gentoo (leap year) resync : 29.02.2020

author: V3n3RiX <venerix@redcorelinux.org> 2020-02-29 18:01:47 +0000
committer: V3n3RiX <venerix@redcorelinux.org> 2020-02-29 18:01:47 +0000
commit: ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (patch)
tree: 9f47ee47c31a0f13f9496879cd88a1042550aa81 /sci-biology
parent: 53cba99042fa967e2a93da9f8db806fe2d035543 (diff)
10 files changed, 360 insertions, 331 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 3301012dde8b..c29ffe1f8aaf 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest
index fc5186011f1b..533808de8b3f 100644
--- a/sci-biology/qrna/Manifest
+++ b/sci-biology/qrna/Manifest
@@ -1,6 +1,6 @@
 AUX 26qrna 30 BLAKE2B 07faad9f2143edab789c29f999182e76a87ae82b9e6fca3346fc6391f7581ce3595a70e2432358e527a0a4178078b0e8f881537fe90a069a0b09211476520648 SHA512 ba47d1fe1cba68ca7dce369e814a67cca24339a1ec213d206001b4f87f8939d81c7e59bc285090e5ec2cec05693f560c9c4883cae8f67891f6053d9bc69cc46b
 AUX qrna-2.0.3c-glibc-2.10.patch 7571 BLAKE2B 3361fa6c31af0fa7f01e3c32bce2a8570df69b06517f9eb46a2f4f249acc972ac15da4fa5b9c1211efeaa91ee7d41f5c5e2392d89ead41252b5f5675826d4c21 SHA512 afa8767baadf99dafbb0ce4fa8b31017f6a12e1eadbcbd41a7e04e571d3f059395356178df3ab28f8c03c10f227123361590357c6ace6256727322ade00228e6
-AUX qrna-2.0.3c-ldflags.patch 1368 BLAKE2B b3f5cee42c370545e348e86627981d4568a84a673faf32d041b0ebbce0e782c8cab1aaa41c2c48f43704886035431c64b035a99b98225363f5ca2d0b8b9c0dc2 SHA512 4b1be14c664056eebb914e8c8223686ef0f345c860bd5aca82dced67b9580a205ef9539c563c0b0c646a9781ed0c58c4cec69d71bceb2c410dc485e9b5881c54
+AUX qrna-2.0.3c-ldflags.patch 18533 BLAKE2B b4901278e494d75895efecf9808e119307ece785437dec6c0776154665205d22cdd95be8526fbdf6f717e45613776b778b6c4a4f7561b3ec4e57ffda1547212e SHA512 6090e90d1723001dcda9a613bb13387bb6cf1b33c1692d4ea40efd1e14bce792779bf6b9acf3eed964c9432f49d2325e4bf910c87cc076e2e7a9329b4f9371d9
 DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5
-EBUILD qrna-2.0.3c-r3.ebuild 1114 BLAKE2B 737bf8541a3812727d8d2c8adba527cc259b52fa88ed411c56c91a5783b3bc41d001da59b67ae79f02df48fda79859fae352a00dae452de291f1a7bce93676cf SHA512 008cb677ee7548fbae56f87e0394f135cc89c9811ad598157cb1b2ce2f708a715bb8a9b841b5348ef2647dd4a488905960d0a6448d5c13fcd05be61361c4de37
+EBUILD qrna-2.0.3c-r3.ebuild 950 BLAKE2B adf9ed2e0efbdc1324e7ab68366f4bea99a1e27192d6d7eebff579a74c647af45b2150649347c581547bf78e266ebcde909ced51eeca63ade688007f51c065c6 SHA512 a59e67d3e608b1b441fd4f8a80bcdeb89431372406d149bb0df84a375a376e4b5b7d4bc74771b0e48daebdf412b63b04e3e83bcc32a583f1436fb30a6f320baf
 MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
index d03f650dd39e..17ca27e6da5a 100644
--- a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
@@ -1,13 +1,156 @@
-diff --git a/src/Makefile b/src/Makefile
-index 1d1631b..4fa3af9 100644
+--- a/squid/Makefile
++++ b/squid/Makefile
+@@ -19,7 +19,6 @@
+ #  On an Alliant, use fxc.
+ #
+ #CC = cc
+-CC = gcc
+ #CC = fxc
+ 
+ ## Any special compiler flags you want.
+@@ -37,7 +36,6 @@
+ #  for instance. If the code builds cleanly but seg faults, try
+ #  rebuilding without optimization.
+ #
+-CFLAGS = -O
+ #CFLAGS = -g 
+ #CFLAGS = -TARG:exc_max -64 -Ofast=ip27    #specific SGI Origin200 compiler#
+ 
+@@ -47,8 +45,6 @@
+ #  Don't worry. The Makefile tests for ranlib existence and will work
+ #  fine on SGIs even if RANLIB is set.
+ #
+-AR     = ar rcv
+-RANLIB = ranlib
+ 
+ ## Machine specific definitions
+ #
+@@ -108,41 +104,41 @@
+ all: $(LIBTARGET)  
+ 
+ alistat: $(OBJ) alistat_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
+ 
+ compalign: $(OBJ) compalign_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
+ 
+ compstruct: $(OBJ) compstruct_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
+ 
+ getseq: $(OBJ) getseq_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
+ 
+ reformat: $(OBJ) reformat_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
+ 
+ revcomp: $(OBJ) revcomp_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
+ 
+ seqstat: $(OBJ) seqstat_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
+ 
+ seqsplit: $(OBJ) seqsplit_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
+ 
+ shuffle: $(OBJ) shuffle_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
+ 
+ translate:  $(OBJ) translate_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
+ 
+ weight: $(OBJ) weight_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
+ 
+ 
+ $(LIBTARGET): $(OBJ)
+-	$(AR) $(LIBTARGET) $(OBJ)
++	$(AR) rcv $(LIBTARGET) $(OBJ)
+ 	-if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi
+ 	-if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi
+ 	-if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi
+@@ -182,4 +178,4 @@
+ 	etags -t $(SRC) $(HDRS)
+ 
+ .c.o:
+-	$(CC) $(CFLAGS) $(MDEFS) -c $<		
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<
+--- a/squid02/Makefile
++++ b/squid02/Makefile
+@@ -27,8 +27,6 @@
+ 
+ ## your compiler and compiler flags
+ #
+-CC     = gcc
+-CFLAGS = -g -O2
+ 
+ ## other defined flags for machine-specific stuff 
+ #
+@@ -37,8 +35,6 @@
+ 
+ ## Archiver command
+ #
+-AR     = ar rcv
+-RANLIB = ranlib
+ 
+ ## instructions for installing man pages
+ #
+@@ -158,10 +154,10 @@
+ all: version.h $(PROGS) libsquid.a
+ 
+ $(PROGS): %: %_main.o version.h $(OBJS) 
+-	$(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
+ 
+ .c.o:
+-	$(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<		
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<
+ ################################################################
+ 
+ 
+@@ -172,7 +168,7 @@
+ module: libsquid.a
+ 
+ libsquid.a: version.h $(OBJS)
+-	$(AR) libsquid.a $(OBJS)
++	$(AR) rcv libsquid.a $(OBJS)
+ 	$(RANLIB) libsquid.a
+ 	chmod 644 libsquid.a
+ #################################################################
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -131,17 +131,17 @@ DEMOS =
+@@ -21,7 +21,6 @@
+ SQUIDSRCDIR02 = ../squid02
+ 
+ ## your compiler
+-CC = gcc
+ #CC = cc
+ 
+ ## any special compiler flags you want
+@@ -30,7 +29,6 @@
+ #CFLAGS = -g -Wall -pedantic 
+ #CFLAGS = -TARG:exc_max 
+ #CFLAGS = -g -fullwarn -wlint,-fviah
+-CFLAGS = -O
+ #CFLAGS = -p # profiling #
+ #CFLAGS = -64 -Ofast=ip27   #specific warhorse compiler#
+ 
+@@ -131,145 +129,145 @@
  all: 	$(PROGS)
  
  main:              $(OBJ) main.o
 -	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
-+	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
  cfgbuild:          $(OBJ) cfgbuild.o
 -	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
 +	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
@@ -25,4 +168,208 @@ index 1d1631b..4fa3af9 100644
 +	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
  
  main.o:            ../src/main.c
- 	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ cfgbuild.o:        ../src/cfgbuild.c
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ eqrna.o:           ../src/eqrna.c
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ eqrna_sample.o:    ../src/eqrna_sample.c
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ shuffle.o:         ../src/shuffle.c
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnamat_main.o:     ../src/rnamat_main.c
+-	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?	
++	           $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ 
+ cfgio.o:                      ../src/cfgio.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ cfgmodel.o:                   ../src/cfgmodel.c
+-		              $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++		                  $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ cfgparse.o:                   ../src/cfgparse.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ codcreatealign.o:             ../src/codcreatealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ coddp.o:                      ../src/coddp.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ coddpscanfast.o:              ../src/coddpscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ codmodel.o:                   ../src/codmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ codon.o:                      ../src/codon.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ codscorealign.o:              ../src/codscorealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ er_math.o:                    ../src/er_math.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ er_vectop.o:                  ../src/er_vectop.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ evd.o:                        ../src/evd.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolcodmodel.o:               ../src/evolcodmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolemissions.o:              ../src/evolemissions.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolmisc.o:                   ../src/evolmisc.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolnullmodel.o:              ../src/evolnullmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolothmodel.o:               ../src/evolothmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolqrnaversion.o:            ../src/evolqrnaversion.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolscorewithmodels.o:        ../src/evolscorewithmodels.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolriboprob.o:               ../src/evolriboprob.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolrnadp.o:                  ../src/evolrnadp.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolrnadpscanfast.o:          ../src/evolrnadpscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolrnamodel.o:               ../src/evolrnamodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolrnascorealign.o:          ../src/evolrnascorealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ evolve.o:                     ../src/evolve.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ globals.o:                    ../src/globals.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ hexamer.o:                    ../src/hexamer.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ matrix.o:                     ../src/matrix.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ misc.o:                       ../src/misc.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ nrnscfg.o:                    ../src/nrnscfg.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ nstack.o:                     ../src/nstack.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ nullmodel.o:                  ../src/nullmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ othcreatealign.o:             ../src/othcreatealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ othdp.o:                      ../src/othdp.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ othdpscanfast.o:              ../src/othdpscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ othmodel.o:                   ../src/othmodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ othscorealign.o:              ../src/othscorealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ posterior.o:                  ../src/posterior.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ qrnaversion.o:                ../src/qrnaversion.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ riboprob.o:                   ../src/riboprob.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnacreatealign.o:             ../src/rnacreatealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnadp.o:                      ../src/rnadp.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnadpscanfast.o:              ../src/rnadpscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnaio.o:                      ../src/rnaio.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnamat.o:                     ../src/rnamat.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ rnamodel.o:                   ../src/rnamodel.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnaoutput.o:                  ../src/rnaoutput.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnascorealign.o:              ../src/rnascorealign.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnascfg.o:                    ../src/rnascfg.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ rnascfgscanfast.o:            ../src/rnascfgscanfast.c
+-	                      $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ scorewithmodels.o:           ../src/scorewithmodels.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ scorewithmodelscanfast.o:    ../src/scorewithmodelscanfast.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ seqio.o:                     ../src/seqio.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ trace.o:                     ../src/trace.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ traceSCFG.o:                 ../src/traceSCFG.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ tying.o:                     ../src/tying.c
+-	                     $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
++	                      $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ 
+ 
+ install: $(PROGS)
+@@ -313,10 +311,10 @@
+ 	/usr/lib/lint/llib-lm.ln
+ 
+ .c.o:
+-	$(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<		
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ 
+ .m.o:
+-	$(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ 
+ 
+ 
diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
index 5c580a24d2a3..34b59e9fb0a3 100644
--- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
+++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 RDEPEND="
 	dev-lang/perl
@@ -26,15 +25,13 @@ PATCHES=(
 
 src_prepare() {
 	default
-	sed \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \
-		-e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \
-		-i {src,squid,squid02}/Makefile || die
 	rm -v squid*/*.a || die
 }
 
+src_configure() {
+	tc-export AR CC RANLIB
+}
+
 src_compile() {
 	local d
 	for d in squid squid02 src; do
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
deleted file mode 100644
index 994f585d8924..000000000000
--- a/sci-biology/tophat/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX tophat-2.1.1-fix-c++14.patch 655 BLAKE2B 760f2d371e6467340d31c688187a62b0266f6a3cd52cf79db6917a9a5ec0538952b8a5212c70a16f7af5413fe7d5e2b002abf8f77c081e9578a0af9c5ca9d36c SHA512 66f46da853ee56821c50d46cb6853f082009dfc4d5237ec82371db9e9f5435a5a84420e03955aec7ae80076d3da492e0be7ae7d34bced06ee2ea845ad23974ca
-AUX tophat-2.1.1-python2-shebangs.patch 758 BLAKE2B 83bda360dc36d3eaa890adee00bdb58698fb5eaaa29255c85b3b63f61536921386115662051a4938d21079a3eb1a103dce752f0320fe1990535d35ae74480fcc SHA512 887e5a8b02c2e43a7fa35c9f98670dd722527c45454ca24d5e2f9d2f372267905d7e0142317769b14830706cf82868cb83ede970ffe527f736d71df794fd6342
-AUX tophat-2.1.1-unbundle-seqan-samtools.patch 5224 BLAKE2B acdf26085b6eab54f478f5e31e2f180a008b9a05b853253f8f161759dc79a0fb5ea0c54bbf3a0f4ebf79da71988c60d17899aaa1ff6e927a308eca01edccbdf1 SHA512 d920cee92a0a694a34d6ac5b949e5b883bf9dcff338f36e227cb014732231b96461c02e75418972c85880169751a96c2367f6a4be6ce8c91f310b4b4f6858248
-DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
-EBUILD tophat-2.1.1-r5.ebuild 2229 BLAKE2B 592ad2da66507557ae794c2372d3502a66c5d10248de271ae1df19ce6e2652aa568c2948940b172ebe62adb0f5f186b476fbaaa5b25d6ecda50abd34488097fa SHA512 32c653dc0abacb77e342142d64e0522c1c9305a34e66475b84ec8d5843c200a8a8ab3acb9138b2d51e48fb6540ab53d70f4bfd8f26447c00f14ef174486c3eb8
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
deleted file mode 100644
index e8168bb91438..000000000000
--- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Fix building with C++14, which errors out due to broken perfect forwarding signature.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594544
-
---- a/src/tophat_reports.cpp
-+++ b/src/tophat_reports.cpp
-@@ -2705,7 +2705,7 @@
- 				junction_stat.gtf_match = true;
- 				junction_stat.accepted = true;
- 
--				gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
-+				gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
- 			}
- 		}
- 		fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());
diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
deleted file mode 100644
index 5c38bcc072ef..000000000000
--- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Make Python 2 explicit in python scripts
-
---- a/src/bed_to_juncs
-+++ b/src/bed_to_juncs
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- bed_to_juncs.py
---- a/src/contig_to_chr_coords
-+++ b/src/contig_to_chr_coords
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- contig_to_chr_coords.py
---- a/src/sra_to_solid
-+++ b/src/sra_to_solid
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- """
- sra_to_solid.py
---- a/src/tophat-fusion-post
-+++ b/src/tophat-fusion-post
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- 
- """
---- a/src/tophat.py
-+++ b/src/tophat.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- # encoding: utf-8
- """
diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
deleted file mode 100644
index 9d0a2694051a..000000000000
--- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
+++ /dev/null
@@ -1,162 +0,0 @@
-Unbundle the included samtools and SeqAn, and use system libraries.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
-
-Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend
-on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594810
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -28,26 +28,15 @@
- AC_PROG_INSTALL
- AM_PATH_PYTHON([2.4])
- 
--m4_include([ax_boost_base.m4])
--m4_include([ax_boost_thread.m4])
- # CXXFLAGS="$CXXFLAGS $threadLib"
- AX_BOOST_BASE([1.38.0])
-+AX_BOOST_SYSTEM
- AX_BOOST_THREAD
--if test -z "$BOOST_THREAD_LIBS"; then
-+if test -z "$BOOST_THREAD_LIB"; then
-   AC_MSG_ERROR([boost.thread not found. Aborting.])
- fi
- 
- 
--# BAM related:
-- ac_bam_path=samtools-0.1.18
-- BAM_LIB="-lbam"
-- BAM_LDFLAGS="-L./$ac_bam_path"
-- BAM_CPPFLAGS="-I./$ac_bam_path"
-- AC_SUBST(BAM_CPPFLAGS)
-- AC_SUBST(BAM_LDFLAGS)
-- AC_SUBST(BAM_LIB)
--
--
- # Checks for header files.
- AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
- 
-@@ -80,32 +69,23 @@
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- user_LDFLAGS="$LDFLAGS"
- 
--AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
--			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
--
- AC_ARG_ENABLE([debug],
-               [AS_HELP_STRING([--enable-debug],
- 	                      [enable debugging info (default is no)])],
-               [], [enable_debug=no])
--AC_ARG_ENABLE([optim],
--              [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
--	                      [set optimization level (default is 3)])],
--              [if test "x$enable_optim" = xyes; then enable_optim=3; fi],
--              [enable_optim=3])
- 
--AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])	
- AS_IF([test "x$enable_debug" = xyes],
-       [debug_CFLAGS="-DDEBUG"],
-       [debug_CFLAGS="-DNDEBUG"])
- 	  
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
- CXXFLAGS="$CFLAGS"
--CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
-+CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
- LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
- 
- AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
-@@ -122,7 +102,7 @@
- -- ${PACKAGE_STRING} Configuration Results --
-   C++ compiler:        ${CXX} ${CXXFLAGS}
-   Linker flags:        ${LDFLAGS}
--  BOOST libraries:     ${BOOST_THREAD_LIBS}"
-+  BOOST libraries:     ${BOOST_THREAD_LIB}"
- 
- if test x"${GCC}" = x"yes" ; then
-    gcc_version=`${CC} --version | head -n 1`
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -683,17 +683,12 @@
- SeqAn-1.4.2/seqan/system/system_thread.h \
- SeqAn-1.4.2/seqan/version.h
- 
--SAMDIR = ./samtools-0.1.18
--SAMLIB = libbam.a
--SAMPROG = samtools_0.1.18
--BAM_LIB = -lbam
--BAM_CPPFLAGS = -I$(SAMDIR)
--BAM_LDFLAGS = -L$(SAMDIR)
-+BAM_LIB = -lbam-0.1-legacy
-+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/
- 
- #-- progs to be installed in $prefix/bin
- 
- bin_PROGRAMS = \
--	$(SAMPROG) \
- 	prep_reads \
- 	gtf_to_fasta \
- 	fix_map_ordering \
-@@ -722,9 +717,6 @@
- 	tophat2 \
- 	tophat
- 
--clean-local:
--	cd $(SAMDIR) && make clean
--
- tophat2: tophat2.sh
- 	cp tophat2.sh tophat2 && chmod 755 tophat2
- 
-@@ -732,7 +724,7 @@
- 	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
- 
- #-- tophat library for linking convienence
--noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
-+noinst_LIBRARIES = libgc.a libtophat.a
- 
- noinst_HEADERS = \
- 	reads.h \
-@@ -801,11 +793,11 @@
- prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) 
- 
- segment_juncs_SOURCES = segment_juncs.cpp
--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
- segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
- 
- long_spanning_reads_SOURCES = long_spanning_reads.cpp
--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
- long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
- 
- gtf_juncs_SOURCES = gtf_juncs.cpp
-@@ -817,7 +809,7 @@
- juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
- 
- tophat_reports_SOURCES = tophat_reports.cpp
--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
- tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
- 
- fix_map_ordering_SOURCES = fix_map_ordering.cpp
-@@ -844,15 +836,5 @@
- gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
- gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
- 
--
--libbam_a_SOURCES = 
--samtools_0_1_18_SOURCES = 
--
--$(SAMPROG): $(SAMLIB)
--	
--
--$(SAMLIB):
--	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
--
- install-data-hook:
- 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/tophat/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
deleted file mode 100644
index 753188771381..000000000000
--- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
-HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
-SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-libs/boost:=[threads]
-	$(python_gen_cond_dep '
-		dev-python/intervaltree[${PYTHON_MULTI_USEDEP}]
-		dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}]
-	')
-	sci-biology/samtools:0.1-legacy
-	sci-biology/bowtie:2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	sci-biology/seqan:1.4
-	>=sys-devel/autoconf-archive-2016.09.16"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
-	"${FILESDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-python2-shebangs.patch
-)
-
-src_prepare() {
-	default
-
-	# remove bundled libs
-	rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
-
-	sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
-		-i src/tophat.py src/common.cpp || die
-
-	sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
-		-e '/^samtools-0\.1\.18\//d' \
-		-e '/^SeqAn-1\.4\.2\//d' \
-		-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
-		-e 's:\$(top_builddir)\/src\/::' \
-		-i src/Makefile.am || die
-	sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
-	append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
-
-	# remove ancient autoconf archive macros, wreaking havoc,
-	# depend on sys-devel/autoconf-archive instead, bug #594810
-	rm {ax_boost_thread,ax_boost_base}.m4 || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable debug)
-}
-
-src_install() {
-	default
-
-	# delete bundled python modules
-	local i
-	for i in intervaltree sortedcontainers; do
-		rm -r "${ED%/}"/usr/bin/${i} || die
-	done
-}
-
-pkg_postinst() {
-	optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
-}
author	V3n3RiX <venerix@redcorelinux.org>	2020-02-29 18:01:47 +0000
committer	V3n3RiX <venerix@redcorelinux.org>	2020-02-29 18:01:47 +0000
commit	ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (patch)
tree	9f47ee47c31a0f13f9496879cd88a1042550aa81 /sci-biology
parent	53cba99042fa967e2a93da9f8db806fe2d035543 (diff)