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* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2014-03-23 22:06 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2014-03-23 22:06 UTC (permalink / raw
  To: gentoo-commits

commit:     99922b305f1d1b746aaab8d7f073dbf097fa6570
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 22:05:00 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 22:05:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=99922b30

sci-biology/eval: new package; needs perl team help to install this evil package with Eval.pm into PERL_PATH

---
 sci-biology/eval/ChangeLog         | 11 +++++++++++
 sci-biology/eval/eval-2.2.8.ebuild | 32 ++++++++++++++++++++++++++++++++
 sci-biology/eval/metadata.xml      |  9 +++++++++
 3 files changed, 52 insertions(+)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
new file mode 100644
index 0000000..2acaa77
--- /dev/null
+++ b/sci-biology/eval/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/eval
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*eval-2.2.8 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +eval-2.2.8.ebuild,
+  +metadata.xml:
+  new package; needs perl team help to install this evil package with Eval.pm
+  into PERL_PATH
+

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
new file mode 100644
index 0000000..a075f69
--- /dev/null
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# This ebuild generated by g-cpan 0.16.4
+
+EAPI="3"
+
+DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz
+		http://mblab.wustl.edu/software/download/eval-documentation.pdf"
+
+DEPEND="dev-lang/perl
+	dev-lang/tk
+	sci-biology/vcftools
+	sci-visualization/gnuplot"
+
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin *.pl *.py
+	dodoc "${DISTDIR}"/eval-documentation.pdf
+	dodoc help/*.ps
+	insinto /usr/share/eval
+	doins *.gtf
+	insinto /usr/share/eval/perl
+	doins *.pm
+	# TODO: need to add this into PERL_PATH
+}

diff --git a/sci-biology/eval/metadata.xml b/sci-biology/eval/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/eval/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] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2014-09-04 21:04 Jauhien Piatlicki
  0 siblings, 0 replies; 11+ messages in thread
From: Jauhien Piatlicki @ 2014-09-04 21:04 UTC (permalink / raw
  To: gentoo-commits

commit:     ff476f948d38f59327666d52c19c6e9e449bd897
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  4 20:42:13 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Sep  4 21:03:27 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ff476f94

sci-biology/eval: Add HOMEPAGE and LICENSE

---
 sci-biology/eval/ChangeLog         | 3 +++
 sci-biology/eval/eval-2.2.8.ebuild | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
index 2acaa77..0b39a96 100644
--- a/sci-biology/eval/ChangeLog
+++ b/sci-biology/eval/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> eval-2.2.8.ebuild:
+  Add HOMEPAGE and LICENSE
+
 *eval-2.2.8 (23 Mar 2014)
 
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +eval-2.2.8.ebuild,

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index a075f69..bd7232a 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -5,8 +5,9 @@
 EAPI="3"
 
 DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
+HOMEPAGE="http://mblab.wustl.edu/software.html"
 
-LICENSE=""
+LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS=""
 IUSE=""


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2014-09-16 17:01 Christoph Junghans
  0 siblings, 0 replies; 11+ messages in thread
From: Christoph Junghans @ 2014-09-16 17:01 UTC (permalink / raw
  To: gentoo-commits

commit:     f06e786820aebf64ca67189423d9efa11a0aa769
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 16:58:45 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 16:58:45 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f06e7868

clean up

Package-Manager: portage-2.2.8-r1

---
 sci-biology/eval/ChangeLog         | 4 +++-
 sci-biology/eval/eval-2.2.8.ebuild | 4 ++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
index 0b39a96..c13870d 100644
--- a/sci-biology/eval/ChangeLog
+++ b/sci-biology/eval/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> eval-2.2.8.ebuild:
+  clean up
+
   04 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> eval-2.2.8.ebuild:
   Add HOMEPAGE and LICENSE
 
@@ -11,4 +14,3 @@
   +metadata.xml:
   new package; needs perl team help to install this evil package with Eval.pm
   into PERL_PATH
-

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index bd7232a..4d1ec45 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
 
-EAPI="3"
+EAPI=5
 
 DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
 HOMEPAGE="http://mblab.wustl.edu/software.html"


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2015-02-13 21:21 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2015-02-13 21:21 UTC (permalink / raw
  To: gentoo-commits

commit:     0420ac8728146d7c6afb7caf4c0545337a671dd7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 13 21:19:29 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 13 21:19:29 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0420ac87

install the perl module properly; added KEYWORDS

Package-Manager: portage-2.2.15

---
 sci-biology/eval/eval-2.2.8.ebuild | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index 4d1ec45..e79577d 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -9,7 +9,7 @@ HOMEPAGE="http://mblab.wustl.edu/software.html"
 
 LICENSE="GPL-2+"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz
 		http://mblab.wustl.edu/software/download/eval-documentation.pdf"
@@ -27,7 +27,14 @@ src_install(){
 	dodoc help/*.ps
 	insinto /usr/share/eval
 	doins *.gtf
-	insinto /usr/share/eval/perl
+	eval `perl '-V:installvendorlib'`
+	vendor_lib_install_dir="${installvendorlib}"
+	dodir ${vendor_lib_install_dir}/eval
+	insinto ${vendor_lib_install_dir}/eval
 	doins *.pm
-	# TODO: need to add this into PERL_PATH
+	echo "PERL5LIB="${vendor_lib_install_dir}"/eval" > ${S}"/99eval"
+	doenvd ${S}"/99eval" || die
 }
+
+# the version of validate_gtf.pl bundled with eval differs a bit from
+# validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2015-02-13 21:22 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2015-02-13 21:22 UTC (permalink / raw
  To: gentoo-commits

commit:     426c2166fb1ca49ce8a941f35e91c27a5d269f81
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 13 21:20:29 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 13 21:20:29 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=426c2166

fix Gentoo copyright header

Package-Manager: portage-2.2.15

---
 sci-biology/eval/ChangeLog         | 5 ++++-
 sci-biology/eval/eval-2.2.8.ebuild | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
index c13870d..0e9cff2 100644
--- a/sci-biology/eval/ChangeLog
+++ b/sci-biology/eval/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/eval
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild:
+  fix Gentoo copyright header
+
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> eval-2.2.8.ebuild:
   clean up
 

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index e79577d..75f38c5 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.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: $
 


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2015-03-19 10:37 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:37 UTC (permalink / raw
  To: gentoo-commits

commit:     be87477142feac27a5fb8c764b057092cef1f968
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:34:13 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:34:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=be874771

removing KEYWORDS until the perl files are installed to some other place. At the moment I get: 'perl-module.eclass: Suspicious environment values found. PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/eval"'

Package-Manager: portage-2.2.15

 sci-biology/eval/ChangeLog         | 5 +++++
 sci-biology/eval/eval-2.2.8.ebuild | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
index 0e9cff2..34f2faa 100644
--- a/sci-biology/eval/ChangeLog
+++ b/sci-biology/eval/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild:
+  removing KEYWORDS until the perl files are installed to some other place. At
+  the moment I get: 'perl-module.eclass: Suspicious environment values found.
+  PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/eval"'
+
   13 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild:
   fix Gentoo copyright header
 

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index 75f38c5..77a8076 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -9,7 +9,7 @@ HOMEPAGE="http://mblab.wustl.edu/software.html"
 
 LICENSE="GPL-2+"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz
 		http://mblab.wustl.edu/software/download/eval-documentation.pdf"


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2015-04-17 23:56 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
  To: gentoo-commits

commit:     e4e5c84b2835673ceac3607cf84dc0d68c3bcfe6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:18:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:18:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4e5c84b

sci-biology/eval: fixed installation of perl-related files

Package-Manager: portage-2.2.18

 sci-biology/eval/ChangeLog         |  3 +++
 sci-biology/eval/eval-2.2.8.ebuild | 23 ++++++++++++-----------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog
index 34f2faa..7de843d 100644
--- a/sci-biology/eval/ChangeLog
+++ b/sci-biology/eval/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild:
+  sci-biology/eval: fixed installation of perl-related files
+
   19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild:
   removing KEYWORDS until the perl files are installed to some other place. At
   the moment I get: 'perl-module.eclass: Suspicious environment values found.

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index 77a8076..c6ddde2 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -4,17 +4,20 @@
 
 EAPI=5
 
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
 DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
 HOMEPAGE="http://mblab.wustl.edu/software.html"
 
 LICENSE="GPL-2+"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz
 		http://mblab.wustl.edu/software/download/eval-documentation.pdf"
 
-DEPEND="dev-lang/perl
+DEPEND="
 	dev-lang/tk
 	sci-biology/vcftools
 	sci-visualization/gnuplot"
@@ -25,16 +28,14 @@ src_install(){
 	dobin *.pl *.py
 	dodoc "${DISTDIR}"/eval-documentation.pdf
 	dodoc help/*.ps
-	insinto /usr/share/eval
+	insinto /usr/share/${PN}
 	doins *.gtf
-	eval `perl '-V:installvendorlib'`
-	vendor_lib_install_dir="${installvendorlib}"
-	dodir ${vendor_lib_install_dir}/eval
-	insinto ${vendor_lib_install_dir}/eval
+	perl_set_version
+	insinto ${VENDOR_LIB}
 	doins *.pm
-	echo "PERL5LIB="${vendor_lib_install_dir}"/eval" > ${S}"/99eval"
-	doenvd ${S}"/99eval" || die
 }
 
-# the version of validate_gtf.pl bundled with eval differs a bit from
-# validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf
+pkg_postinst(){
+	ewarn "The version of validate_gtf.pl bundled with eval differs a bit from"
+	ewarn "validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf"
+}


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2015-09-21 17:44 Justin Lecher
  0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2015-09-21 17:44 UTC (permalink / raw
  To: gentoo-commits

commit:     66c67667985dacbe5da287859f9b3b6d02d441af
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:20:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:20:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=66c67667

sci-biology/eval: Use python eclass

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/eval/eval-2.2.8.ebuild | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index ff2512e..613b651 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -4,30 +4,35 @@
 
 EAPI=5
 
+PYTHON_COMPAT=( python2_7 )
 PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module eutils python-r1 toolchain-funcs
 
 DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
 HOMEPAGE="http://mblab.wustl.edu/software.html"
+SRC_URI="
+	http://mblab.wustl.edu/software/download/${PN}-${PV}.tar.gz
+	http://mblab.wustl.edu/software/download/eval-documentation.pdf"
 
 LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
-SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz
-		http://mblab.wustl.edu/software/download/eval-documentation.pdf"
 
-DEPEND="
-	dev-lang/tk
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	dev-lang/tk:0=
 	sci-biology/vcftools
 	sci-visualization/gnuplot"
-
 RDEPEND="${DEPEND}"
 
 src_install(){
-	dobin *.pl *.py
-	dodoc "${DISTDIR}"/eval-documentation.pdf
-	dodoc help/*.ps
+	dobin *.pl
+	python_foreach_impl python_doscript *.py
+	dodoc \
+		"${DISTDIR}"/eval-documentation.pdf \
+		help/*.ps
 	insinto /usr/share/${PN}
 	doins *.gtf
 	perl_set_version


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2017-01-08 16:39 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-01-08 16:39 UTC (permalink / raw
  To: gentoo-commits

commit:     a4fd373b45de86b4a6b5d631c2a4ddc148e290eb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan  8 16:39:38 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan  8 16:39:38 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4fd373b

sci-biology/eval: fix shebang line according to bug #602580

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/eval/eval-2.2.8.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index 613b651..b7c6720 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -29,6 +29,9 @@ RDEPEND="${DEPEND}"
 
 src_install(){
 	dobin *.pl
+	# TODO: prepend shebang lines to *.py files
+	# https://bugs.gentoo.org/show_bug.cgi?id=602580
+	sed -i -e "1i #!/usr/bin/env ${EPYTHON}" RangeFinder.py || die
 	python_foreach_impl python_doscript *.py
 	dodoc \
 		"${DISTDIR}"/eval-documentation.pdf \


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2017-01-17  9:44 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-01-17  9:44 UTC (permalink / raw
  To: gentoo-commits

commit:     91d9ac3dd8937f2091118f1f3ac1d638898445d9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 17 09:44:27 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 17 09:44:27 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=91d9ac3d

sci-biology/eval: drop EPYTHON variable which was empty and let fix_shebangs to its work

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/eval/eval-2.2.8.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
index b7c6720..39ce41e 100644
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ b/sci-biology/eval/eval-2.2.8.ebuild
@@ -31,7 +31,7 @@ src_install(){
 	dobin *.pl
 	# TODO: prepend shebang lines to *.py files
 	# https://bugs.gentoo.org/show_bug.cgi?id=602580
-	sed -i -e "1i #!/usr/bin/env ${EPYTHON}" RangeFinder.py || die
+	sed -i -e "1i #!/usr/bin/env python" RangeFinder.py || die
 	python_foreach_impl python_doscript *.py
 	dodoc \
 		"${DISTDIR}"/eval-documentation.pdf \


^ permalink raw reply related	[flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eval/
@ 2021-01-19 14:10 Andrew Ammerlaan
  0 siblings, 0 replies; 11+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 14:10 UTC (permalink / raw
  To: gentoo-commits

commit:     ea4f3085d2e5a027085bb889f42a7e22cdc3b887
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 14:10:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 14:10:31 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea4f3085

sci-biology/eval: remove pack, does not fetch, invalid cert

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/eval/eval-2.2.8.ebuild | 48 --------------------------------------
 sci-biology/eval/metadata.xml      | 12 ----------
 2 files changed, 60 deletions(-)

diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
deleted file mode 100644
index 074f39707..000000000
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils python-r1 toolchain-funcs
-
-DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
-HOMEPAGE="http://mblab.wustl.edu/software.html"
-SRC_URI="
-	http://mblab.wustl.edu/software/download/${PN}-${PV}.tar.gz
-	http://mblab.wustl.edu/software/download/eval-documentation.pdf"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	dev-lang/tk:0=
-	sci-biology/vcftools
-	sci-visualization/gnuplot"
-RDEPEND="${DEPEND}"
-
-src_install(){
-	dobin *.pl
-	# TODO: prepend shebang lines to *.py files
-	# https://bugs.gentoo.org/show_bug.cgi?id=602580
-	sed -i -e "1i #!/usr/bin/env python" RangeFinder.py || die
-	python_foreach_impl python_doscript *.py
-	dodoc \
-		"${DISTDIR}"/eval-documentation.pdf \
-		help/*.ps
-	insinto /usr/share/${PN}
-	doins *.gtf
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins *.pm
-}
-
-pkg_postinst(){
-	ewarn "The version of validate_gtf.pl bundled with eval differs a bit from"
-	ewarn "validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf"
-}

diff --git a/sci-biology/eval/metadata.xml b/sci-biology/eval/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/eval/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>


^ permalink raw reply related	[flat|nested] 11+ messages in thread
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2015-03-19 10:37 Martin Mokrejs
2015-02-13 21:22 Martin Mokrejs
2015-02-13 21:21 Martin Mokrejs
2014-09-16 17:01 Christoph Junghans
2014-09-04 21:04 Jauhien Piatlicki
2014-03-23 22:06 Martin Mokrejs

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