- Update to 35.3.5

- Switch to .tar.gz distfile so that we don't define our do-extract
- While I'm here, using substitution for version numbers in pkg-plist
  for easier upgrade

PR:		ports/121690
Submitted by:	Wen heping <wenheping at gmail.com>
Approved by:	maintainer timeout (2 weeks)

3 files changed, 49 insertions, 53 deletions

diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile
index a02bbc17f9aa..489e08950a80 100644
--- a/biology/fasta3/Makefile
+++ b/biology/fasta3/Makefile
@@ -7,17 +7,16 @@
 #
 
 PORTNAME=	fasta3
-PORTVERSION=	34.26.2
+PORTVERSION=	35.3.5
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.virginia.edu/pub/fasta/
+MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/
 DISTNAME=	fasta-${PORTVERSION}
-EXTRACT_SUFX=	.shar.Z
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of programs for searching DNA and protein databases
 
 NO_CDROM=	May not be sold or incorporated into a commercial product
-WRKSRC=		${WRKDIR}/${PORTNAME}
+WRKSRC=		${WRKDIR}/${DISTNAME}
 SUB_FILES=	pkg-message
 MAKEFILE=	Makefile.freebsd
 
@@ -36,13 +35,7 @@ MAN1=		fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
 MLINKS=		fasta3.1 tfasta3.1 fasta3.1 fastx3.1  fasta3.1 tfastx3.1  \
 		fasta3.1 fasty3.1  fasta3.1 tfasty3.1 fasta3.1 ssearch3.1 \
 		fastf3.1 tfastf3.1 fasts3.1 tfasts3.1
-
-do-extract:
-	@ ${RM} -rf ${WRKDIR}
-	@ ${MKDIR} ${WRKSRC}
-	@ for file in ${EXTRACT_ONLY}; do \
-	  cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \
-	done
+PLIST_SUB=	VER=${PORTVERSION:R:R}
 
 post-install:
 	${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
diff --git a/biology/fasta3/distinfo b/biology/fasta3/distinfo
index 9d8e0f764bab..a491baf9ee90 100644
--- a/biology/fasta3/distinfo
+++ b/biology/fasta3/distinfo
@@ -1,3 +1,3 @@
-MD5 (fasta-34.26.2.shar.Z) = 5fec360037baa1a0ab8cc4b11f3259a4
-SHA256 (fasta-34.26.2.shar.Z) = cd6494cb508892e9121b7a42d18d629b7cb3d431c04d47f6b31364f40f1094ae
-SIZE (fasta-34.26.2.shar.Z) = 853267
+MD5 (fasta-35.3.5.tar.gz) = d93ebf3fadf5225c10447fa428b92ff1
+SHA256 (fasta-35.3.5.tar.gz) = 02af2d016029a5c8d5aec32c498286643ef4bbfacb84b5ef22af77562f00589d
+SIZE (fasta-35.3.5.tar.gz) = 614736
diff --git a/biology/fasta3/pkg-plist b/biology/fasta3/pkg-plist
index b518e67cce40..4c400aec1c94 100644
--- a/biology/fasta3/pkg-plist
+++ b/biology/fasta3/pkg-plist
@@ -1,32 +1,33 @@
-bin/fasta34
-bin/prss34_t
-bin/tfastf34_t
-bin/fastf34_t
-bin/fastm34_t
-bin/tfasts34_t
-bin/tfasty34_t
-bin/fasty34_t
-bin/tfastx34_t
-bin/fastx34_t
-bin/tfasta34_t
-bin/fasts34_t
-bin/fasta34_t
-bin/ssearch34_t
-bin/tfastf34
-bin/fastf34
-bin/prfx34
-bin/prss34
-bin/tfastm34
-bin/fastm34
-bin/tfasts34
-bin/tfasty34
-bin/fasty34
-bin/tfastx34
-bin/fastx34
-bin/fasts34
-bin/tfasta34
-bin/ssearch34
-bin/prfx34_t
+bin/fasta%%VER%%
+bin/fasta%%VER%%_t
+bin/fastf%%VER%%
+bin/fastf%%VER%%_t
+bin/fastm%%VER%%
+bin/fastm%%VER%%_t
+bin/fasts%%VER%%
+bin/fasts%%VER%%_t
+bin/fastx%%VER%%
+bin/fastx%%VER%%_t
+bin/fasty%%VER%%
+bin/fasty%%VER%%_t
+bin/ggsearch%%VER%%
+bin/ggsearch%%VER%%_t
+bin/glsearch%%VER%%
+bin/glsearch%%VER%%_t
+bin/lalign%%VER%%
+bin/lav2ps
+bin/lav2svg
+bin/ssearch%%VER%%
+bin/ssearch%%VER%%_t
+bin/tfastf%%VER%%
+bin/tfastf%%VER%%_t
+bin/tfastm%%VER%%
+bin/tfasts%%VER%%
+bin/tfasts%%VER%%_t
+bin/tfastx%%VER%%
+bin/tfastx%%VER%%_t
+bin/tfasty%%VER%%
+bin/tfasty%%VER%%_t
 etc/fastlibs.sample
 %%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
@@ -47,18 +48,28 @@ etc/fastlibs.sample
 %%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
 %%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
 %%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
+%%PORTDOCS%%%%DOCSDIR%%/readme.v35
 %%PORTDOCS%%%%DOCSDIR%%/readme.w32
 %%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
+%%EXAMPLESDIR%%/bovgh.seq
+%%EXAMPLESDIR%%/bovprl.seq
 %%EXAMPLESDIR%%/egmsmg.aa
+%%EXAMPLESDIR%%/gst.seq
+%%EXAMPLESDIR%%/gstt1_drome.aa
 %%EXAMPLESDIR%%/gtm1_human.aa
 %%EXAMPLESDIR%%/gtt1_drome.aa
 %%EXAMPLESDIR%%/h10_human.aa
 %%EXAMPLESDIR%%/hahu.aa
+%%EXAMPLESDIR%%/hsgstm1b.seq
+%%EXAMPLESDIR%%/humgstd.seq
 %%EXAMPLESDIR%%/lcbo.aa
 %%EXAMPLESDIR%%/m1r.aa
 %%EXAMPLESDIR%%/m2.aa
 %%EXAMPLESDIR%%/mchu.aa
 %%EXAMPLESDIR%%/mgstm1.aa
+%%EXAMPLESDIR%%/mgstm1.lc
+%%EXAMPLESDIR%%/mgstm1.seq
+%%EXAMPLESDIR%%/mgtt2_x.seq
 %%EXAMPLESDIR%%/ms1.aa
 %%EXAMPLESDIR%%/musplfm.aa
 %%EXAMPLESDIR%%/mwkw.aa
@@ -75,18 +86,10 @@ etc/fastlibs.sample
 %%EXAMPLESDIR%%/prio_atepa.aa
 %%EXAMPLESDIR%%/qrhuld.aa
 %%EXAMPLESDIR%%/titin_hum.aa
+%%EXAMPLESDIR%%/titin_hum.seq
 %%EXAMPLESDIR%%/xurt8c.aa
-%%EXAMPLESDIR%%/xurtg.aa
-%%EXAMPLESDIR%%/mgstm1.lc
 %%EXAMPLESDIR%%/xurt8c.lc
-%%EXAMPLESDIR%%/bovgh.seq
-%%EXAMPLESDIR%%/bovprl.seq
-%%EXAMPLESDIR%%/gst.seq
-%%EXAMPLESDIR%%/hsgstm1b.seq
-%%EXAMPLESDIR%%/humgstd.seq
-%%EXAMPLESDIR%%/mgstm1.seq
-%%EXAMPLESDIR%%/mgtt2_x.seq
-%%EXAMPLESDIR%%/titin_hum.seq
+%%EXAMPLESDIR%%/xurtg.aa
 %%DATADIR%%/blosum45.mat
 %%DATADIR%%/blosum50.mat
 %%DATADIR%%/blosum62.mat