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

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

[Martin Mokrejs]

commit:     aeae301a7d5eba2e10398a056622b6efd6c24654
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan  8 22:34:09 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan  8 22:34:09 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aeae301a

sci-biology/parafly: new package

Package-Manager: portage-2.2.7

---
 sci-biology/parafly/ChangeLog               |  9 +++++++++
 sci-biology/parafly/metadata.xml            |  9 +++++++++
 sci-biology/parafly/parafly-20130121.ebuild | 23 +++++++++++++++++++++++
 3 files changed, 41 insertions(+)

diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog
new file mode 100644
index 0000000..eb3df3e
--- /dev/null
+++ b/sci-biology/parafly/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/parafly
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*parafly-20130121 (08 Jan 2015)
+
+  08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +parafly-20130121.ebuild:
+  sci-biology/parafly: new package

diff --git a/sci-biology/parafly/metadata.xml b/sci-biology/parafly/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/parafly/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>

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
new file mode 100644
index 0000000..2f9c3ff
--- /dev/null
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Some dependency for transdecoder"
+HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
+SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
+
+src_configure(){
+	./configure --prefix=/usr
+}

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

[Martin Mokrejs]

commit:     b39d83c6d58ed27b5ee057320a727ab4228cf4dc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 20 23:33:19 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 20 23:33:19 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b39d83c6

sci-biology/parafly: document a recent upstream bugreport from github

Package-Manager: portage-2.2.18

 sci-biology/parafly/ChangeLog               | 4 ++++
 sci-biology/parafly/parafly-20130121.ebuild | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog
index 8a13e38..5a69c8c 100644
--- a/sci-biology/parafly/ChangeLog
+++ b/sci-biology/parafly/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  parafly-20130121.ebuild:
+  sci-biology/parafly: document a recent upstream bugreport from github
+
 *parafly-20130121 (08 Jan 2015)
 
   08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index 4d7ab90..8b0ebd3 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -18,6 +18,8 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
 
+# maybe we once the CXXFLAGS and LDFLAGS mentioned
+#   in https://github.com/trinityrnaseq/trinityrnaseq/issues/65 ?
 src_configure(){
 	./configure --prefix=/usr
 }

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

[Martin Mokrejs]

commit:     c830a39b5cc3807dd44a11c3e85201c1610effcd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 31 22:56:44 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 31 22:56:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c830a39b

sci-biology/parafly: updating moved SRC_URI of a last release left on sourceforge

Package-Manager: portage-2.2.26

 sci-biology/parafly/ChangeLog               | 5 +++++
 sci-biology/parafly/parafly-20130121.ebuild | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog
index 5a69c8c..89c98ec 100644
--- a/sci-biology/parafly/ChangeLog
+++ b/sci-biology/parafly/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  parafly-20130121.ebuild:
+  sci-biology/parafly: updating moved SRC_URI of a last release left on
+  sourceforge
+
   20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   parafly-20130121.ebuild:
   sci-biology/parafly: document a recent upstream bugreport from github

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index 8b0ebd3..c56dd41 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 DESCRIPTION="Some dependency for transdecoder"
 HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
+SRC_URI="http://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"
 
 LICENSE="BSD-BroadInstitute"
 SLOT="0"

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

[Martin Mokrejs]

commit:     00d3568beccc13ad25832c62da494a05ca18a9f3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 31 23:40:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 31 23:40:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=00d3568b

sci-biology/parafly: note code bundled under trinity-plugins

Package-Manager: portage-2.2.26

 sci-biology/parafly/ChangeLog               | 4 ++++
 sci-biology/parafly/parafly-20130121.ebuild | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog
index 89c98ec..a0b2db8 100644
--- a/sci-biology/parafly/ChangeLog
+++ b/sci-biology/parafly/ChangeLog
@@ -4,6 +4,10 @@
 
   31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   parafly-20130121.ebuild:
+  sci-biology/parafly: note code bundled under trinity-plugins
+
+  31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  parafly-20130121.ebuild:
   sci-biology/parafly: updating moved SRC_URI of a last release left on
   sourceforge
 

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index c56dd41..e696182 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -7,6 +7,8 @@ EAPI=5
 DESCRIPTION="Some dependency for transdecoder"
 HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
 SRC_URI="http://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"
+# are current sources available only from here?
+# https://github.com/trinityrnaseq/trinityrnaseq/tree/f81f0497a211c84ba4299063086604760933e6e3/trinity-plugins/parafly-code
 
 LICENSE="BSD-BroadInstitute"
 SLOT="0"

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

[Martin Mokrejs]

commit:     53b0f877dc7973925e9c6c738450b81e7fa27e30
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 16:08:26 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 16:08:26 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53b0f877

sci-biology/parafly: respect EPREFIX

Package-Manager: portage-2.2.28

 sci-biology/parafly/parafly-20130121.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index e696182..77c0629 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -23,5 +23,5 @@ S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
 # maybe we once the CXXFLAGS and LDFLAGS mentioned
 #   in https://github.com/trinityrnaseq/trinityrnaseq/issues/65 ?
 src_configure(){
-	./configure --prefix=/usr
+	./configure --prefix="${EPREFIX}"/usr
 }

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

[Martin Mokrejs]

commit:     145641db815aee901f393e76a6d81bdddf414738
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 16:11:52 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 16:11:52 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=145641db

sci-biology/parafly: respect EPREFIX also during src_install

Package-Manager: portage-2.2.28

 sci-biology/parafly/parafly-20130121.ebuild | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index 77c0629..5dd1d66 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -25,3 +25,7 @@ S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
 src_configure(){
 	./configure --prefix="${EPREFIX}"/usr
 }
+
+src_install(){
+	emake install DESTDIR="${D}"/"${EPREFIX}"
+}

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

[Martin Mokrejs]

commit:     0309c08ff0230c570f20c23b0a4c76c50178c332
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 16:56:59 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 16:56:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0309c08f

Revert "sci-biology/parafly: respect EPREFIX also during src_install"

This reverts commit 145641db815aee901f393e76a6d81bdddf414738 because
it was not necessary. My test setup was screwed, sorry for that.

 sci-biology/parafly/parafly-20130121.ebuild | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
index 5dd1d66..77c0629 100644
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -25,7 +25,3 @@ S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
 src_configure(){
 	./configure --prefix="${EPREFIX}"/usr
 }
-
-src_install(){
-	emake install DESTDIR="${D}"/"${EPREFIX}"
-}

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

[Andrew Ammerlaan]

commit:     454d4e4876455ed72069bf2343c499b2a5184901
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 13:15:13 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 13:15:13 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=454d4e48

sci-biology/parafly: fix this, EAPI bump

- fixed description
- fixed homepage
- fixed src_uri

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

 sci-biology/parafly/parafly-0.1.0.ebuild    | 21 +++++++++++++++++++++
 sci-biology/parafly/parafly-20130121.ebuild | 26 --------------------------
 2 files changed, 21 insertions(+), 26 deletions(-)

diff --git a/sci-biology/parafly/parafly-0.1.0.ebuild b/sci-biology/parafly/parafly-0.1.0.ebuild
new file mode 100644
index 000000000..ce1084020
--- /dev/null
+++ b/sci-biology/parafly/parafly-0.1.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Parallel cmd processing utility"
+HOMEPAGE="https://github.com/ParaFly/ParaFly"
+SRC_URI="https://github.com/ParaFly/ParaFly/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ParaFly-${PV}"
+
+src_configure(){
+	./configure --prefix="${EPREFIX}"/usr
+}

diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
deleted file mode 100644
index fe3e26c6c..000000000
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Some dependency for transdecoder"
-HOMEPAGE="https://sourceforge.net/projects/transdecoder/"
-SRC_URI="https://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"
-# are current sources available only from here?
-# https://github.com/trinityrnaseq/trinityrnaseq/tree/f81f0497a211c84ba4299063086604760933e6e3/trinity-plugins/parafly-code
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
-
-# maybe we once the CXXFLAGS and LDFLAGS mentioned
-#   in https://github.com/trinityrnaseq/trinityrnaseq/issues/65 ?
-src_configure(){
-	./configure --prefix="${EPREFIX}"/usr
-}