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-rw-r--r--sci-biology/yass/Manifest6
-rw-r--r--sci-biology/yass/files/1.14-as-needed.patch207
-rw-r--r--sci-biology/yass/metadata.xml12
-rw-r--r--sci-biology/yass/yass-1.14-r2.ebuild32
4 files changed, 257 insertions, 0 deletions
diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest
new file mode 100644
index 000000000000..fed19b131f6d
--- /dev/null
+++ b/sci-biology/yass/Manifest
@@ -0,0 +1,6 @@
+AUX 1.14-as-needed.patch 6046 SHA256 16a8e8e042ef6af33b49145fca2da1f4c1dae4f5fcd692509eda8d867cbb8ecd SHA512 4b9227bb16556084121336b01d6d02257ccf7e35765db53b4a6ba2b0a41946a6b600a9dd05156b763b4b37f18d30d2c9111eeca79a1656f757199ba1cda5b3dd WHIRLPOOL 5c4ad2c59472ed93df27c4e9a8d5d29cb9c9e7b84b6318b2e21a799c671cc5b9f7f27408148ac79065f89b5d2fe2957dd7db55f30d01c1f0615a315d3a5cfc2c
+DIST yass-1.14.tar.gz 235530 SHA256 f23da1c16cf98317ad11c085feede9790401e888a95d486b550f0c081d4c9018 SHA512 fdfac6f391848d0bd35829a966721a242697b0832803092bd7ea2116149332642ddf3bf5f095fe707f6edbbb9454efe068852fe6d5cdfe937445d9d32a521fa2 WHIRLPOOL e5aabfabe7a1b001e5b41c2fd17dfc345ae66ba06d42decaacfd7948fc60aa38d90ca9d2d7a05cb0d7fa3216dbf125ec64d2341ee4e9c1ffa91b69f60e8a3728
+EBUILD yass-1.14-r2.ebuild 663 SHA256 34ba5ddb35fe3ce8bcc7bfa78a4eb156c57911214d797d30c769c622acc8bdbe SHA512 ac373f6d89d678ca71d0e84d76965cc2d3eed9ccf51d33c799613bcdb588f5adfc7ca588b823a92ea6bb12c39bb91fca6cdd685af3a8ec943a43192b633246cc WHIRLPOOL e1ff4e60a01bdcf1df0684b2ca1596853a0009fe48532a8c3b07f5e9a04670951eb36b02bab0afb0103a97d59fd57826c9741b63f4c6d340d9f31063d2c9ce1c
+MISC ChangeLog 2808 SHA256 36408d37a9418e7618211341f457a4dce25fc9f0ca711db9862d215e855a6519 SHA512 46095a17fa40a05dc57a00c78b1d326dd55dc8620ddcf340f2dbbedad22aa561c68726241aeb5096b6c67f42fdef91707ef4569565de25c87732b1559c62074d WHIRLPOOL de75615af31a0051077809b0d56d1b02174b1ec40b72b61e373fed913e4c65cc9bba1810e0ea43c1832c1526b431202e821771ee6eb14a5ea573701a6da8e7b7
+MISC ChangeLog-2015 675 SHA256 ae16ce2beb0da9bd6036d65853da5d15e0b357d5d351dd871aea5f4eec0f4265 SHA512 13ae8cfa681e40ee21cf3dca9f47ebcf7bf0dc14b4c446cd503e5be9bfeb70e87b701d15ff86b7f2603f5ff0233e1354910399d5baaeead597ed6d5074cebea9 WHIRLPOOL efd335d71098594ebfe42a080d923111c3acd3c861db0e5dc6331cbc2eac4cd36a7b504de5babbced9349428f3a895810a6c0299b317e3a76e7b9dc384b191a7
+MISC metadata.xml 439 SHA256 9d66ed15ddabe6d56a5a820c57b95fc4cb91f1b4ac9a3a0221072e04d077693b SHA512 e2f368f4a1b1b46ee31e1308c9a57846b08d9a4958a53caed2f2a9c8f228459cf305e1d07ac4f294bd6eca622094a36be0ec2859f86bd9eecf10070ea832d7af WHIRLPOOL 7747dec3f247172eaddc2e58e24a179e74708a9c7340d9dfc917e9f16be3cf9df66b130e6f385c62f06d9b4d5c9ddab597957053c9de7a6ecc97d28148ca8c13
diff --git a/sci-biology/yass/files/1.14-as-needed.patch b/sci-biology/yass/files/1.14-as-needed.patch
new file mode 100644
index 000000000000..e57503801c7a
--- /dev/null
+++ b/sci-biology/yass/files/1.14-as-needed.patch
@@ -0,0 +1,207 @@
+diff --git a/configure.ac b/configure.ac
+index 68453ef..3ecfd21 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul])
+ dnl 1) threads options
+
+ dnl abc) : with-threads option
+-AC_ARG_WITH(
+- threads,
+- [ --with-threads compile with all threads],
+- [threads="yes"],
+- [threads="no"])
++AC_ARG_ENABLE(
++ [threads],
++ AS_HELP_STRING([--enable-threads], [compile with all threads]))
+
+-if test "$threads" = "yes"; then
++AS_IF([test "x$enable_threads" = "xyes"], [
+ AC_MSG_RESULT(detected cpu parameter: threads);
+
+ dnl pthread library here ? (UNIX system)
+@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then
+ AC_MSG_RESULT(yes)
+ AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+ CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK "
+- LDFLAGS="$LDFLAGS -lpthread"
++ LIBS="$LIBS -lpthread"
+ else
+ AC_MSG_RESULT(no : disabling \"--with-threads\" parameter)
+ fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-threads\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
+-
+-
+-dnl a) : with-thread-fr option
+-AC_ARG_WITH(
+- thread-fr,
+- [ --with-thread-fr compile with two separate threads for Forward and Reverse sequence],
+- [thread_forward_reverse="yes"],
+- [thread_forward_reverse="no"])
+-
+-if test "$thread_forward_reverse" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-fr);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-fr\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
+-
+-
+-dnl b) : with-thread-aa option
+-AC_ARG_WITH(
+- thread-aa,
+- [ --with-thread-aa compile with two separate threads for Assemble and Align steps],
+- [thread_assemble_align="yes"],
+- [thread_assemble_align="no"])
+-
+-if test "$thread_assemble_align" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-aa);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-aa\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-dnl c) : with-thread-qc option
+-AC_ARG_WITH(
+- thread-qc,
+- [ --with-thread-qc compile with threads for the query chunks],
+- [thread_query_chunk="yes"],
+- [thread_query_chunk="no"])
+-
+-if test "$thread_query_chunk" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-qc);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-qc\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
++])
+
+ dnl 2) : low-memory option
+-AC_ARG_WITH(
+- low-memory,
+- [ --with-low-memory use less memory, but can miss some repeats],
+- [low_memory="yes"],
+- [low_memory="no"])
++AC_ARG_ENABLE(
++ [lowmemory],
++ AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats]))
+
+-if test "$low_memory" = "yes"; then
++AS_IF([test "x$enable_lowmemory" = "xyes"], [
+ AC_MSG_RESULT(detected memory parameter: low memory);
+ CFLAGS=" $CFLAGS -DLOW_MEMORY "
+-else
+- AC_MSG_RESULT(detected memory parameter : plain memory)
+-fi
+-
+-
+-CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer "
+-LDFLAGS="$LDFLAGS -lm"
++])
+
+ AC_SUBST(CFLAGS)
+ AC_SUBST(LDFLAGS)
++
+ AM_WITH_DMALLOC
+ AM_INIT_AUTOMAKE
+ AC_CONFIG_FILES([Makefile
+diff --git a/src/Makefile.am b/src/Makefile.am
+index e456f94..8d90ca9 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -6,3 +6,4 @@
+ bin_PROGRAMS = yass
+ yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \
+ align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h
++yass_LDADD = -lm
diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml
new file mode 100644
index 000000000000..67dfef524416
--- /dev/null
+++ b/sci-biology/yass/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <use>
+ <flag name="dmalloc">Enable debugging with the dmalloc library</flag>
+ <flag name="lowmem">Build for environments with low amounts of memory</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/yass/yass-1.14-r2.ebuild b/sci-biology/yass/yass-1.14-r2.ebuild
new file mode 100644
index 000000000000..cdbe54f0bef6
--- /dev/null
+++ b/sci-biology/yass/yass-1.14-r2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds"
+HOMEPAGE="http://bioinfo.lifl.fr/yass/"
+SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="dmalloc lowmem threads"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dmalloc? ( dev-libs/dmalloc )"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch )
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_enable threads) \
+ $(use_enable lowmem lowmemory) \
+ $(use_with dmalloc)
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-30 11:54:02 +0000