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authorV3n3RiX <venerix@redcorelinux.org>2017-10-09 18:53:29 +0100
committerV3n3RiX <venerix@redcorelinux.org>2017-10-09 18:53:29 +0100
commit4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch)
treeba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/maq
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/maq')
-rw-r--r--sci-biology/maq/Manifest10
-rw-r--r--sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch16
-rw-r--r--sci-biology/maq/files/maq-0.7.1-flags.patch24
-rw-r--r--sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch34
-rw-r--r--sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch19
-rw-r--r--sci-biology/maq/maq-0.7.1-r2.ebuild42
-rw-r--r--sci-biology/maq/metadata.xml11
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>