diff options
Diffstat (limited to 'sci-biology/maq')
| -rw-r--r-- | sci-biology/maq/Manifest | 10 | ||||
| -rw-r--r-- | sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch | 16 | ||||
| -rw-r--r-- | sci-biology/maq/files/maq-0.7.1-flags.patch | 24 | ||||
| -rw-r--r-- | sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch | 34 | ||||
| -rw-r--r-- | sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch | 19 | ||||
| -rw-r--r-- | sci-biology/maq/maq-0.7.1-r2.ebuild | 42 | ||||
| -rw-r--r-- | sci-biology/maq/metadata.xml | 11 |
7 files changed, 156 insertions, 0 deletions
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest new file mode 100644 index 000000000000..f26a3ced4353 --- /dev/null +++ b/sci-biology/maq/Manifest @@ -0,0 +1,10 @@ +AUX maq-0.7.1-bfr-overfl.patch 527 SHA256 ff7521f696d4deb311f3dec07997bd8cce068749369d6cd3d3e65fb6cce19e56 SHA512 953587e9354f2d3a070aae67ee999105b96678b2b781b9fbe8416d040a594d1db2ed6e7de0516cd29c2020de5129bbc26b78b7bfa5a258ebb5cb9fd4715f8bcf WHIRLPOOL ab41e0d61d75caf9780920eb87bd2def0b6b1006860b60d43d5fa8f96dc6a1956147073b2e6b186a64cb977c055a4e6133f12eb7d925aecf7c650a1cfdd3fed7 +AUX maq-0.7.1-flags.patch 799 SHA256 f1949b063ed015182e403668dc19466d079eacc6d351d11cc5d099d2aeeb18f9 SHA512 f13d8af7884691f2d8c8e9bd9d370c5ca12e863aaf05e156a964ba88053d86dcb63f24169fbc3b2a9264423510061c26d88904b87ea8aeb8bf446b51e190aedb WHIRLPOOL 6091105a0f1606bc96a5da85026da7dc4acf4d9900e9d26f64e353486eb3e1fc90862c5b16f3709a19019ace12313bb60af4e7603a4c8c49716f878c96486cfe +AUX maq-0.7.1-gcc-4.7.patch 1429 SHA256 df958693a9eb428069ca09410f549b22444fbd1818fab6101aaa03e658f00250 SHA512 e2936757fff7f32d8dea3da3181839b7b4190a15f4bfb5c3b6cb6a723a10ba8f6e4f762eca32387345a4263c9bf525a425d5e58c78f387a1813508fdc5fb364c WHIRLPOOL 244d7656f0ca1db364068910bd1042363ebcc7933506ad2e17c653e74e76ddc8b9862a2b84d82eed87aaa35776b964eaeaf70069f9e47418a1f3f850f3a91f4d +AUX maq-0.7.1-remove-64bit-flag.patch 787 SHA256 83b88bfc8f9035528460c5f194195bf33ccd9affb574e0a78198828143bee894 SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1 WHIRLPOOL f77db9e0358681e9e140004b74544754d8c91fbf254d11610610af4acbe5f1ba045127d93e00fffc8e7df2f36a5cea4e3b5641ed026d5f8a7aa67f7d9c6d79fe +DIST calib-36.dat.gz 196371 SHA256 d4480e04446eb273f1908add709dd5a24262c08a59a1647b9a2d053f4d30181b SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7 WHIRLPOOL cf060f27ba191f234f5db2a8c43a70bb03e4f9625fb73dcdcccdc342a9baa8686602fc92eaab5a68d4864d334852a90d665cc50421dacdf6257fb96f47f5829b +DIST maq-0.7.1.tar.bz2 368645 SHA256 e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2 SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c WHIRLPOOL 5e00112a0cca7646433b53f799e9baa088048f9b6b5577e3a633d23ac78c2d79169fe00f3d28ea7e304b73605b7e6a5c97e0d051881072955a936f1b3b0b8a21 +EBUILD maq-0.7.1-r2.ebuild 799 SHA256 1478f732dea1917bb9816dcec3cb2d967659a47e4f7069a9cc5a90c9fbdf4637 SHA512 5e52158937efbb822f9e521ec19b76a3dab1d6823da94cc154947d1024d2aa59bab00b111eb9d3d3e23a59782f2069ff4aa079133fa4608a4aa37e623e14c265 WHIRLPOOL 0c77259845a10adb180d6a6879934f30e09e87ba422539981c737e05d281c9dd3ab4539ff0663299053e41ec9a8b24487788af481ecfb4b35332245323c35911 +MISC ChangeLog 2569 SHA256 8678a35c30639699aa4992f76cc26d96a039e15b1ed73220307f251c40636fc1 SHA512 17db6913d41be3493da79df5015173007215efa4b8dd309bf7b8b826eea134460bbecd85a64c0c83a7ff2584e7aa5ec24aaa75ee5fb1dda40a295a160872cb37 WHIRLPOOL bd5b06241e6bb89c3db4f2fc711c96a9e9cad0436853005048499442569b95d0d340e42389b1c53df5ba83808f733a2669a83315835b90d5f91278d8d2383a4f +MISC ChangeLog-2015 1593 SHA256 11a721662c24da57a4547df5500eb4f67e45ba788b9c12ede57861992cadd88b SHA512 dcc4634336b513ef01f06c269d65c2b1ca55b6cc0436521cf552d6bdd7cafcb29617cba552ac0cbcbfcffea20154aa1c92b68ced341f3d9a423d9c9d7db2d99a WHIRLPOOL 55d882686d50124d8251fa3101361aa180feaf7db0dd254208e6661c7d83a3cee433bf12cb64c45ea2f0d6ae659e877a70b36088dc5b099a0c6f5aead25609cc +MISC metadata.xml 344 SHA256 e7635c034b39ae80b82be3d5b388b8cbe8642e948d699f8b7a208b75618f4991 SHA512 01962a043f6efd23e14570c486b43f89319c47d040fe94324b67e077cbc755435d236eb736e70c5fc582798c8765daa0f85a1f39a3d18ab27bff171fa7765e45 WHIRLPOOL 9d8641cdc4d97433980cd5f9366ddb94e44d1b179e75c5fc17b54a64d0e64e6b17076039efc9cb5c5449fa1439aa8185579afa5a7554472b400461d7f995f3d0 diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch new file mode 100644 index 000000000000..9f4247d441f5 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch @@ -0,0 +1,16 @@ + simulate.c | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/simulate.c b/simulate.c +index 788c440..67ba2ba 100644 +--- a/simulate.c ++++ b/simulate.c +@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres) + memset(wc_single, 0, 40); memset(tot_single, 0, 40); + memset(wc_pair, 0, 40); memset(tot_pair, 0, 40); + memset(abpair, 0, 4 * 256 * 10); +- memset(tc[2], 0, 4 * sizeof(int)); ++ memset(tc, 0, 4 * sizeof(int)); + while (maqmap_read1(fp, m1)) { + int is_correct; + bit32_t p1, p2; diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch new file mode 100644 index 000000000000..721e53248b7a --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-flags.patch @@ -0,0 +1,24 @@ + configure.ac | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ad2f1e6..4f9d7be 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -8,6 +8,7 @@ AC_PROG_CXX + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} ++user_CXXFLAGS=${CXXFLAGS} + generic_CFLAGS="-Wall" + ext_CFLAGS="" + case "${host_cpu}-${host_os}" in +@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread, [ --enable-shortreads use shortread mode], + AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], + [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}" +-CXXFLAGS=$CFLAGS ++CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}" + + AC_STDC_HEADERS + AC_CHECK_HEADER(zlib.h) diff --git a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch new file mode 100644 index 000000000000..4b97da89be48 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch @@ -0,0 +1,34 @@ + stdhash.hh | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..16cd1a3 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -412,7 +412,7 @@ public: + inline bool insert(const keytype_t &key) { + __lh3_hash_base_class<keytype_t>::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); + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } + else ++(this->n_size); // then ret == 2 +@@ -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); } +@@ -503,7 +503,7 @@ public: + inline bool insert(const keytype_t &key, valtype_t **q) { + 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); + *q = vals + i; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch new file mode 100644 index 000000000000..3bcbc2b5fd51 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch @@ -0,0 +1,19 @@ +Do not hardcode -m64 into the build system + +--- a/configure.ac ++++ b/configure.ac +@@ -21,12 +21,12 @@ + [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"], + [ext_CFLAGS="-arch i386 -arch ppc"]);; + 0) CFLAGS="-m64" +- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"], []);; ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""], []);; + esac;; + *) + AC_MSG_CHECKING([if gcc accepts -m64]) + CFLAGS="-m64" +- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])], ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""; AC_MSG_RESULT([yes])], + [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);; + esac + AC_ARG_ENABLE(experimental, [ --enable-experimental enable experimental features], diff --git a/sci-biology/maq/maq-0.7.1-r2.ebuild b/sci-biology/maq/maq-0.7.1-r2.ebuild new file mode 100644 index 000000000000..14b0284b7f58 --- /dev/null +++ b/sci-biology/maq/maq-0.7.1-r2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.bz2 + mirror://sourceforge/${PN}/calib-36.dat.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-bfr-overfl.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-remove-64bit-flag.patch +) + +src_prepare() { + default + eautoreconf +} + +src_install() { + default + + insinto /usr/share/${PN} + doins "${WORKDIR}"/*.dat + + doman maq.1 + dodoc ${PN}.pdf +} diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml new file mode 100644 index 000000000000..0b39d2a8530d --- /dev/null +++ b/sci-biology/maq/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">maq</remote-id> + </upstream> +</pkgmetadata> |