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* [gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/, sci-biology/glimmer/files/
@ 2015-05-25 20:57 Martin Mokrejs
  0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-25 20:57 UTC (permalink / raw
  To: gentoo-commits

commit:     f58ff05630e47bad8736bd30d9e6985fe0910754
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 20:56:53 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 20:56:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f58ff056

avoid file collision on /usr/bin/extract (bug #247394)

Package-Manager: portage-2.2.18

 sci-biology/glimmer/ChangeLog                      |  47 ++++++
 .../glimmer/files/glimmer-3.02-glibc210.patch      |  24 +++
 .../glimmer/files/glimmer-3.02-jobserver-fix.patch |  22 +++
 .../glimmer/files/glimmer-3.02-ldflags.patch       |  88 ++++++++++
 .../files/glimmer-3.02-rename_extract.patch        | 185 +++++++++++++++++++++
 sci-biology/glimmer/glimmer-3.02-r3.ebuild         |  53 ++++++
 sci-biology/glimmer/metadata.xml                   |   5 +
 7 files changed, 424 insertions(+)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
new file mode 100644
index 0000000..c3d61e9
--- /dev/null
+++ b/sci-biology/glimmer/ChangeLog
@@ -0,0 +1,47 @@
+# ChangeLog for sci-biology/glimmer
+# Copyright 1999-2013 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 $
+
+  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-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
new file mode 100644
index 0000000..f6051ec
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
@@ -0,0 +1,24 @@
+diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
+--- glimmer3.02-orig/src/Common/gene.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/Common/gene.cc	2009-12-28 13:36:06.914974685 +0000
+@@ -443,7 +443,7 @@
+ //  Return a subscript corresponding to character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (CONVERSION_STRING, tolower (ch));
+    if  (p == NULL)
+diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
+--- glimmer3.02-orig/src/ICM/icm.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/ICM/icm.cc	2009-12-28 13:36:44.649451803 +0000
+@@ -1981,7 +1981,7 @@
+ //  model) for character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+    if  (p == NULL)

diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
new file mode 100644
index 0000000..91498b1
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
@@ -0,0 +1,22 @@
+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-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
new file mode 100644
index 0000000..0a04fbe
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
@@ -0,0 +1,88 @@
+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-3.02-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
new file mode 100644
index 0000000..07c8cd3
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
@@ -0,0 +1,185 @@
+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"

diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
new file mode 100644
index 0000000..c8a09d8
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -0,0 +1,53 @@
+# 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="2"
+
+inherit eutils
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh
+	!app-crypt/pkcrack
+	!media-libs/libextractor"
+
+S="${WORKDIR}/${PN}${PV}"
+
+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) $(TGT) || exit 1/' src/c_make.gen || die
+	# GCC 4.3 include fix
+	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	# avoid file collision on /usr/bin/extract #247394
+	epatch "${FILESDIR}/${P}-glibc210.patch"
+	epatch "${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
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/glimmer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/, sci-biology/glimmer/files/
@ 2015-05-25 21:17 Martin Mokrejs
  0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-25 21:17 UTC (permalink / raw
  To: gentoo-commits

commit:     baac64492c3678422d948c8b3fbd8a2ac66cabf8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 21:16:30 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 21:16:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=baac6449

updated patch with a fixed target name glimmer_extract

Package-Manager: portage-2.2.18

 sci-biology/glimmer/ChangeLog                               |  4 ++++
 sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch | 11 +++++++++++
 2 files changed, 15 insertions(+)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index 2871a0a..95afa54 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -3,6 +3,10 @@
 # $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>
+  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
 

diff --git a/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
index 07c8cd3..6eebc56 100644
--- a/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
+++ b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
@@ -183,3 +183,14 @@ diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
         "\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
+ 


^ permalink raw reply related	[flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/, sci-biology/glimmer/files/
@ 2015-05-25 21:46 Martin Mokrejs
  0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-25 21:46 UTC (permalink / raw
  To: gentoo-commits

commit:     e1144b215d807165cb00d2fbadfadeea27c9f5b7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 21:46:08 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 21:46:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1144b21

version bump to 3.02b which has the glimmer-3.02-glibc210.patch applied

Package-Manager: portage-2.2.18

 sci-biology/glimmer/ChangeLog                      | 10 +++++++++
 .../glimmer/files/glimmer-3.02-glibc210.patch      | 24 ----------------------
 ...fix.patch => glimmer-3.02b-jobserver-fix.patch} |  0
 ...2-ldflags.patch => glimmer-3.02b-ldflags.patch} |  0
 ...ct.patch => glimmer-3.02b-rename_extract.patch} |  0
 ...glimmer-3.02-r3.ebuild => glimmer-3.02b.ebuild} |  6 +++---
 6 files changed, 13 insertions(+), 27 deletions(-)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index 95afa54..c3157e4 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -2,6 +2,16 @@
 # 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 $
 
+*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

diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
deleted file mode 100644
index f6051ec..0000000
--- a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
---- glimmer3.02-orig/src/Common/gene.cc	2009-12-28 13:34:21.577437056 +0000
-+++ glimmer3.02/src/Common/gene.cc	2009-12-28 13:36:06.914974685 +0000
-@@ -443,7 +443,7 @@
- //  Return a subscript corresponding to character  ch .
- 
-   {
--   char  * p;
-+   const char  * p;
- 
-    p = strchr (CONVERSION_STRING, tolower (ch));
-    if  (p == NULL)
-diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
---- glimmer3.02-orig/src/ICM/icm.cc	2009-12-28 13:34:21.577437056 +0000
-+++ glimmer3.02/src/ICM/icm.cc	2009-12-28 13:36:44.649451803 +0000
-@@ -1981,7 +1981,7 @@
- //  model) for character  ch .
- 
-   {
--   char  * p;
-+   const char  * p;
- 
-    p = strchr (ALPHA_STRING, tolower (Filter (ch)));
-    if  (p == NULL)

diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
similarity index 100%
rename from sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
rename to sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch

diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
similarity index 100%
rename from sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
rename to sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch

diff --git a/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
similarity index 100%
rename from sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
rename to sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch

diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
similarity index 90%
rename from sci-biology/glimmer/glimmer-3.02-r3.ebuild
rename to sci-biology/glimmer/glimmer-3.02b.ebuild
index 94a2fa0..cc3411f 100644
--- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -10,7 +10,7 @@ MY_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
 HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
-SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
@@ -22,7 +22,8 @@ RDEPEND="app-shells/tcsh
 	!app-crypt/pkcrack
 	!media-libs/libextractor"
 
-S="${WORKDIR}/${PN}${PV}"
+#S="${WORKDIR}/${PN}${PV}"
+S="${WORKDIR}/${PN}3.02"
 
 src_prepare() {
 	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
@@ -32,7 +33,6 @@ src_prepare() {
 	# GCC 4.3 include fix
 	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
 	# avoid file collision on /usr/bin/extract #247394
-	epatch "${FILESDIR}/${P}-glibc210.patch"
 	epatch "${FILESDIR}/${P}-jobserver-fix.patch"
 	epatch "${FILESDIR}/${P}-ldflags.patch"
 	epatch "${FILESDIR}/${P}-rename_extract.patch"


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