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 <[email protected]> - 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 <[email protected]> - +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 <[email protected]> - files/glimmer-3.02-rename_extract.patch: - updated patch with a fixed target name glimmer_extract - - 25 May 2015; Martin Mokrejs <[email protected]> - glimmer-3.02-r3.ebuild: - EAPI bump - - 11 Mar 2013; Justin Lecher <[email protected]> metadata.xml: - Drop Andrey as maintainer so that bugs get assigned to sci-biology directly - - 16 Jul 2010; Markos Chandras <[email protected]> glimmer-3.02-r2.ebuild: - Stable on amd64 wrt bug #328415 - - 16 Jul 2010; Christian Faulhammer <[email protected]> - glimmer-3.02-r2.ebuild: - stable x86, bug 328415 - -*glimmer-3.02-r2 (03 Apr 2010) - - 03 Apr 2010; Justin Lecher <[email protected]> +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 <[email protected]> glimmer-3.02-r1.ebuild: - amd64 stable, bug 298762 - - 29 Dec 2009; Christian Faulhammer <[email protected]> - glimmer-3.02-r1.ebuild: - stable x86, bug 298762 - - 28 Dec 2009; Andrey Kislyuk <[email protected]> - +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 <[email protected]> -glimmer-3.02.ebuild, - +glimmer-3.02-r1.ebuild: - Collision block, bug 247394 - - 30 Sep 2008; Jeremy Olexa <[email protected]> glimmer-3.02.ebuild: - add ~amd64 kw based on Chad's testing. bug #239162 - -*glimmer-3.02 (07 Sep 2008) - - 07 Sep 2008; weaver <[email protected]> +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>
