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

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

[Justin Lecher]

commit:     ebb7fad94eae960c7f63251f72bcd88116d357c1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 26 06:24:13 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 26 06:24:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebb7fad9

Moved to tree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/glimmer/ChangeLog                      |  69 --------
 .../files/glimmer-3.02b-jobserver-fix.patch        |  22 ---
 .../glimmer/files/glimmer-3.02b-ldflags.patch      |  88 ---------
 .../files/glimmer-3.02b-rename_extract.patch       | 196 ---------------------
 sci-biology/glimmer/glimmer-3.02b.ebuild           |  57 ------
 sci-biology/glimmer/metadata.xml                   |   5 -
 6 files changed, 437 deletions(-)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
deleted file mode 100644
index f1aa5cd..0000000
--- a/sci-biology/glimmer/ChangeLog
+++ /dev/null
@@ -1,69 +0,0 @@
-# ChangeLog for sci-biology/glimmer
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10 2013/03/11 15:17:43 jlec Exp $
-
-  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  glimmer-3.02b.ebuild:
-  added dependency on sci-biology/elph as in Fedora; also stole from Fedora few
-  more sed(1) tricks to remove yet missed hardcoded paths
-
-*glimmer-3.02b (25 May 2015)
-
-  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +files/glimmer-3.02b-jobserver-fix.patch, +files/glimmer-3.02b-ldflags.patch,
-  +files/glimmer-3.02b-rename_extract.patch, +glimmer-3.02b.ebuild,
-  -files/glimmer-3.02-glibc210.patch, -files/glimmer-3.02-jobserver-fix.patch,
-  -files/glimmer-3.02-ldflags.patch, -files/glimmer-3.02-rename_extract.patch,
-  -glimmer-3.02-r3.ebuild:
-  version bump to 3.02b which has the glimmer-3.02-glibc210.patch applied
-
-  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  files/glimmer-3.02-rename_extract.patch:
-  updated patch with a fixed target name glimmer_extract
-
-  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  glimmer-3.02-r3.ebuild:
-  EAPI bump
-
-  11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
-
-  16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> glimmer-3.02-r2.ebuild:
-  Stable on amd64 wrt bug #328415
-
-  16 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
-  glimmer-3.02-r2.ebuild:
-  stable x86, bug 328415
-
-*glimmer-3.02-r2 (03 Apr 2010)
-
-  03 Apr 2010; Justin Lecher <jlec@gentoo.org> +glimmer-3.02-r2.ebuild,
-  +files/glimmer-3.02-jobserver-fix.patch:
-  jobserver fix, #299482, Thanks Myckel Habets
-  LDFLAGS/CFLAGS etc repected
-
-  03 Jan 2010; Pacho Ramos <pacho@gentoo.org> glimmer-3.02-r1.ebuild:
-  amd64 stable, bug 298762
-
-  29 Dec 2009; Christian Faulhammer <fauli@gentoo.org>
-  glimmer-3.02-r1.ebuild:
-  stable x86, bug 298762
-
-  28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org>
-  +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild:
-  QA fixes, including bug 298223
-
-*glimmer-3.02-r1 (04 Jan 2009)
-
-  04 Jan 2009; weaver <weaver@gentoo.org> -glimmer-3.02.ebuild,
-  +glimmer-3.02-r1.ebuild:
-  Collision block, bug 247394
-
-  30 Sep 2008; Jeremy Olexa <darkside@gentoo.org> glimmer-3.02.ebuild:
-  add ~amd64 kw based on Chad's testing. bug #239162
-
-*glimmer-3.02 (07 Sep 2008)
-
-  07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml,
-  +glimmer-3.02.ebuild:
-  Import from science overlay

diff --git a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
deleted file mode 100644
index 91498b1..0000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
---- glimmer3.02-orig/src/Makefile	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Makefile	2010-03-18 14:30:15.000000000 +0100
-@@ -2,12 +2,12 @@
- 
- 
- all:
--	@ TGT=objs
--	@ $(dosubdirs)
--	@ TGT=libs
--	@ $(dosubdirs)
--	@ TGT=progs
--	@ $(dosubdirs)
-+	@+ TGT=objs
-+	@+ $(dosubdirs)
-+	@+ TGT=libs
-+	@+ $(dosubdirs)
-+	@+ TGT=progs
-+	@+ $(dosubdirs)
- 
- 
- install: all

diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
deleted file mode 100644
index 0a04fbe..0000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-diff --git a/src/c_make.gen b/src/c_make.gen
-index 414dead..84c3030 100644
---- a/src/c_make.gen
-+++ b/src/c_make.gen
-@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
- #### Do not redefine if (a) passed in on command line, or (b)
- #### defined in an environment variable.
- 
--ifneq "$(origin CC)" "environment"
--CC      = cc
--endif
--
--ifneq "$(origin CPPFLAGS)" "environment"
--CPPFLAGS=
--endif
--
--ifneq "$(origin CFLAGS)" "environment"
--CFLAGS  =
--endif
--
--ifneq "$(origin CDEFS)" "environment"
--CDEFS  =
--endif
--
--ifneq "$(origin CXX)" "environment"
--CXX	= g++
--endif
--
--ifneq "$(origin CXXFLAGS)" "environment"
--CXXFLAGS=
--endif
--
--ifneq "$(origin CXXDEFS)" "environment"
--CXXDEFS= -D__cplusplus
--endif
--
--ifneq "$(origin AR)" "environment"
--AR      = ar
--endif
--
--ifneq "$(origin ARFLAGS)" "environment"
--ARFLAGS = rvs
--endif
--
--ifneq "$(origin LDFLAGS)" "environment"
--LDFLAGS =
--endif
-+CC      ?= cc
-+CXX	?= g++
-+CXXFLAGS ?=
-+CXXDEFS = -D__cplusplus
-+AR      ?= ar
-+ARFLAGS ?= rvs
- 
- #### Delete default suffix rules
- .SUFFIXES:
-@@ -359,13 +326,13 @@ $(PROGS):
- 	  cd $(LOCAL_OBJ); \
- 	    if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
-                $(LD_DIRS) $(filter-out lib%.a, $+) \
--	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- 			true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
- 	else \
- 	  cd $(LOCAL_OBJ); \
- 	    if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
-                $(LD_DIRS) $(filter-out lib%.a, $+) \
--	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- 			true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
- 	fi ;
- 
-diff --git a/src/c_make.glm b/src/c_make.glm
-index 0decc17..b82131c 100644
---- a/src/c_make.glm
-+++ b/src/c_make.glm
-@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen
- 
- SUBDIRS = Common ICM Glimmer Util
- 
--CFLAGS = -g -Wall
--CXXFLAGS = -g -Wall
--
--LDFLAGS = -g -lm
-+LIBS = -lm
- 
- 
- #AS_BUILD_DIR =$(LOCAL_WORK)

diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
deleted file mode 100644
index 6eebc56..0000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
+++ /dev/null
@@ -1,196 +0,0 @@
-diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
---- glimmer3.02.old/docs/notes.tex	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/docs/notes.tex	2015-05-25 22:41:39.450340098 +0200
-@@ -306,7 +306,7 @@
-   The script would then run the commands:
- \BSV\begin{verbatim}
-   long-orfs -n -t 1.15 genom.seq run1.longorfs
--  extract -t genom.seq run1.longorfs > run1.train
-+  glimmer_extract -t genom.seq run1.longorfs > run1.train
-   build-icm -r run1.icm < run1.train
-   glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
- \end{verbatim}\ESV
-@@ -330,9 +330,9 @@
- \end{verbatim}\ESV
-   The script would then run the commands:
- \BSV\begin{verbatim}
--  extract -t genom.seq train.coords > run2.train
-+  glimmer_extract -t genom.seq train.coords > run2.train
-   build-icm -r run2.icm < run2.train
--  upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
-+  upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream
-   elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
-   set startuse = `start-codon-distrib -3 genom.seq train.coords`
-   glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
-@@ -358,11 +358,11 @@
-   The script would then run the commands:
- \BSV\begin{verbatim}
-   long-orfs -n -t 1.15 genom.seq run3.longorfs
--  extract -t genom.seq run3.longorfs > run3.train
-+  glimmer_extract -t genom.seq run3.longorfs > run3.train
-   build-icm -r run3.icm < run3.train
-   glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
-   tail +2 run3.run1.predict > run3.coords
--  upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
-+  upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream
-   elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
-   set startuse = `start-codon-distrib -3 genom.seq run3.coords`
-   glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
-@@ -1081,12 +1081,12 @@
-   \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
- \eq
- 
--\subsubsection{\Pg{extract} Program}
-+\subsubsection{\Pg{glimmer_extract} Program}
- This program reads a genome sequence and a list of coordinates
- for it and outputs a multi-fasta file of the regions specified
- by the coordinates.  Output goes to standard output.
- \bq
--  \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
-+  \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
- \eq
- 
- \subsubsection{\Pg{multi-extract} Program}
-diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh
---- glimmer3.02.old/sample-run/g3-from-scratch.csh	2006-06-12 21:46:35.000000000 +0200
-+++ glimmer3.02/sample-run/g3-from-scratch.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -50,7 +50,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh
---- glimmer3.02.old/sample-run/g3-from-training.csh	2006-06-12 21:46:35.000000000 +0200
-+++ glimmer3.02/sample-run/g3-from-training.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -42,7 +42,7 @@
- step1:
- # Extract the training sequences from the genome file
- echo "Step 1 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $coords > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -66,7 +66,7 @@
- # upstream of the start locations in $coords
- echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh
---- glimmer3.02.old/sample-run/g3-iterated.csh	2006-06-13 14:15:28.000000000 +0200
-+++ glimmer3.02/sample-run/g3-iterated.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -57,7 +57,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -103,7 +103,7 @@
- # upstream of the start locations in $tag.coords
- echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $tag.coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh
---- glimmer3.02.old/scripts/g3-from-scratch.csh	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/scripts/g3-from-scratch.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -50,7 +50,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh
---- glimmer3.02.old/scripts/g3-from-training.csh	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/scripts/g3-from-training.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -42,7 +42,7 @@
- step1:
- # Extract the training sequences from the genome file
- echo "Step 1 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $coords > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -66,7 +66,7 @@
- # upstream of the start locations in $coords
- echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh
---- glimmer3.02.old/scripts/g3-iterated.csh	2006-06-13 14:15:46.000000000 +0200
-+++ glimmer3.02/scripts/g3-iterated.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -57,7 +57,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -103,7 +103,7 @@
- # upstream of the start locations in $tag.coords
- echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $tag.coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
---- glimmer3.02.old/src/Util/Makefile	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
-@@ -8,7 +8,7 @@
- SOURCES = $(UTIL_SRCS)
- OBJECTS = $(UTIL_OBJS)
- 
--PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \
-+PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \
-   uncovered window-acgt
- 
- LIBRARIES = 
-diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
---- glimmer3.02.old/src/Util/extract.cc	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Util/extract.cc	2015-05-25 22:44:01.760342470 +0200
-@@ -297,7 +297,7 @@
- 
-   {
-    fprintf (stderr,
--       "USAGE:  extract [options] <sequence-file> <coords>\n"
-+       "USAGE:  glimmer_extract [options] <sequence-file> <coords>\n"
-        "\n"
-        "Read fasta-format <sequence-file> and extract from it the\n"
-        "subsequences specified by <coords>.  By default, <coords>\n"
---- glimmer3.02.old/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
-+++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile	2015-05-25 23:13:34.230372010 +0200
-@@ -21,7 +21,7 @@
- 
- entropy-score:  entropy-score.o libGLMcommon.a
- 
--extract:  extract.o libGLMcommon.a
-+glimmer_extract:  extract.o libGLMcommon.a
- 
- multi-extract:  multi-extract.o libGLMcommon.a
- 

diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
deleted file mode 100644
index 1f7db36e..0000000
--- a/sci-biology/glimmer/glimmer-3.02b.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r2.ebuild,v 1.3 2010/07/16 17:29:32 hwoarang Exp $
-
-EAPI="5"
-
-inherit eutils
-
-MY_PV=${PV//./}
-
-DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
-SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh
-	sci-biology/elph"
-
-#S="${WORKDIR}/${PN}${PV}"
-S="${WORKDIR}/${PN}3.02"
-
-src_prepare() {
-	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
-		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
-	# Fix Makefile to die on failure
-	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
-	# GCC 4.3 include fix
-	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
-	#
-	sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die
-	sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die
-	sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die
-	sed -i "s/@ if/if/" src/c_make.gen || die
-	# avoid file collision on /usr/bin/extract #247394
-	epatch "${FILESDIR}/${P}-jobserver-fix.patch"
-	epatch "${FILESDIR}/${P}-ldflags.patch"
-	epatch "${FILESDIR}/${P}-rename_extract.patch"
-}
-
-src_compile() {
-	emake -C src || die
-}
-
-src_install() {
-	rm -f bin/test
-	dobin bin/* || die
-
-	insinto /usr/share/${PN}/scripts
-	doins scripts/* || die
-
-	dodoc glim302notes.pdf
-}

diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/glimmer/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-</pkgmetadata>