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authorDavid Seifert <soap@gentoo.org>2020-11-01 19:35:59 +0100
committerDavid Seifert <soap@gentoo.org>2020-11-01 19:35:59 +0100
commite44c9cbdd06cfb672155e0d6747d11e955d90dca (patch)
treee34ef0491768b5d25b48a94313f50d16e03668ac /sci-biology
parentsci-biology/paml: Remove old 4.4c-r1 (diff)
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sci-biology/gmap: Version bump to 2020.10.27
Bug: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/gmap/Manifest1
-rw-r--r--sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch22
-rw-r--r--sci-biology/gmap/gmap-2020.10.27.ebuild17
3 files changed, 40 insertions, 0 deletions
diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest
index a43611ecf589..226efe61e422 100644
--- a/sci-biology/gmap/Manifest
+++ b/sci-biology/gmap/Manifest
@@ -1 +1,2 @@
DIST gmap-gsnap-2015-12-31.v5.tar.gz 4169874 BLAKE2B bbbf53b72b5b7f97ba0eb05db7daa3d1f8a9330f32b96c2460a904a9f9f22078093f6fa585a12d4275e0943145ee78ef99348de4f19349dfa4e81d5f65572e1c SHA512 d42623c60c298d9d3009893432f3eef8cb764bf7cf26b42e6a95b27a468fffab20c8307597c4c8e1afdd61f35652246568c3162137ce59fc4850aaab1062bb48
+DIST gmap-gsnap-2020-10-27.tar.gz 4480720 BLAKE2B 9f8e8bfab19c079111d42ec466dd145385d35e3fde0a809e46776ed1b62b599664f12618803ea4475b6961a053423a8794d0b77eb0b308bdfa927b5bcaa7d49c SHA512 22e59adf404f5ef524b3cd472fb3124d03c8c55aa7946b9dc3901f5070339dc765f8f1ecc7e394b69a14bf80923f7a9db8d545e45328a346996b3288115a535b
diff --git a/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch
new file mode 100644
index 000000000000..cc225a78c26e
--- /dev/null
+++ b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch
@@ -0,0 +1,22 @@
+--- a/src/dynprog_end.c
++++ b/src/dynprog_end.c
+@@ -109,7 +109,7 @@
+ static Trieoffset_T *trieoffsets_max;
+ static Triecontent_T *triecontents_max;
+
+-bool homopolymerp;
++static bool homopolymerp;
+
+ void
+ Dynprog_end_setup (Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in,
+--- a/src/dynprog_single.c
++++ b/src/dynprog_single.c
+@@ -91,7 +91,7 @@
+
+ #define T Dynprog_T
+
+-bool homopolymerp;
++static bool homopolymerp;
+
+ void
+ Dynprog_single_setup (bool homopolymerp_in) {
diff --git a/sci-biology/gmap/gmap-2020.10.27.ebuild b/sci-biology/gmap/gmap-2020.10.27.ebuild
new file mode 100644
index 000000000000..a90f0f631068
--- /dev/null
+++ b/sci-biology/gmap/gmap-2020.10.27.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MY_PV="$(ver_rs 1- '-')"
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://research-pub.gene.com/gmap/"
+SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/gmap-${MY_PV}"
+PATCHES=( "${FILESDIR}"/${PN}-2020.10.27-fno-common.patch )