jlec 15/05/26 06:22:16
Added: glimmer-3.02b-jobserver-fix.patch
glimmer-3.02b-ldflags.patch
glimmer-3.02b-rename_extract.patch
Log:
Version Bump and patch for file collision, thanks Martin Mokrejs for the fix,
bug #247394; Respect CXX, CXXFLAGS and LDFLAGS
(Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key
E9402A79B03529A2!)
Revision Changes Path
1.1 sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch?rev=1.1&content-type=text/plain
Index: glimmer-3.02b-jobserver-fix.patch
===================================================================
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
+ @+ $(dosubdirs)
install: all
1.1 sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch?rev=1.1&content-type=text/plain
Index: glimmer-3.02b-ldflags.patch
===================================================================
diff --git a/src/c_make.gen b/src/c_make.gen
index 414dead..84c3030 100644
--- a/src/c_make.gen
+++ b/src/c_make.gen
@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(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)
1.1
sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch?rev=1.1&content-type=text/plain
Index: glimmer-3.02b-rename_extract.patch
===================================================================
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
