[gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/
commit: af272af3acae1acbae751c484d550f1206679550
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 13:04:01 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 13:04:01 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=af272af3
sci-biology/nxtrim: EAPI bump, vers 0.4.3, fix install
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
.../nxtrim/{nxtrim-.ebuild => nxtrim-0.4.3.ebuild} | 18 +-
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/sci-biology/nxtrim/nxtrim-.ebuild
b/sci-biology/nxtrim/nxtrim-0.4.3.ebuild
similarity index 54%
rename from sci-biology/nxtrim/nxtrim-.ebuild
rename to sci-biology/nxtrim/nxtrim-0.4.3.ebuild
index 9a12a0226..6ccd90101 100644
--- a/sci-biology/nxtrim/nxtrim-.ebuild
+++ b/sci-biology/nxtrim/nxtrim-0.4.3.ebuild
@@ -1,23 +1,23 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-
-inherit git-r3 eutils
+EAPI=7
DESCRIPTION="Trim Illumina TruSeq adapters and split reads by Nextera MatePair
linker"
HOMEPAGE="https://github.com/sequencing/NxTrim;
-EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git;
+SRC_URI="https://github.com/sequencing/NxTrim/archive/v${PV}.tar.gz ->
${P}.tar.gz"
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS="" # https://github.com/sequencing/NxTrim/issues/32
-IUSE=""
+KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}"
+S="${WORKDIR}/NxTrim-${PV}"
+
src_install(){
- dobin nxtrim mergeReads
- dodoc README.md
+ dobin nxtrim scripts/*
+ einstalldocs
+ dodoc -r docs/*
}
[gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/, sci-biology/nxtrim/files/
commit: a3f4a06e9718b69c63c9fcf6a50e4268c26759dd
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Apr 12 17:46:57 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Apr 12 17:46:57 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3f4a06e
sci-biology/nxtrim: drop patch accepted by upstream now
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/nxtrim/files/Makefile.patch | 43 -
sci-biology/nxtrim/nxtrim-.ebuild | 5
2 files changed, 48 deletions(-)
diff --git a/sci-biology/nxtrim/files/Makefile.patch
b/sci-biology/nxtrim/files/Makefile.patch
deleted file mode 100644
index fb7da0a50..0
--- a/sci-biology/nxtrim/files/Makefile.patch
+++ /dev/null
@@ -1,43 +0,0 @@
Makefile.ori 2017-04-06 23:38:08.591353594 +0200
-+++ Makefile 2017-04-06 23:41:34.127107768 +0200
-@@ -1,12 +1,12 @@
--Cxx = g++
-+CXX ?= g++
-
-
--CFLAGS = -O3
--LFLAGS= -lz
-+CXXFLAGS ?= -O3
-+LFLAGS = -lz
-
- all: mergeReads nxtrim
-
--debug: CFLAGS = -Wall -g
-+debug: CXXFLAGS += -Wall -g
- debug: all
-
- GIT_HASH := $(shell git describe --abbrev=4 --always )
-@@ -21,17 +21,17 @@
-
-
- unit_test: test.cpp fastqlib.o utilityfunc.o matepair.o
-- $(CXX) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o
unit_test $(LFLAGS)
-+ $(CXX) $(CXXFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o
unit_test $(LFLAGS)
- nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o version.h
-- $(CXX) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o
nxtrim $(LFLAGS)
-+ $(CXX) $(CXXFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o
nxtrim $(LFLAGS)
- mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h
version.h
-- $(CXX) $(CFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads
$(LFLAGS)
-+ $(CXX) $(CXXFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o
mergeReads $(LFLAGS)
- matepair.o: matepair.cpp matepair.h fastqlib.h
-- $(CXX) $(CFLAGS) -c matepair.cpp
-+ $(CXX) $(CXXFLAGS) -c matepair.cpp
- fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h
-- $(CXX) $(CFLAGS) -c fastqlib.cpp
-+ $(CXX) $(CXXFLAGS) -c fastqlib.cpp
- utilityfunc.o: utilityfunc.cpp utilityfunc.h
-- $(CXX) $(CFLAGS) -c utilityfunc.cpp
-+ $(CXX) $(CXXFLAGS) -c utilityfunc.cpp
- test: nxtrim
- bash example/run_test.sh
- clean:
diff --git a/sci-biology/nxtrim/nxtrim-.ebuild
b/sci-biology/nxtrim/nxtrim-.ebuild
index 4eb879880..9a12a0226 100644
--- a/sci-biology/nxtrim/nxtrim-.ebuild
+++ b/sci-biology/nxtrim/nxtrim-.ebuild
@@ -17,11 +17,6 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}"
-src_prepare(){
- eapply_user
- epatch "${FILESDIR}"/Makefile.patch #
https://github.com/sequencing/NxTrim/pull/31
-}
-
src_install(){
dobin nxtrim mergeReads
dodoc README.md
[gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/
commit: 575f04f3597dd07b5d6332be5300aacc0175b685 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Apr 6 23:18:13 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Apr 6 23:18:13 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=575f04f3 sci-biology/nxtrim: use proper protocol name Package-Manager: Portage-2.3.5, Repoman-2.3.1 sci-biology/nxtrim/nxtrim-.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/nxtrim/nxtrim-.ebuild b/sci-biology/nxtrim/nxtrim-.ebuild index b71255f03..4eb879880 100644 --- a/sci-biology/nxtrim/nxtrim-.ebuild +++ b/sci-biology/nxtrim/nxtrim-.ebuild @@ -5,7 +5,7 @@ EAPI=6 inherit git-r3 eutils -DESCRIPTION="Trim Illumina TruSeq adapters and split reads by NEBnext MatePair linker" +DESCRIPTION="Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker" HOMEPAGE="https://github.com/sequencing/NxTrim; EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git;
[gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/, sci-biology/nxtrim/files/
commit: 77bec8065ed5b62840430e4d0e90814616757a6f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Apr 6 21:53:28 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 6 21:53:28 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=77bec806
sci-biology/nxtrim: new package
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/nxtrim/files/Makefile.patch | 43 +
sci-biology/nxtrim/metadata.xml | 12 +
sci-biology/nxtrim/nxtrim-.ebuild | 28 +
3 files changed, 83 insertions(+)
diff --git a/sci-biology/nxtrim/files/Makefile.patch
b/sci-biology/nxtrim/files/Makefile.patch
new file mode 100644
index 0..fb7da0a50
--- /dev/null
+++ b/sci-biology/nxtrim/files/Makefile.patch
@@ -0,0 +1,43 @@
+--- Makefile.ori 2017-04-06 23:38:08.591353594 +0200
Makefile 2017-04-06 23:41:34.127107768 +0200
+@@ -1,12 +1,12 @@
+-Cxx = g++
++CXX ?= g++
+
+
+-CFLAGS = -O3
+-LFLAGS= -lz
++CXXFLAGS ?= -O3
++LFLAGS = -lz
+
+ all: mergeReads nxtrim
+
+-debug: CFLAGS = -Wall -g
++debug: CXXFLAGS += -Wall -g
+ debug: all
+
+ GIT_HASH := $(shell git describe --abbrev=4 --always )
+@@ -21,17 +21,17 @@
+
+
+ unit_test: test.cpp fastqlib.o utilityfunc.o matepair.o
+- $(CXX) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o
unit_test $(LFLAGS)
++ $(CXX) $(CXXFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o
unit_test $(LFLAGS)
+ nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o version.h
+- $(CXX) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o
nxtrim $(LFLAGS)
++ $(CXX) $(CXXFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o
nxtrim $(LFLAGS)
+ mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h
version.h
+- $(CXX) $(CFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads
$(LFLAGS)
++ $(CXX) $(CXXFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o
mergeReads $(LFLAGS)
+ matepair.o: matepair.cpp matepair.h fastqlib.h
+- $(CXX) $(CFLAGS) -c matepair.cpp
++ $(CXX) $(CXXFLAGS) -c matepair.cpp
+ fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h
+- $(CXX) $(CFLAGS) -c fastqlib.cpp
++ $(CXX) $(CXXFLAGS) -c fastqlib.cpp
+ utilityfunc.o: utilityfunc.cpp utilityfunc.h
+- $(CXX) $(CFLAGS) -c utilityfunc.cpp
++ $(CXX) $(CXXFLAGS) -c utilityfunc.cpp
+ test: nxtrim
+ bash example/run_test.sh
+ clean:
diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml
new file mode 100644
index 0..f68a1b6fa
--- /dev/null
+++ b/sci-biology/nxtrim/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
diff --git a/sci-biology/nxtrim/nxtrim-.ebuild
b/sci-biology/nxtrim/nxtrim-.ebuild
new file mode 100644
index 0..856f63662
--- /dev/null
+++ b/sci-biology/nxtrim/nxtrim-.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit git-r3 eutils
+
+DESCRIPTION="Trim Illumina TruSeq adapters and split reads by NEBnext MatePair
linker"
+HOMEPAGE="https://github.com/sequencing/NxTrim;
+EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git;
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ eapply_user
+ epatch "${FILESDIR}"/Makefile.patch #
https://github.com/sequencing/NxTrim/pull/31
+}
+
+src_install(){
+ dobin nxtrim mergeReads
+ dodoc README.md
+}
