reinit the tree, so we can have metadata

5 files changed, 240 insertions, 0 deletions

diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
new file mode 100644
index 000000000000..3e16dd3c9ae4
--- /dev/null
+++ b/sci-biology/embassy-hmmer/Manifest
@@ -0,0 +1,7 @@
+AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2860 SHA256 6d05b00b1fa6946594cb3e5dea4e3d1652decab49bcb5313801d8ed4a33e51ac SHA512 f215e5c338aa1f0bf791de223f3ee9a13622f70e142c5ad4812dfe171f7d602aab750e1dfe4233324752adc645abf289e63d8981b8497787c785c07de64c7944 WHIRLPOOL 19d3b640de27436d40b95c451c0d39458b1f4a69eed7cb536e7417606d792dea91c677e719cde5b82873060549f36794ec6f36ba71a7549d619fe7f645d8fa62
+AUX embassy-hmmer-2.3.2.660-slotted-hmmer2.patch 3392 SHA256 d2ccf44c1f012300b7578553d697a950714c0eb93cf630799d16b662951f73da SHA512 18d1595b7cd6091917f9657310b286d2f0d1f6a61c045840b1c551b66162142997b837cc50b47a3a5fa7efec4ffa78e5b9b52804e3c4d41efeed9b4edb6e5507 WHIRLPOOL 7e1894fc952af1ffca66785790c94851b1dbdb6bb9530f18abef2862adbde171a731ab4d61f60dc2add66a7638dde778a3effc078047b8d9a39e70be2686b0c7
+DIST embassy-hmmer-2.3.2.660.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83
+EBUILD embassy-hmmer-2.3.2.660.ebuild 501 SHA256 7750aa84f23f0fb4748984397ae166c2677ab167749526bf26ff0e21f7c548b1 SHA512 bee21c5e7950f2f11be84c0287010630754681d840fc7393f9fc8e0c05fd14169e03f37a6d99bc4dfb28dae5b9f78a9f509a163cee6722796a3300b0cdab0651 WHIRLPOOL e2682a83bfa88731f25b9789a181e0c3c4207b183f1c4f73e16ba26a2a95395fc780c3149d46541eed1b2991ed553b44ba6bd71bbd807b6d6c00c1afd3bba5f7
+MISC ChangeLog 3694 SHA256 6632a1ac5d0fba8f1e0e9fe844e366120f360bb50ee7fcc48921f1c43d272a7c SHA512 2ec9e47acbd20102d2041c75376ef8b65781bd8593a9d5d3a866a9981e97bac5ecc32ad5b8272dea4db9a1106c94db35515169e5ca9c890459c2a4829d0953fc WHIRLPOOL 783eb072d06f81c664d86f20fa2165190310f9714b82bbb5b1eb72cdae7096c26dee4104ae7f5098671e82693fc098c961dded8826d34cf50148ae650271c2a4
+MISC ChangeLog-2015 5450 SHA256 f37958058bb7d3d532c9970a9aaa2f146fd9da610aa362e8e697b6aa4811150c SHA512 ff79da3b23f057604319a93af4e3b50b72d293abf6d4441aacac3e0074fc8fd4ce9027cfe26529c0555238bb5091fe75d2c4f24d7f1cf8ee8feea4438bf1eda9 WHIRLPOOL 2a9bfb84467181d90356468d17387a8fb21cabdf0c533239e1152ec61d34b3454d5097678e794303e479419282efc1bb005af03ef2dd4d59e70da7b751f025cc
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild
new file mode 100644
index 000000000000..4fa2defa1f7d
--- /dev/null
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+RDEPEND="sci-biology/hmmer:2"
+
+S="${WORKDIR}/HMMER-2.3.2.650"
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.3.2.650_fix-build-system.patch
+	# sci-biology/hmmer:2 has renamed commandline program names
+	"${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch
+)
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
new file mode 100644
index 000000000000..90c45632eada
--- /dev/null
+++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 037ca00..f539ab6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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 ");
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-hmmer/metadata.xml
@@ -0,0 +1,11 @@
+<?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>
+  <upstream>
+    <remote-id type="sourceforge">emboss</remote-id>
+  </upstream>
+</pkgmetadata>