Version Bump and patch for file collision, thanks Martin Mokrejs for the fix, bug #247394; Respect CXX, CXXFLAGS and LDFLAGS

Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!

7 files changed, 437 insertions, 26 deletions

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index c3d61e9970ae..9dc6606b7d70 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -1,6 +1,16 @@
 # 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 $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.11 2015/05/26 06:22:16 jlec Exp $
+
+*glimmer-3.02b (26 May 2015)
+*glimmer-3.02-r3 (26 May 2015)
+
+  26 May 2015; Justin Lecher <jlec@gentoo.org>
+  +files/glimmer-3.02b-jobserver-fix.patch, +files/glimmer-3.02b-ldflags.patch,
+  +files/glimmer-3.02b-rename_extract.patch, +glimmer-3.02-r3.ebuild,
+  +glimmer-3.02b.ebuild, -glimmer-3.02-r1.ebuild:
+  Version Bump and patch for file collision, thanks Martin Mokrejs for the fix,
+  bug #247394; Respect CXX, CXXFLAGS and LDFLAGS
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -44,4 +54,3 @@
   07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml,
   +glimmer-3.02.ebuild:
   Import from science overlay
-
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index 8e7e5936a8e9..56d418d12038 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -1,18 +1,35 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX glimmer-3.02-glibc210.patch 799 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b WHIRLPOOL 797232ac343731e37800495a50bbdb4c254d04c52ec9ad5b3e57b2ad623bb93c4024fe150f7d8bc2dc4f0d0a83cd75d511d985a62bf4a02bcb04ec813528c606
 AUX glimmer-3.02-jobserver-fix.patch 433 SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d WHIRLPOOL a93193e48512a0cd8c6996d77ee8f1fd91b18cf00e6c99ec6c59dc9953bcb5ee5a90180b317ffb99337666e451da91f77f14a805f43026c1819ec596bb1268c1
 AUX glimmer-3.02-ldflags.patch 2057 SHA256 95d391acdbf6d84440c2f3d96791e9f97776b7a248c9546738cc9df88711a28e SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 WHIRLPOOL d68752a5c3f78195bfabd116d19ca22ba90af7b817bfa29b9e0cc5614391e32cc3dd8cdd72e3ab642f4b52c48305ed8c7ab32ed622826b720b6228617ed682fe
-DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221
-EBUILD glimmer-3.02-r1.ebuild 1270 SHA256 33e1a316e31371a6194055b7e31bb6122d446ef2352e2af9c8cbc0d945de96a0 SHA512 dba90fcb00ffa7f44be0af0a69e2ce1de804e8d446269e0aa9edfe8e305edef1a9d4593ba4417a6b0edb08afa1b14520f6290bf04823616662879b8067f2b04b WHIRLPOOL 4e221f8a3036f06783290a6fc94c841dcd921b362253888bbd48ee654ad7389ce398ce1869783cea0fabebdad9491f76e93dbc284387202f5fbda1b03dfc0cd3
+AUX glimmer-3.02b-jobserver-fix.patch 433 SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d WHIRLPOOL a93193e48512a0cd8c6996d77ee8f1fd91b18cf00e6c99ec6c59dc9953bcb5ee5a90180b317ffb99337666e451da91f77f14a805f43026c1819ec596bb1268c1
+AUX glimmer-3.02b-ldflags.patch 2057 SHA256 95d391acdbf6d84440c2f3d96791e9f97776b7a248c9546738cc9df88711a28e SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 WHIRLPOOL d68752a5c3f78195bfabd116d19ca22ba90af7b817bfa29b9e0cc5614391e32cc3dd8cdd72e3ab642f4b52c48305ed8c7ab32ed622826b720b6228617ed682fe
+AUX glimmer-3.02b-rename_extract.patch 9286 SHA256 275f783f675729e5b39bea26e9a506dd2a1b675ef20f9a611ca50cb94b1ad272 SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342 WHIRLPOOL b5cc7d1d3734fc373c2a96d82bbcbb2a531bdc8040a7543d0ffdfcc9f4889ba9c89854ba4f99f9b4c1be30eb7a477530ee707bfadcc4ef180b1d6fcda26e7334
+DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c WHIRLPOOL c3eedb4a3a65043a69d632360608f04382117b8f7f3718eae328a1aa14f9f5d6d9ae6f05e0a83a09af5eb9e6b0c7b0ae26cb820813341aa5d7fa3f6002938ce8
+DIST glimmer302b.tar.gz 5637975 SHA256 ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 WHIRLPOOL bbce6f57546e6cc77801ac7f5e783510feafc2e120a8727e848a95dd9e2d966538e56cb7be597c2a463d9b372c8586a389d639e1377708a27bd56f81b37fea1f
 EBUILD glimmer-3.02-r2.ebuild 1322 SHA256 6ab8d0b9d4552eaa86d0172350bf107bfa7395fde5a0930b0f3b2b8f53f3c9f3 SHA512 02429bade2542dcd9acb27f6fac7cb392a76bb490df655c8bb2d6065fd9f77848ad3579c331fa63194d6527134d80148fa2aef2b407eb1ebec8a217e057e86bd WHIRLPOOL 81d6e280bc9cfe9301758e68b3e07810b828b1900117112a9087689167109739eb417cefb71e65b27c5983afd96bdb0990d173255263a96609300b1fefca0be2
-MISC ChangeLog 1565 SHA256 c027af4e4f0cd9264aa06e8fcda6c25659079db990091e4c78e695c7178c8eca SHA512 97b373c76db323963cad022dbd6178c11554f0104379cf07fc45031463bea445b0b21eab1fc6254eb40f1893eb57bc18547bbb46fe2f94caa02bd95f02a6e37f WHIRLPOOL dd23e4b60c3c1ec0606edff73a5e4930e8308b3434432fd6cc6bf4793f5c20c5e235c7a8c38db0f6dde0caee9bc8904902cec6a05dd537d13621c866fe88733d
+EBUILD glimmer-3.02-r3.ebuild 1471 SHA256 1d94a19265532a214503ea7ee2460ef009dbb266e87b1e70f4d9f0af7672e1a3 SHA512 fa16d3811ce467ca3224971ef18df9fa6a35ce82cfa6b8f50d6c5943a55e1891ea4768837b5baca979bfeda0b88778c5f1a04ce41616e72f1234e6b9c023cde7 WHIRLPOOL a64543c04c4ef94bbf40fe97d86053fbdbfbf62c908d16ba3d8758c37bbcd0effe5ca27d695e730fd97be162c2ea72346466e266433c1c385fceeab449bdf386
+EBUILD glimmer-3.02b.ebuild 1813 SHA256 9a12cfb1ff260933b83d87335521fd21c9ff3d076c4377005ad73010c65a47fc SHA512 8e52bbbc4317691461a8e83e7861e8191249a371e54ddf5f3cff28f4856e98caa57c4f0f79fa95f3dcdabbeca7a23d3ccfef919cbf1417f726258c8723eb1b29 WHIRLPOOL 0878a4568342cff4c9d21044e441a8fff868b22af9963b89769ff6b53c31554adf18a6fb72f82b9f6a7550e5dce14e8e05135ac4541ff4835c54630ab0b4985f
+MISC ChangeLog 2002 SHA256 42b378c186359056a2c0504a08478e8b910e8d55dec75395ee6f1e1098450925 SHA512 698127e334e2e83aac18af153328fa4c66c6c9950226a1e14a9a32b3751de20b0a592c6e14c620f21c5971837238bcb218a857116b1f8b9e394046e4cb87701d WHIRLPOOL 6b2606c744ca8e9d281f65910239d8842bd35b08c052a931aae773aff9761c7ff0276737022b629739a90808e528948d1450fcc5d2780fc1b18b4de275d0c327
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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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] <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-3.02-r1.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
index 532c3bc51c07..b182561f4671 100644
--- a/sci-biology/glimmer/glimmer-3.02-r1.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2010 Gentoo Foundation
+# 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-r1.ebuild,v 1.4 2010/01/03 14:17:04 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r3.ebuild,v 1.1 2015/05/26 06:22:16 jlec Exp $
 
-EAPI="2"
+EAPI="5"
 
-inherit eutils
+inherit eutils toolchain-funcs
 
 MY_PV=${PV//./}
 
@@ -15,15 +15,20 @@ SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
 LICENSE="Artistic"
 SLOT="0"
 IUSE=""
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
-RDEPEND="app-shells/tcsh
-	!app-crypt/pkcrack
-	!media-libs/libextractor"
+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"
@@ -31,20 +36,26 @@ src_prepare() {
 	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
 	# GCC 4.3 include fix
 	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
-	epatch "${FILESDIR}/${PN}-${PV}-glibc210.patch"
+	epatch "${PATCHES[@]}"
 }
 
 src_compile() {
-	emake -C src || die
+	emake \
+		-C src \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		AR=$(tc-getAR) \
+		CXXFLAGS="${CXXFLAGS}" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
-	rm bin/test
-	dobin bin/* || die
+	rm bin/test || die
+	dobin bin/*
 
-	dodir /usr/share/${PN}/scripts
-	insinto /usr/share/${PN}/scripts
-	doins scripts/* || die
+	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..1890c5332896
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -0,0 +1,68 @@
+# 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-3.02b.ebuild,v 1.1 2015/05/26 06:22:16 jlec Exp $
+
+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) $(TGT) || exit 1/' src/c_make.gen || die
+	# GCC 4.3 include fix
+	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	#
+	sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${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 "${PATCHES[@]}"
+}
+
+src_compile() {
+	emake \
+		-C src \
+		CC=$(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
+}