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biology/hmmer: update to 3.2.1

Browse source 
PR:		229693
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer)
This commit is contained in:
Steve Wills 2018-07-11 15:15:03 +00:00
parent 649969e00d
commit 40ce9dc0d0
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=474455
4 changed files with 23 additions and 46 deletions
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33
biology/hmmer/Makefile
View file

@ -2,30 +2,37 @@
# $FreeBSD$
PORTNAME= hmmer
PORTVERSION= 3.1b2
PORTVERSION= 3.2.1
CATEGORIES= biology
MASTER_SITES= http://eddylab.org/software/hmmer3/${PORTVERSION}/
MASTER_SITES= http://eddylab.org/software/hmmer/
MAINTAINER= mzaki@niid.go.jp
COMMENT= Profile hidden Markov models for biological sequence analysis
LICENSE= GPLv3
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE
USES= gmake
ONLY_FOR_ARCHS= amd64 i386 ia64 powerpc powerpc64
ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions
USES= gmake perl5 shebangfix
GNU_CONFIGURE= yes
MAKE_ARGS= V=1
OPTIONS_DEFINE= DOCS EXAMPLES TEST
TEST_TEST_TARGET= check
TEST_USES= shebangfix perl5
TEST_VARS= shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
TEST_TARGET= check
USE_PERL5= test
SHEBANG_GLOB= *.pl
SHEBANG_FILES= easel/devkit/*
DOCFILES= COPYRIGHT Userguide.pdf
EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \
Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \
globins4.hmm globins4.out globins4.sto globins45.fa \
minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
OPTIONS_DEFINE= DOCS EXAMPLES TEST
DOCFILES= Userguide.pdf
EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
globins4.hmm globins4.sto globins45.fa
TEST_VARS= use_perl5=build
post-build-TEST-on: do-test

6
biology/hmmer/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1510218548
SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536
SIZE (hmmer-3.1b2.tar.gz) = 5965253
TIMESTAMP = 1531293655
SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c
SIZE (hmmer-3.2.1.tar.gz) = 7670274

10
biology/hmmer/files/patch-configure
View file

@ -1,10 +0,0 @@
--- configure.orig 2015-02-26 12:45:55 UTC
+++ configure
@@ -3912,6 +3912,7 @@ fi
if test "$impl_choice" = "none"; then
case $host in
ia64-*-*) impl_choice=sse;;
+ amd64-*-*) impl_choice=sse;;
i?86-*-*) impl_choice=sse;;
x86*-*-*) impl_choice=sse;;
powerpc*-*-*) impl_choice=vmx;;

20
biology/hmmer/pkg-plist
View file

@ -1,10 +1,8 @@
bin/alimask
bin/hmmalign
bin/hmmbuild
bin/hmmc2
bin/hmmconvert
bin/hmmemit
bin/hmmerfm-exactmatch
bin/hmmfetch
bin/hmmlogo
bin/hmmpgmd
@ -18,15 +16,6 @@ bin/makehmmerdb
bin/nhmmer
bin/nhmmscan
bin/phmmer
include/cachedb.h
include/hmmer.h
include/impl_sse.h
include/p7_config.h
include/p7_gbands.h
include/p7_gmxb.h
include/p7_gmxchk.h
include/p7_hmmcache.h
lib/libhmmer.a
man/man1/alimask.1.gz
man/man1/hmmalign.1.gz
man/man1/hmmbuild.1.gz
@ -46,25 +35,16 @@ man/man1/makehmmerdb.1.gz
man/man1/nhmmer.1.gz
man/man1/nhmmscan.1.gz
man/man1/phmmer.1.gz
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p