From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- .../embassy-hmmer-2.3.2.650_fix-build-system.patch | 100 ++++++++++++++++++++ .../embassy-hmmer-2.3.2.660-slotted-hmmer2.patch | 101 +++++++++++++++++++++ 2 files changed, 201 insertions(+) create mode 100644 sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch create mode 100644 sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch (limited to 'sci-biology/embassy-hmmer/files') diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch new file mode 100644 index 000000000000..90c45632eada --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 037ca00..f539ab6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index dc789bc..5a8c38e 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch new file mode 100644 index 000000000000..f202ddf3d0b5 --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch @@ -0,0 +1,101 @@ +Amend command-line names for Gentoo SLOTed hmmer:2 + +--- a/src/ehmmalign.c ++++ b/src/ehmmalign.c +@@ -99,7 +99,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2")); + if(mapali) + ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali)); + if(withali) +--- a/src/ehmmbuild.c ++++ b/src/ehmmbuild.c +@@ -146,7 +146,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2")); + if(prior) + ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior)); + if(null) +--- a/src/ehmmcalibrate.c ++++ b/src/ehmmcalibrate.c +@@ -98,7 +98,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2")); + if(cpu) + ajFmtPrintAppS(&cmd, " --cpu %d ", cpu); + if(fixed) +--- a/src/ehmmconvert.c ++++ b/src/ehmmconvert.c +@@ -72,7 +72,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2")); + + /* ACD option only allows one selection */ + option = ajStrGetCharFirst(format); +--- a/src/ehmmemit.c ++++ b/src/ehmmemit.c +@@ -79,7 +79,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2")); + ajFmtPrintAppS(&cmd, " --seed %d ", seed); + if(a) + ajStrAppendC(&cmd, " -a "); +--- a/src/ehmmfetch.c ++++ b/src/ehmmfetch.c +@@ -74,7 +74,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2")); + if(nhmm) + ajStrAppendC(&cmd, " -n "); + /* Note the output redirected to outfname */ +--- a/src/ehmmindex.c ++++ b/src/ehmmindex.c +@@ -68,7 +68,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2")); + ajStrAppendC(&cmd, ajFileGetNameC(database)); + + +--- a/src/ehmmpfam.c ++++ b/src/ehmmpfam.c +@@ -122,7 +122,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2")); + if(nuc) + ajStrAppendC(&cmd, " -n "); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); +--- a/src/ehmmsearch.c ++++ b/src/ehmmsearch.c +@@ -102,7 +102,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2")); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); + if(compat) + ajStrAppendC(&cmd, " --compat "); -- cgit v1.2.3