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 --- sci-biology/maqview/Manifest | 8 ++++ sci-biology/maqview/files/0.2.5-ldflags.patch | 46 ++++++++++++++++++++++ sci-biology/maqview/files/0.2.5-zlib.patch | 33 ++++++++++++++++ .../maqview/files/maqview-0.2.5-gcc4.7.patch | 16 ++++++++ sci-biology/maqview/maqview-0.2.5-r3.ebuild | 34 ++++++++++++++++ sci-biology/maqview/metadata.xml | 11 ++++++ 6 files changed, 148 insertions(+) create mode 100644 sci-biology/maqview/Manifest create mode 100644 sci-biology/maqview/files/0.2.5-ldflags.patch create mode 100644 sci-biology/maqview/files/0.2.5-zlib.patch create mode 100644 sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch create mode 100644 sci-biology/maqview/maqview-0.2.5-r3.ebuild create mode 100644 sci-biology/maqview/metadata.xml (limited to 'sci-biology/maqview') diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest new file mode 100644 index 000000000000..105b15262568 --- /dev/null +++ b/sci-biology/maqview/Manifest @@ -0,0 +1,8 @@ +AUX 0.2.5-ldflags.patch 1335 SHA256 0876b98428f7964be91fb27f853458ba557ca8bf7eb313e416ece5a869a31efe SHA512 ae034ae1279e49c71f9daf658aece35063c56afc7ac3269d21d21a2f5b6f8e7974be48c82b52f4d250a9dcacfd5e8c9208b40c904ff73af8592c7f39395c6b6e WHIRLPOOL 8b4530a4220b8cd70fd1c33bb6dd19e6cecf8e9c434d9ca55df5e956b19ffa03f8ee7385ae369b6e7e291ddcab5e6d4ca6663744573aaad1080201314001a400 +AUX 0.2.5-zlib.patch 1437 SHA256 0952ca78e6ec4474063e2049294f432abe28890e76923fdb69b262a8a0b73d26 SHA512 7925f70d1f68bfa4fa87134d8ef20b05a6f022b1a9478a8e594e7b655852d858c0928b101f7eafd4e1ef44a17f8d353d49a6d1ede4072ac85ec452f75bd06c03 WHIRLPOOL 4b5fffeae840e49d372c3e8399da7cef708fbd6fbe45e2f5074751a37bdf0b66bb299c33ea2cc61b20abbe55e108b14f9d3bfc640c4aa89af3b0520dd34f606b +AUX maqview-0.2.5-gcc4.7.patch 575 SHA256 c5474002f6624d688fce6fea700334d09971987720a11321363631217c87e20e SHA512 277086e1d6d536ae368083032421029d64d5173e643edaafbad2833d56e8ec283152a49d9874a7142333e0fee976d3600ed118b6beb0482ec7e0e95f4a36fba4 WHIRLPOOL dfbbaf4cfe1f85b8aaa0a7517cbe62f3df861e3ccc8c64a45b865270b50091eb9b41d9c1cfb8286e736817b62a9f21358a58ff0413eaae5a4c04a6bccae41163 +DIST maqview-0.2.5.tar.gz 383410 SHA256 156794f114a00bb455a47ccefa50782441dc1b9668b6e7439ce0674060c085cb SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 WHIRLPOOL 0ba5a15a1317b4bb78458b9e282348983be9e2c30980aef4e35a9f5dacfff57226eaa4403fb0b9d9d448ba033409d548db224ed544ad365226a8fb59be8b743e +EBUILD maqview-0.2.5-r3.ebuild 608 SHA256 719fe87c607582da8c2b6cf50f9dd0296b5b935b2fd70bb28dac877b1e5d8d20 SHA512 71d33765c88d05e9d2c9c24c7d3bed6cefc194bbb4844a274ccb5b16380d8e1608acfb929b9dd8631adf9542ee3af5bcfd1cfed50f420b2d352d9b0d31eaf7bf WHIRLPOOL f590b13a08d314b3bfab5790f98707966cc10f8e6b582035ae7b7fa4c22ac5839bcc90d6b87f841260be19b8864c4b57d3882e9f5466f3ceea8fd325ba70d162 +MISC ChangeLog 2526 SHA256 c6ff0d1b78a0da57fd34e3779221f644aadfc9b5ff5e469b14616d2120701763 SHA512 b3a8b31668d4af69db4daea90f302c39b42b57e22a2c48eb64cf44405070ced1af360a70f48b49efd265c47b0480aa0d53693dbccf0871e6da62e1977e3b859a WHIRLPOOL 239e1d9c3873789680882540b6005d0bdd9a38d9ad1bc180b3041322d6a389ff7df136a2be13755655cbad41a61bfe1999361e56b0f298c1e15021b97c249e49 +MISC ChangeLog-2015 1735 SHA256 7a4e5bbd005f3618c3e7d610da81bbe06577af3e840eff90098da8dcc753a09b SHA512 4f350d0d119bf3b8394584e4f306529a91be264ded36af621bac3d971cc27e8b83da78679b9fe0afb54991bde515b2ddb6b0fc560bfcd6d0695c5a13a89d0147 WHIRLPOOL f6350b623c52b046a37e73eeed2b027f6dfdca84d8cbf49de989499c9f62add437363d58c39b524e0e9818c8f2548bd1c3e60f380e6f18b746a8ac38e1008214 +MISC metadata.xml 344 SHA256 e7635c034b39ae80b82be3d5b388b8cbe8642e948d699f8b7a208b75618f4991 SHA512 01962a043f6efd23e14570c486b43f89319c47d040fe94324b67e077cbc755435d236eb736e70c5fc582798c8765daa0f85a1f39a3d18ab27bff171fa7765e45 WHIRLPOOL 9d8641cdc4d97433980cd5f9366ddb94e44d1b179e75c5fc17b54a64d0e64e6b17076039efc9cb5c5449fa1439aa8185579afa5a7554472b400461d7f995f3d0 diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch new file mode 100644 index 000000000000..92b9a3ed58ac --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-ldflags.patch @@ -0,0 +1,46 @@ + configure.ac | 18 +++--------------- + 1 files changed, 3 insertions(+), 15 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 90e612b..5a00d15 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -9,17 +9,10 @@ AC_PROG_INSTALL + AC_STDC_HEADERS + + is_static=0 +-case ${prefix} in +- NONE);; +- *) is_static=1 +- AC_MSG_WARN([Library libglut will be statically linked.]) +- LDFLAGS="-L${prefix}/lib" +- CPPFLAGS="-I${prefix}/include";; +-esac + + # set CFLAGS and LDFLAGS + +-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" ++true_CFLAGS="-DMAQ_LONGREADS" + case "${host_os}" in + darwin*) + GLLIBS="-framework OpenGL -framework GLUT" +@@ -30,17 +23,12 @@ case "${host_os}" in + i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; + esac + AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"]) +- AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], +- [is_static=1]) +- case $is_static in +- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; +- 0) GLLIBS="-lGL -lglut -lm";; +- esac ++ GLLIBS="-lGL -lglut -lm -lGLU" + AC_SUBST([GLLIBS]);; + # *) AC_MSG_ERROR([OS is not supported]);; + esac + AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1]) +-CFLAGS=$true_CFLAGS ++CFLAGS="${CFLAGS} $true_CFLAGS" + + AC_CONFIG_FILES([Makefile]) + AC_OUTPUT diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch new file mode 100644 index 000000000000..cd35273de66b --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-zlib.patch @@ -0,0 +1,33 @@ + Makefile.am | 6 +++--- + zrio.c | 2 +- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index dad515a..9617eb7 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,8 +1,8 @@ + bin_PROGRAMS = zrio maqindex maqview maqindex_socks +-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \ +- infback.c inftrees.c trees.c uncompr.c zutil.c +-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src) ++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c ++LIBS = -lz + zrio_SOURCES = zrio_main.c $(generic_src) ++zrio_LDADD = -lz + maqindex_SOURCES = maqmap_index_main.c $(generic_src) + maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \ + $(generic_src) +diff --git a/zrio.c b/zrio.c +index ffed00a..fe744df 100644 +--- a/zrio.c ++++ b/zrio.c +@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void + totin += strm.avail_in; + totout += strm.avail_out; + tmp = strm.avail_out; +- ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */ ++ ret = inflate(&strm, Z_BLOCK); /* return at end of block */ + totin -= strm.avail_in; + totout -= strm.avail_out; + if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout); diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch new file mode 100644 index 000000000000..043208bb79b5 --- /dev/null +++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch @@ -0,0 +1,16 @@ + stdhash.hh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..f22c5a6 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maqview/maqview-0.2.5-r3.ebuild b/sci-biology/maqview/maqview-0.2.5-r3.ebuild new file mode 100644 index 000000000000..2d6574217029 --- /dev/null +++ b/sci-biology/maqview/maqview-0.2.5-r3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI="mirror://sourceforge/maq/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + media-libs/freeglut + sys-libs/zlib" +RDEPEND="${DEPEND} + sci-biology/maq" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-zlib.patch + "${FILESDIR}"/${P}-gcc4.7.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml new file mode 100644 index 000000000000..0b39d2a8530d --- /dev/null +++ b/sci-biology/maqview/metadata.xml @@ -0,0 +1,11 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + maq + + -- cgit v1.2.3