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authorJohann Visagie <wjv@FreeBSD.org>2001-08-22 13:18:10 +0000
committerJohann Visagie <wjv@FreeBSD.org>2001-08-22 13:18:10 +0000
commit4e8aeac4406cdf01cd8373c1c45da1c2f3e67ab4 (patch)
tree9cb58a7cacd54f28a1b9b65ef7164e13633a165e /biology
parent8aff3a669c1f00e3f5931b88b2e49f7cd8257521 (diff)
downloadports-4e8aeac4406cdf01cd8373c1c45da1c2f3e67ab4.tar.gz
ports-4e8aeac4406cdf01cd8373c1c45da1c2f3e67ab4.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/hmmer/Makefile25
-rw-r--r--biology/hmmer/distinfo2
-rw-r--r--biology/hmmer/files/patch-Makefile.in19
-rw-r--r--biology/hmmer/pkg-plist211
4 files changed, 34 insertions, 223 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 4259aba6335c..f3c5ead9cd28 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -6,28 +6,29 @@
#
PORTNAME= hmmer
-PORTVERSION= 2.1.1
+PORTVERSION= 2.2.g
CATEGORIES= biology
-MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
-EXTRACT_SUFX= .tar.Z
+MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/
+DISTNAME= ${PORTNAME}-${VERSIONSTRING}
MAINTAINER= wjv@FreeBSD.org
GNU_CONFIGURE= yes
USE_PERL5= yes
+VERSIONSTRING= ${PORTVERSION:C|\.([^.]*)$|\1|}
-MAN1= hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
- hmmer.1 hmmpfam.1 hmmsearch.1 hmmfetch.1 hmmindex.1 alistat.1 \
- getseq.1 seqstat.1 sreformat.1
-
-HMMER_DOCDIR= ${PREFIX}/share/doc/${PORTNAME}
+DOCFILES= 00README COPYRIGHT NOTES Userguide.pdf
+MAN1= afetch.1 alistat.1 hmmalign.1 hmmbuild.1 hmmcalibrate.1 \
+ hmmconvert.1 hmmemit.1 hmmer.1 hmmfetch.1 hmmindex.1 \
+ hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \
+ sreformat.1
post-install:
.if !defined(NOPORTDOCS)
- @ ${MKDIR} ${HMMER_DOCDIR}
- @ ${INSTALL_DATA} ${WRKSRC}/Userguide/Userguide.pdf ${HMMER_DOCDIR}
- @ ${INSTALL_DATA} ${WRKSRC}/Userguide/Userguide.ps ${HMMER_DOCDIR}
- @ ${TAR} xzfC ${WRKSRC}/Userguide/hmmer-html.tar.Z ${HMMER_DOCDIR}
+ @ ${MKDIR} ${DOCSDIR}
+.for docfile in ${DOCFILES}
+ @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
+.endfor
.endif
.if !defined(BATCH)
@ ${CAT} ${PKGMESSAGE}
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 6dbe81b02fd8..99b8a3003bed 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1 +1 @@
-MD5 (hmmer-2.1.1.tar.Z) = 0f98910a3507b4d52fbe82adc6fa89b5
+MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c
diff --git a/biology/hmmer/files/patch-Makefile.in b/biology/hmmer/files/patch-Makefile.in
index deade1eaceeb..40e1561681b4 100644
--- a/biology/hmmer/files/patch-Makefile.in
+++ b/biology/hmmer/files/patch-Makefile.in
@@ -1,5 +1,5 @@
---- Makefile.in.orig Thu Dec 10 01:11:07 1998
-+++ Makefile.in Wed Jul 4 15:41:09 2001
+--- Makefile.in.orig Mon Aug 6 01:55:36 2001
++++ Makefile.in Wed Aug 22 14:52:30 2001
@@ -34,7 +34,7 @@
# how to install the man pages;
# cp is generally fine, unless you preformat your pages.
@@ -9,12 +9,19 @@
MANSUFFIX = 1
# your compiler and compiler flags
-@@ -142,7 +142,7 @@
- # installs man pages in MANDIR/man1/ (if MANSUFFIX is 1)
+@@ -144,12 +144,12 @@
+ # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
install:
for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
- cp binaries/$$file $(BINDIR)/;\
+ $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\
done
- for file in hmmer $(PROGS) $(SQUIDPROGS); do\
- $(INSTMAN) Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+- for file in hmmer $(PROGS) $(SQUIDPROGS); do\
++ for file in hmmer $(PROGS); do\
+ $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ done
+- for file in $(SQUIDPROGS); do\
++ for file in afetch alistat seqstat sfetch shuffle sreformat; do\
+ $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ done
+
diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
index 86b1ac45a9be..b633cb15c522 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -1,5 +1,5 @@
+bin/afetch
bin/alistat
-bin/getseq
bin/hmmalign
bin/hmmbuild
bin/hmmcalibrate
@@ -10,209 +10,12 @@ bin/hmmindex
bin/hmmpfam
bin/hmmsearch
bin/seqstat
+bin/sfetch
+bin/shuffle
+bin/sindex
bin/sreformat
+%%PORTDOCS%%share/doc/hmmer/00README
+%%PORTDOCS%%share/doc/hmmer/COPYRIGHT
+%%PORTDOCS%%share/doc/hmmer/NOTES
%%PORTDOCS%%share/doc/hmmer/Userguide.pdf
-%%PORTDOCS%%share/doc/hmmer/Userguide.ps
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/IMG_PARAMS.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/ID_MAP.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/ORIG_MAP.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/aux_preamble
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/dependent
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/depends_on
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/env_style
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/envstyles.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/expanded.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/global.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/main-expanded
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_command
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_environment
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_theorem
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/part001
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/preamble
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/prelatex
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/styleID
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/styleIDs.db
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/styles
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/txt_style
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/txtstyles.db
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-%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/verbatim_counter
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-%%PORTDOCS%%share/doc/hmmer/hmmer-html/contents_motif.gif
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/figure.pl
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/footnode.html
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/images.aux
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/images.log
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/images.pl
-%%PORTDOCS%%share/doc/hmmer/hmmer-html/images.tex
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-%%PORTDOCS%%share/doc/hmmer/hmmer-html/img3.gif
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-%%PORTDOCS%%share/doc/hmmer/hmmer-html/img9.gif
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