/

2019-02-19 Thread Martin Mokrejs 
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/

2019-02-19 Thread Martin Mokrejs 
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/

2019-02-19 Thread Martin Mokrejs 
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/

2019-02-18 Thread Martin Mokrejs 
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" \
+

[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/

2015-10-15 Thread Justin Lecher 
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

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

2015-10-12 Thread Marius Brehler 
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/

2015-10-12 Thread Marius Brehler 
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/

2015-10-12 Thread Marius Brehler 
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/

2015-05-01 Thread Martin Mokrejs 
commit: a6949bfe7f087ab37f5ebf875ecc154dda9d8593
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri May  1 20:37:44 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT 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 mmokr...@fold.natur.cuni.cz 
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/

2015-04-28 Thread Martin Mokrejs 
commit: 56eef21f8af41d10246dc582ce51ec09cd514c3e
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Mon Apr 27 11:00:54 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT 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 mmokr...@fold.natur.cuni.cz
+  +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 ted.tanbe...@gmail.com bowtie-1.1.1.ebuild,
   bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
   system bugs
 
   28 Sep 2013; Justin Lecher j...@gentoo.org 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/, sci-biology/bowtie/files/

2015-02-08 Thread Christoph Junghans 
commit: 9944df7ebb74c77f354dba013b5ac9d4bdab0c8f
Author: Ted Tanberry ted.tanberry AT gmail DOT com
AuthorDate: Fri Feb  6 21:15:40 2015 +
Commit: Christoph Junghans ottxor AT gentoo DOT 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 ted.tanbe...@gmail.com bowtie-1.1.1.ebuild,
+  bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
+  system bugs
+
   28 Sep 2013; Justin Lecher j...@gentoo.org 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)

[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/

2015-02-08 Thread Christoph Junghans 
commit: 59c62dccda24a226ceb535dee59e081c4f1002eb
Author: Ted Tanberry ted.tanberry AT gmail DOT com
AuthorDate: Thu Feb  5 21:54:51 2015 +
Commit: Christoph Junghans ottxor AT gentoo DOT 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
+++

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

2015-02-08 Thread Christoph Junghans 
commit: d9b4902dd52631d0ff4cbf2d92a1448c722989fd
Author: Ted Tanberry ted.tanberry AT gmail DOT com
AuthorDate: Sat Feb  7 13:03:26 2015 +
Commit: Christoph Junghans ottxor AT gentoo DOT 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/

2015-02-08 Thread Christoph Junghans 
commit: 60ba53b88755c62f589c3787765bd6f39da78eef
Author: Ted Tanberry ted.tanberry AT gmail DOT com
AuthorDate: Fri Feb  6 08:52:03 2015 +
Commit: Christoph Junghans ottxor AT gentoo DOT 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