From ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 29 Feb 2020 18:01:47 +0000 Subject: gentoo (leap year) resync : 29.02.2020 --- sci-biology/Manifest.gz | Bin 23827 -> 23662 bytes sci-biology/qrna/Manifest | 4 +- sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 357 ++++++++++++++++++++- sci-biology/qrna/qrna-2.0.3c-r3.ebuild | 15 +- sci-biology/tophat/Manifest | 6 - .../tophat/files/tophat-2.1.1-fix-c++14.patch | 14 - .../files/tophat-2.1.1-python2-shebangs.patch | 42 --- .../tophat-2.1.1-unbundle-seqan-samtools.patch | 162 ---------- sci-biology/tophat/metadata.xml | 8 - sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 ----- 10 files changed, 360 insertions(+), 331 deletions(-) delete mode 100644 sci-biology/tophat/Manifest delete mode 100644 sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch delete mode 100644 sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch delete mode 100644 sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch delete mode 100644 sci-biology/tophat/metadata.xml delete mode 100644 sci-biology/tophat/tophat-2.1.1-r5.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 3301012dde8b..c29ffe1f8aaf 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ 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(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 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - 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 -} -- cgit v1.2.3