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* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2014-07-02 23:15 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2014-07-02 23:15 UTC (permalink / raw
  To: gentoo-commits

commit:     67b7a57059dc518a94c8c2af71a2ef0317b2cded
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul  2 23:13:20 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul  2 23:13:20 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=67b7a570

sci-biology/jellyfish: new package, works

Package-Manager: portage-2.2.7

---
 sci-biology/jellyfish/ChangeLog              |  9 +++++++++
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 18 ++++++++++++++++++
 sci-biology/jellyfish/metadata.xml           |  9 +++++++++
 3 files changed, 36 insertions(+)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
new file mode 100644
index 0000000..a5df6d9
--- /dev/null
+++ b/sci-biology/jellyfish/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/jellyfish
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jellyfish-2.1.3 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +jellyfish-2.1.3.ebuild, +metadata.xml:
+  sci-biology/jellyfish: new package, works

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
new file mode 100644
index 0000000..4ac06b2
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="k-mer counter withing reads for assemblies"
+HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/jellyfish/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-01-07 21:43 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:43 UTC (permalink / raw
  To: gentoo-commits

commit:     a02cb28232bd985520b07b000bd19ae6bc8fb025
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan  7 21:42:09 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan  7 21:42:09 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a02cb282

added a comment on old version

Package-Manager: portage-2.2.7

---
 sci-biology/jellyfish/ChangeLog              | 6 +++++-
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 4 +++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index a5df6d9..cf2f8f7 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/jellyfish
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-2.1.3.ebuild:
+  added a comment on old version
+
 *jellyfish-2.1.3 (02 Jul 2014)
 
   02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 4ac06b2..51f683c 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -9,6 +9,8 @@ HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
 
+# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
+
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-03-31 19:50 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-03-31 19:50 UTC (permalink / raw
  To: gentoo-commits

commit:     ca1d210fcb7805b9b0facbf1e6896d84e123f4cc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 31 19:50:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 31 19:50:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca1d210f

sci-biology/jellyfish: fix installation of header *.hpp files into /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog              | 5 +++++
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 9 ++++++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index cf2f8f7..5a84c98 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-2.1.3.ebuild:
+  sci-biology/jellyfish: fix installation of header *.hpp files into
+  /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code
+
   07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-2.1.3.ebuild:
   added a comment on old version

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 51f683c..cceca4b 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-DESCRIPTION="k-mer counter withing reads for assemblies"
+DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
@@ -18,3 +18,10 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
+
+src_install(){
+	default
+	mkdir -p ${D}/usr/include/${PN} || die
+	mv ${D}/usr/include/${P}/${PN}/* ${D}/usr/include/${PN}/ || die
+	rm -rf ${D}/usr/include/${P}
+}


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-03-31 22:34 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-03-31 22:34 UTC (permalink / raw
  To: gentoo-commits

commit:     3b210b2d6e82815216cd3c46bdec443ddbd49018
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 31 22:33:51 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 31 22:33:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b210b2d

sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog              | 4 ++++
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 7 ++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index 5a84c98..d3ea5cd 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -4,6 +4,10 @@
 
   31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-2.1.3.ebuild:
+  sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc
+
+  31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-2.1.3.ebuild:
   sci-biology/jellyfish: fix installation of header *.hpp files into
   /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code
 

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index cceca4b..c217e42 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -21,7 +21,8 @@ RDEPEND="${DEPEND}"
 
 src_install(){
 	default
-	mkdir -p ${D}/usr/include/${PN} || die
-	mv ${D}/usr/include/${P}/${PN}/* ${D}/usr/include/${PN}/ || die
-	rm -rf ${D}/usr/include/${P}
+	sed -e 's#jellyfish-2.1.3#jellyfish#' -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
+	mkdir -p "${D}/usr/include/${PN}" || die
+	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
+	rm -rf "${D}/usr/include/${P}"
 }


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-04-30 10:11 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-04-30 10:11 UTC (permalink / raw
  To: gentoo-commits

commit:     50d3d1d5b5c59652a2348b4105490cc698125b89
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 10:10:36 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 10:10:36 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=50d3d1d5

sci-biology/jellyfish: version bump; ebuild cleanup

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/jellyfish-2.1.3.ebuild                          | 4 ++--
 .../jellyfish/{jellyfish-2.1.3.ebuild => jellyfish-2.1.4.ebuild}      | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index c217e42..0d45b48 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}"
 
 src_install(){
 	default
-	sed -e 's#jellyfish-2.1.3#jellyfish#' -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
 	mkdir -p "${D}/usr/include/${PN}" || die
 	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
 	rm -rf "${D}/usr/include/${P}"

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
similarity index 83%
copy from sci-biology/jellyfish/jellyfish-2.1.3.ebuild
copy to sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index c217e42..0d45b48 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}"
 
 src_install(){
 	default
-	sed -e 's#jellyfish-2.1.3#jellyfish#' -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
 	mkdir -p "${D}/usr/include/${PN}" || die
 	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
 	rm -rf "${D}/usr/include/${P}"


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-04-30 20:32 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-04-30 20:32 UTC (permalink / raw
  To: gentoo-commits

commit:     2084f45bf4de01d7c6c603fb294b54b35386e97b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 20:32:21 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 20:32:21 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2084f45b

sci-biology/jellyfish: added missing DEPEND on virtual/pkgconfig so that the jellyfish-2.0.pc gets installed properly

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog              | 5 +++++
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 4 +++-
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild | 4 +++-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index d3ea5cd..ddaab96 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild:
+  sci-biology/jellyfish: added missing DEPEND on virtual/pkgconfig so that the
+  jellyfish-2.0.pc gets installed properly
+
   31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-2.1.3.ebuild:
   sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 0d45b48..243cd46 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -17,10 +17,12 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	virtual/pkgconfig"
 
 src_install(){
 	default
+	# beware the filename say 2.0 instead of 2.1. does it matter?
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
 	mkdir -p "${D}/usr/include/${PN}" || die
 	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index 0d45b48..243cd46 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -17,10 +17,12 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	virtual/pkgconfig"
 
 src_install(){
 	default
+	# beware the filename say 2.0 instead of 2.1. does it matter?
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
 	mkdir -p "${D}/usr/include/${PN}" || die
 	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-04-30 21:28 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-04-30 21:28 UTC (permalink / raw
  To: gentoo-commits

commit:     d5bb19eb26c17d1639a37265acd3ea31d65a79b3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 21:27:46 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 21:27:46 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d5bb19eb

sci-biology/jellyfish: added older version, added HalfLICENSE to all ebuilds

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog                                    | 6 ++++++
 .../jellyfish/{jellyfish-2.1.3.ebuild => jellyfish-1.1.11.ebuild}  | 7 ++++---
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild                       | 2 +-
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild                       | 2 +-
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index ddaab96..fe0d9c4 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*jellyfish-1.1.11 (30 Apr 2015)
+
+  30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +jellyfish-1.1.11.ebuild, jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild:
+  sci-biology/jellyfish: added older version, added HalfLICENSE to all ebuilds
+
   30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild:
   sci-biology/jellyfish: added missing DEPEND on virtual/pkgconfig so that the

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
similarity index 76%
copy from sci-biology/jellyfish/jellyfish-2.1.3.ebuild
copy to sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index 243cd46..082ef0c 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -6,12 +6,13 @@ EAPI=5
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
+	http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
+# also was bundled in quorum-0.2.1 and MaSuRca-2.1.0
 
-LICENSE="GPL-3"
+LICENSE="GPL-3+ HalfLICENSE"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 243cd46..1cc3010 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
-LICENSE="GPL-3"
+LICENSE="GPL-3+ HalfLICENSE"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index 243cd46..1cc3010 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
-LICENSE="GPL-3"
+LICENSE="GPL-3+ HalfLICENSE"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-04-30 21:29 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-04-30 21:29 UTC (permalink / raw
  To: gentoo-commits

commit:     22c41949bd2a07f4d261391d89b9a527952d221f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 21:29:18 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 21:29:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=22c41949

sci-biology/jellyfish: fixed homepage for the old version

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog               | 4 ++++
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index fe0d9c4..ffe60b9 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-1.1.11.ebuild:
+  sci-biology/jellyfish: fixed homepage for the old version
+
 *jellyfish-1.1.11 (30 Apr 2015)
 
   30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index 082ef0c..ae87af1 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -5,7 +5,7 @@
 EAPI=5
 
 DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
 SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
 	http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf"
 


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-04-30 22:02 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-04-30 22:02 UTC (permalink / raw
  To: gentoo-commits

commit:     807e154c5033cdff04e4f1db51cb7e15b1b8fe75
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 22:01:38 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 22:01:38 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=807e154c

sci-biology/jellyfish: added a note

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog               | 4 ++++
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 1 +
 2 files changed, 5 insertions(+)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index ffe60b9..8791b67 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -4,6 +4,10 @@
 
   30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-1.1.11.ebuild:
+  sci-biology/jellyfish: added a note
+
+  30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-1.1.11.ebuild:
   sci-biology/jellyfish: fixed homepage for the old version
 
 *jellyfish-1.1.11 (30 Apr 2015)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index ae87af1..4686679 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -11,6 +11,7 @@ SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 # also was bundled in quorum-0.2.1 and MaSuRca-2.1.0
+# also bundled in SEECER-0.1.3
 
 LICENSE="GPL-3+ HalfLICENSE"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-05-04 14:45 Justin Lecher
  0 siblings, 0 replies; 29+ messages in thread
From: Justin Lecher @ 2015-05-04 14:45 UTC (permalink / raw
  To: gentoo-commits

commit:     fa9b7040b13664449a9b5258bc99c7a7431bba5a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May  4 14:45:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May  4 14:45:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa9b7040

sci-biology/jellyfish: Correct license from HalfLICENSE to BSD as they are identical

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog               | 5 +++++
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 4 ++--
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild  | 4 ++--
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild  | 4 ++--
 4 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index 8791b67..63efcad 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 May 2015; Justin Lecher <jlec@gentoo.org> jellyfish-1.1.11.ebuild,
+  jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild:
+  sci-biology/jellyfish: Correct license from HalfLICENSE to BSD as they are
+  identical
+
   30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   jellyfish-1.1.11.ebuild:
   sci-biology/jellyfish: added a note

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index 4686679..4708a9b 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -13,13 +13,13 @@ SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
 # also was bundled in quorum-0.2.1 and MaSuRca-2.1.0
 # also bundled in SEECER-0.1.3
 
-LICENSE="GPL-3+ HalfLICENSE"
+LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}
+DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
 src_install(){

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 1cc3010..6003a48 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -11,13 +11,13 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
-LICENSE="GPL-3+ HalfLICENSE"
+LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}
+DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
 src_install(){

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index 1cc3010..6003a48 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -11,13 +11,13 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
-LICENSE="GPL-3+ HalfLICENSE"
+LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}
+DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
 src_install(){


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2015-11-13 19:11 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2015-11-13 19:11 UTC (permalink / raw
  To: gentoo-commits

commit:     e563ef0844dacf85a0dffc25c134f108465c7255
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 13 19:10:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 13 19:10:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e563ef08

sci-biology/jellyfish: fix filename generated by pkgconfig

Package-Manager: portage-2.2.18

 sci-biology/jellyfish/ChangeLog               | 4 ++++
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 3 +--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
index 5abd4ea..9132f22 100644
--- a/sci-biology/jellyfish/ChangeLog
+++ b/sci-biology/jellyfish/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  jellyfish-1.1.11.ebuild:
+  sci-biology/jellyfish: fix filename generated by pkgconfig
+
   04 May 2015; Justin Lecher <jlec@gentoo.org> jellyfish-1.1.11.ebuild,
   jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild:
   sci-biology/jellyfish: Correct license from HalfLICENSE to BSD as they are

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index 2154ee6..9d36444 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -24,8 +24,7 @@ DEPEND="${RDEPEND}
 
 src_install(){
 	default
-	# beware the filename say 2.0 instead of 2.1. does it matter?
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-1.1.pc || die
 	mkdir -p "${D}/usr/include/${PN}" || die
 	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
 	rm -rf "${D}/usr/include/${P}"


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2016-03-06 19:44 Justin Lecher
  0 siblings, 0 replies; 29+ messages in thread
From: Justin Lecher @ 2016-03-06 19:44 UTC (permalink / raw
  To: gentoo-commits

commit:     c5a275736294026002e61d4d3582c1c8e3e8ca51
Author:     mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Jan 23 19:31:54 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 19:43:28 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5a27573

sci-biology/jellyfish: bump EAPI=6 and QA

* respect ${EPREFIX}, fix pkg-config paths
* add missing die

 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 12 ++++++------
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild  | 13 ++++++-------
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild  | 13 ++++++-------
 3 files changed, 18 insertions(+), 20 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index 9d36444..acb7729 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
@@ -24,8 +24,8 @@ DEPEND="${RDEPEND}
 
 src_install(){
 	default
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-1.1.pc || die
-	mkdir -p "${D}/usr/include/${PN}" || die
-	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
-	rm -rf "${D}/usr/include/${P}"
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.pc || die
+	mkdir -p "${ED}/usr/include/${PN}" || die
+	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" || die
+	rm -r "${ED}/usr/include/${P}" || die
 }

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index 226b260..d38d7bb 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
@@ -22,9 +22,8 @@ DEPEND="${RDEPEND}
 
 src_install(){
 	default
-	# beware the filename say 2.0 instead of 2.1. does it matter?
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
-	mkdir -p "${D}/usr/include/${PN}" || die
-	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
-	rm -rf "${D}/usr/include/${P}"
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
+	mkdir -p "${ED}/usr/include/${PN}" || die
+	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" || die
+	rm -r "${ED}/usr/include/${P}" || die
 }

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index 226b260..d38d7bb 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
@@ -22,9 +22,8 @@ DEPEND="${RDEPEND}
 
 src_install(){
 	default
-	# beware the filename say 2.0 instead of 2.1. does it matter?
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die
-	mkdir -p "${D}/usr/include/${PN}" || die
-	mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die
-	rm -rf "${D}/usr/include/${P}"
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
+	mkdir -p "${ED}/usr/include/${PN}" || die
+	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" || die
+	rm -r "${ED}/usr/include/${P}" || die
 }


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2016-12-09 16:24 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2016-12-09 16:24 UTC (permalink / raw
  To: gentoo-commits

commit:     a5b2a38c915c223d7c2712301c6802b3e6c3389f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec  9 16:23:50 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec  9 16:23:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a5b2a38c

sci-biology/jellyfish: version bump; respect sse CPU USE flag

Package-Manager: portage-2.3.3

 sci-biology/jellyfish/jellyfish-1.1.11.ebuild              | 14 +++++++++++++-
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild               | 14 +++++++++++++-
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild               | 14 +++++++++++++-
 .../{jellyfish-2.1.3.ebuild => jellyfish-2.2.0.ebuild}     | 14 +++++++++++++-
 4 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
index acb7729..9475622 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=6
 
+inherit eutils flag-o-matic
+
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
 SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
@@ -16,12 +18,22 @@ SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
 LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
 DEPEND=""
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
+src_prepare(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf econf ${myconf[@]}
+	eapply_user
+}
+
 src_install(){
 	default
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.pc || die

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
index d38d7bb..7501aef 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=6
 
+inherit eutils flag-o-matic
+
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
@@ -14,12 +16,22 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
 DEPEND=""
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
+src_prepare(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf econf ${myconf[@]}
+	eapply_user
+}
+
 src_install(){
 	default
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
index d38d7bb..7501aef 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=6
 
+inherit eutils flag-o-matic
+
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
@@ -14,12 +16,22 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
 DEPEND=""
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
+src_prepare(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf econf ${myconf[@]}
+	eapply_user
+}
+
 src_install(){
 	default
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.2.0.ebuild
similarity index 72%
copy from sci-biology/jellyfish/jellyfish-2.1.3.ebuild
copy to sci-biology/jellyfish/jellyfish-2.2.0.ebuild
index d38d7bb..7501aef 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.0.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=6
 
+inherit eutils flag-o-matic
+
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
@@ -14,12 +16,22 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
 LICENSE="GPL-3+ BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
 DEPEND=""
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
+src_prepare(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf econf ${myconf[@]}
+	eapply_user
+}
+
 src_install(){
 	default
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2017-05-15 14:17 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2017-05-15 14:17 UTC (permalink / raw
  To: gentoo-commits

commit:     89745927430667600a2190593e887ccf4eac14e5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 14:17:46 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 14:17:46 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=89745927

sci-biology/jellyfish: version bump, add new CDEPEND on dev-lang/yaggo

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 .../{jellyfish-2.2.0.ebuild => jellyfish-2.2.6.ebuild} | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.0.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
similarity index 70%
rename from sci-biology/jellyfish/jellyfish-2.2.0.ebuild
rename to sci-biology/jellyfish/jellyfish-2.2.6.ebuild
index fd71046ac..99e258e91 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit eutils flag-o-matic
+inherit eutils flag-o-matic autotools
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
+SRC_URI="https://github.com/gmarcais/Jellyfish/archive/v2.2.6.tar.gz -> ${P}.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -17,18 +17,26 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-DEPEND=""
+CDEPEND="dev-lang/yaggo"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
+S="${WORKDIR}/Jellyfish-${PV}"
+
 src_prepare(){
+	eautoreconf
+	default
+}
+
+# TODO: enable compilation of Bindings to Ruby, Python and Perl
+# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
+src_configure(){
 	#  --with-sse              enable SSE
 	#  --with-half             enable half float (16 bits)
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
 	econf econf ${myconf[@]}
-	eapply_user
 }
 
 src_install(){


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2017-05-15 14:21 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2017-05-15 14:21 UTC (permalink / raw
  To: gentoo-commits

commit:     dccca8150240011802245e34055dc76a5dfdabbd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 14:21:04 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 14:21:04 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dccca815

sci-biology/jellyfish: CDEPEND does not work?

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/jellyfish/jellyfish-2.2.6.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
index 99e258e91..6c3ce948b 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
@@ -17,7 +17,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-CDEPEND="dev-lang/yaggo"
+RDEPEND="dev-lang/yaggo"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2017-05-15 15:56 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2017-05-15 15:56 UTC (permalink / raw
  To: gentoo-commits

commit:     bcdbe7d68fad5b1056f370020f236e543952ee4f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 15:56:39 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 15:56:39 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bcdbe7d6

sci-biology/jellyfish: point SRC_URI to proper tarball, drop yaggo DEPENDency

This tarball really doe snot need yaggo for building. See
for whole discussion: https://github.com/gmarcais/Jellyfish/issues/87

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/jellyfish/jellyfish-2.2.6.ebuild | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
index 6c3ce948b..af91bd892 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
@@ -7,7 +7,7 @@ inherit eutils flag-o-matic autotools
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/archive/v2.2.6.tar.gz -> ${P}.tar.gz
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz
 	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -17,12 +17,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-RDEPEND="dev-lang/yaggo"
+RDEPEND=""
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
-S="${WORKDIR}/Jellyfish-${PV}"
-
 src_prepare(){
 	eautoreconf
 	default


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2017-11-21 16:09 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2017-11-21 16:09 UTC (permalink / raw
  To: gentoo-commits

commit:     03271b4b44f838754e7af1b70c62366c42f4d4d2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 21 16:08:54 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 21 16:08:54 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=03271b4b

sci-biology/jellyfish: rename jellyfish to jellyfish1

This will facilitate simultaneous installs of jeelyfish2
and jellyfish, so that sci-biology/SEECER and sci-biology/quorum
could be installed at the same time (both calling "jellyfish"
but quorum needs version 2 and SEECER version 1.
See list of files at https://packages.debian.org/unstable/jellyfish1

Package-Manager: Portage-2.3.14, Repoman-2.3.6

 .../jellyfish/{jellyfish-1.1.11.ebuild => jellyfish-1.1.11-r1.ebuild} | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
similarity index 85%
rename from sci-biology/jellyfish/jellyfish-1.1.11.ebuild
rename to sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
index 9134a98d4..923784ada 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -34,6 +34,8 @@ src_prepare(){
 }
 
 src_install(){
+	# install the binary under jellyfish1 name like Debian/Ubuntu to avoid name clash with jellyfish2 and allow simultaneous installs
+	mv bin/jellyfish bin/jellyfish1 || die
 	default
 	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.pc || die
 	mkdir -p "${ED}/usr/include/${PN}" || die


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2018-04-21 19:43 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2018-04-21 19:43 UTC (permalink / raw
  To: gentoo-commits

commit:     0b235984987db697c4d43270887884e66cf894a3
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 19:43:04 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 19:43:04 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0b235984

sci-biology/jellyfish: install the pdf manual too

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
index 21b002b9c..54cc724eb 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
@@ -48,4 +48,5 @@ src_install(){
 	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
 	rm -r "${ED}/usr/include/${P}" || die
 	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
+	dodoc "${DISTDIR}"/JellyfishUserGuide.pdf
 }


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2018-04-23 19:13 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2018-04-23 19:13 UTC (permalink / raw
  To: gentoo-commits

commit:     026f3272fc9085f69f1a6caf4a1ccb8b9d887ab7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 23 19:13:21 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 23 19:13:21 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=026f3272

sci-biology/jellyfish: install bundled PDF manual

And do not download an old version at all.

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild                      | 5 ++---
 .../jellyfish/{jellyfish-2.2.6-r1.ebuild => jellyfish-2.2.9.ebuild}  | 5 ++---
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
index 54cc724eb..692c9e9ee 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
@@ -7,8 +7,7 @@ inherit eutils flag-o-matic autotools
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
@@ -48,5 +47,5 @@ src_install(){
 	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
 	rm -r "${ED}/usr/include/${P}" || die
 	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-	dodoc "${DISTDIR}"/JellyfishUserGuide.pdf
+	dodoc doc/jellyfish.pdf
 }

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.9.ebuild
similarity index 92%
copy from sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
copy to sci-biology/jellyfish/jellyfish-2.2.9.ebuild
index 54cc724eb..692c9e9ee 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.9.ebuild
@@ -7,8 +7,7 @@ inherit eutils flag-o-matic autotools
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 
@@ -48,5 +47,5 @@ src_install(){
 	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
 	rm -r "${ED}/usr/include/${P}" || die
 	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-	dodoc "${DISTDIR}"/JellyfishUserGuide.pdf
+	dodoc doc/jellyfish.pdf
 }


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2018-05-01 22:13 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2018-05-01 22:13 UTC (permalink / raw
  To: gentoo-commits

commit:     39d413c0adc6a8d96442cc9562c516c53021add8
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  1 22:13:29 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  1 22:13:29 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=39d413c0

sci-biology/jellyfish: version bump and a few tweaks

Install properly PDF documentation.

Use ${PV} in SRC_URI.

Update SRC_URI to reflect github hosting these days.

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 .../jellyfish/{jellyfish-1.1.11-r2.ebuild => jellyfish-1.1.12.ebuild} | 4 ++--
 .../jellyfish/{jellyfish-2.2.9.ebuild => jellyfish-2.2.10.ebuild}     | 0
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
similarity index 91%
rename from sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild
rename to sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index a9b0ce4d1..a22be5187 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -7,8 +7,7 @@ inherit eutils flag-o-matic
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
-SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
-	http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf"
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
 # also was bundled in quorum-0.2.1 and MaSuRca-2.1.0
@@ -45,4 +44,5 @@ src_install(){
 	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
 	rm -r "${ED}/usr/include/${P}" || die
 	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
+	newdoc doc/jellyfish.pdf jellyfish"${SLOT}".pdf
 }

diff --git a/sci-biology/jellyfish/jellyfish-2.2.9.ebuild b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
similarity index 100%
rename from sci-biology/jellyfish/jellyfish-2.2.9.ebuild
rename to sci-biology/jellyfish/jellyfish-2.2.10.ebuild


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2018-09-11 11:21 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2018-09-11 11:21 UTC (permalink / raw
  To: gentoo-commits

commit:     3018cbc70e35cdf24bb18df11e7d59141f65437c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 11 11:21:38 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 11 11:21:38 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3018cbc7

sci-biology/jellyfish: remove doubled econf call

Package-Manager: Portage-2.3.48, Repoman-2.3.10

 sci-biology/jellyfish/jellyfish-1.1.12.ebuild   | 2 +-
 sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild | 2 +-
 sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild | 2 +-
 sci-biology/jellyfish/jellyfish-2.2.10.ebuild   | 2 +-
 sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index a22be5187..d39fb6104 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -28,7 +28,7 @@ src_prepare(){
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf econf ${myconf[@]}
+	econf ${myconf[@]}
 	eapply_user
 }
 

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
index 115848f30..5404d6bfb 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
@@ -27,7 +27,7 @@ src_prepare(){
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf econf ${myconf[@]}
+	econf ${myconf[@]}
 	eapply_user
 }
 

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
index 248e2cef4..11a4a4805 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
@@ -27,7 +27,7 @@ src_prepare(){
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf econf ${myconf[@]}
+	econf ${myconf[@]}
 	eapply_user
 }
 

diff --git a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
index 692c9e9ee..89f9fa231 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
@@ -33,7 +33,7 @@ src_configure(){
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf econf ${myconf[@]}
+	econf ${myconf[@]}
 }
 
 src_install(){

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
index 692c9e9ee..89f9fa231 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
@@ -33,7 +33,7 @@ src_configure(){
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf econf ${myconf[@]}
+	econf ${myconf[@]}
 }
 
 src_install(){


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2019-07-18 16:10 Martin Mokrejs
  0 siblings, 0 replies; 29+ messages in thread
From: Martin Mokrejs @ 2019-07-18 16:10 UTC (permalink / raw
  To: gentoo-commits

commit:     149f20f4275c9b8530d623935f370a2edd84af8d
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 18 16:10:11 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 18 16:10:11 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=149f20f4

sci-biology/jellyfish: version bump

Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../jellyfish/{jellyfish-2.2.6-r1.ebuild => jellyfish-2.3.0.ebuild}     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
similarity index 97%
rename from sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
rename to sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index 89f9fa231..eba4dcc9c 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2021-03-06 11:34 Andrew Ammerlaan
  0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 11:34 UTC (permalink / raw
  To: gentoo-commits

commit:     c85df1ad01fd17212b53c14fda2a36b760f95769
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:33:39 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:33:39 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c85df1ad

sci-biology/jellyfish: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/jellyfish/jellyfish-1.1.12.ebuild | 10 +++++-----
 sci-biology/jellyfish/jellyfish-2.3.0.ebuild  | 12 ++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index d39fb6104..f7b7e1d29 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils flag-o-matic
+inherit flag-o-matic
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
@@ -19,8 +19,8 @@ KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
 DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_prepare(){
 	#  --with-sse              enable SSE

diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index eba4dcc9c..6bd33a14c 100644
--- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils flag-o-matic autotools
+inherit flag-o-matic autotools
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
@@ -16,9 +16,9 @@ SLOT="2"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+DEPEND=""
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_prepare(){
 	eautoreconf


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2021-03-06 11:34 Andrew Ammerlaan
  0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 11:34 UTC (permalink / raw
  To: gentoo-commits

commit:     0ab5b07fa7e7699f34c1c2463d1607156b354487
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:33:59 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:33:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0ab5b07f

sci-biology/jellyfish: cleanup old

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild | 45 ----------------------
 sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild | 45 ----------------------
 sci-biology/jellyfish/jellyfish-2.2.10.ebuild   | 51 -------------------------
 3 files changed, 141 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
deleted file mode 100644
index 5404d6bfb..000000000
--- a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-	eapply_user
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-	sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-}

diff --git a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
deleted file mode 100644
index 11a4a4805..000000000
--- a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-	eapply_user
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-}

diff --git a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
deleted file mode 100644
index 89f9fa231..000000000
--- a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic autotools
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	eautoreconf
-	default
-}
-
-# TODO: enable compilation of Bindings to Ruby, Python and Perl
-# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
-src_configure(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-	dodoc doc/jellyfish.pdf
-}


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2021-06-06  0:38 Jakov Smolić
  0 siblings, 0 replies; 29+ messages in thread
From: Jakov Smolić @ 2021-06-06  0:38 UTC (permalink / raw
  To: gentoo-commits

commit:     53e334d850765ddcf72f8a7316b93c337bcaee45
Author:     Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr>
AuthorDate: Sun Jun  6 00:31:52 2021 +0000
Commit:     Jakov Smolić <jakov.smolic <AT> sartura <DOT> hr>
CommitDate: Sun Jun  6 00:32:14 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53e334d8

sci-biology/jellyfish: Call econf in src_configure in 1.1.12

Closes: https://bugs.gentoo.org/755752
Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr>

 sci-biology/jellyfish/jellyfish-1.1.12.ebuild | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index f7b7e1d29..15a2d7bca 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -18,21 +18,18 @@ SLOT="1"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-DEPEND=""
-DEPEND="${RDEPEND}"
 BDEPEND="virtual/pkgconfig"
 
-src_prepare(){
+src_configure() {
 	#  --with-sse              enable SSE
 	#  --with-half             enable half float (16 bits)
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
 	econf ${myconf[@]}
-	eapply_user
 }
 
-src_install(){
+src_install() {
 	default
 	# install the binary under jellyfish1 name like Debian/Ubuntu to avoid name clash with jellyfish2 and allow simultaneous installs
 	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish1 || die


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2022-01-14 10:10 Andrew Ammerlaan
  0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2022-01-14 10:10 UTC (permalink / raw
  To: gentoo-commits

commit:     f4a2efc5cc14bdcde3643e259fc069af29818570
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 14 10:06:05 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 14 10:06:05 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f4a2efc5

sci-biology/jellyfish: fix configure phase, add missing deps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/jellyfish/jellyfish-2.3.0.ebuild | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index 7a8176f75..e8e3c8fd0 100644
--- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -3,8 +3,6 @@
 
 EAPI=7
 
-inherit autotools
-
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
 SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
@@ -16,15 +14,13 @@ SLOT="2"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-DEPEND=""
+RDEPEND="
+	sci-biology/samtools:0
+	sci-libs/htslib
+"
 DEPEND="${RDEPEND}"
 BDEPEND="virtual/pkgconfig"
 
-src_prepare(){
-	eautoreconf
-	default
-}
-
 # TODO: enable compilation of Bindings to Ruby, Python and Perl
 # '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
 src_configure(){


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2023-04-20  4:11 Horea Christian
  0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-20  4:11 UTC (permalink / raw
  To: gentoo-commits

commit:     1824864d7672cec024e6a09bbd68abfb005f200d
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 20 03:27:41 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 20 03:27:41 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1824864d

sci-biology/jellyfish: add github upstream metadata

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/jellyfish/metadata.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml
index 138cb7705..f2c1cd819 100644
--- a/sci-biology/jellyfish/metadata.xml
+++ b/sci-biology/jellyfish/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">gmarcais/Jellyfish</remote-id>
+	</upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2023-04-20  4:11 Horea Christian
  0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-20  4:11 UTC (permalink / raw
  To: gentoo-commits

commit:     f8c26f3c6899cc2c9de3d1d422f3fd2032c899aa
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 20 04:11:31 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 20 04:11:31 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8c26f3c

sci-biology/jellyfish: update EAPI 7 -> 8

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/jellyfish/jellyfish-1.1.12.ebuild | 4 ++--
 sci-biology/jellyfish/jellyfish-2.3.0.ebuild  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index f008096d6..a6989c2bf 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="https://genome.umd.edu/jellyfish.html"

diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index bd2d2be0d..2237173e0 100644
--- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 DESCRIPTION="k-mer counter within reads for assemblies"
 HOMEPAGE="https://genome.umd.edu/jellyfish.html"


^ permalink raw reply related	[flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
@ 2023-04-20  4:11 Horea Christian
  0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-20  4:11 UTC (permalink / raw
  To: gentoo-commits

commit:     119665a77ed75950a41f19c1b4ea83ea9030569c
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 20 03:26:31 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 20 03:26:31 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=119665a7

sci-biology/jellyfish: update HOMEPAGE

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/jellyfish/jellyfish-1.1.12.ebuild | 2 +-
 sci-biology/jellyfish/jellyfish-2.3.0.ebuild  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index b2e6ea25b..f008096d6 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -4,7 +4,7 @@
 EAPI=7
 
 DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
+HOMEPAGE="https://genome.umd.edu/jellyfish.html"
 SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11

diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index e8e3c8fd0..bd2d2be0d 100644
--- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -4,7 +4,7 @@
 EAPI=7
 
 DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+HOMEPAGE="https://genome.umd.edu/jellyfish.html"
 SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11


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