From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/glimmer/Manifest | 13 ++ .../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-3.02b-jobserver-fix.patch | 22 +++ .../glimmer/files/glimmer-3.02b-ldflags.patch | 88 +++++++++ .../files/glimmer-3.02b-rename_extract.patch | 196 +++++++++++++++++++++ sci-biology/glimmer/glimmer-3.02-r3.ebuild | 60 +++++++ sci-biology/glimmer/glimmer-3.02b.ebuild | 67 +++++++ sci-biology/glimmer/metadata.xml | 8 + 10 files changed, 588 insertions(+) create mode 100644 sci-biology/glimmer/Manifest create mode 100644 sci-biology/glimmer/files/glimmer-3.02-glibc210.patch create mode 100644 sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch create mode 100644 sci-biology/glimmer/files/glimmer-3.02-ldflags.patch create mode 100644 sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch create mode 100644 sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch create mode 100644 sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch create mode 100644 sci-biology/glimmer/glimmer-3.02-r3.ebuild create mode 100644 sci-biology/glimmer/glimmer-3.02b.ebuild create mode 100644 sci-biology/glimmer/metadata.xml (limited to 'sci-biology/glimmer') diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest new file mode 100644 index 000000000000..3d68f9533801 --- /dev/null +++ b/sci-biology/glimmer/Manifest @@ -0,0 +1,13 @@ +AUX glimmer-3.02-glibc210.patch 799 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b WHIRLPOOL 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file mode 100644 index 000000000000..f6051ec82054 --- /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 000000000000..91498b116d12 --- /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 ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(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-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-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 ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(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-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch new file mode 100644 index 000000000000..6eebc5610414 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch @@ -0,0 +1,196 @@ +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 = $(UTIL_OBJS) + +-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \ ++PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \ + uncovered window-acgt + + LIBRARIES = +diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc +--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200 +@@ -297,7 +297,7 @@ + + { + fprintf (stderr, +- "USAGE: extract [options] \n" ++ "USAGE: glimmer_extract [options] \n" + "\n" + "Read fasta-format and extract from it the\n" + "subsequences specified by . By default, \n" +--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 ++++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200 +@@ -21,7 +21,7 @@ + + entropy-score: entropy-score.o libGLMcommon.a + +-extract: extract.o libGLMcommon.a ++glimmer_extract: extract.o libGLMcommon.a + + multi-extract: multi-extract.o libGLMcommon.a + diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild new file mode 100644 index 000000000000..992a6d327fcb --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" +SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/${PN}${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-glibc210.patch + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${PN}-3.02b-rename_extract.patch +) + +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) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include /include /' src/Common/delcher.hh || die + epatch "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild new file mode 100644 index 000000000000..9653024a1de2 --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${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" + +PATCHES=( + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-rename_extract.patch +) + +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) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include /include /' src/Common/delcher.hh || die + # + sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${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 "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/glimmer/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + -- cgit v1.2.3