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authorMartin Wilke <miwi@FreeBSD.org>2008-05-22 00:49:42 +0000
committerMartin Wilke <miwi@FreeBSD.org>2008-05-22 00:49:42 +0000
commit21d58ada2303ef006025b0daee9bac1ec4190010 (patch)
tree91c83d33cda04401a74c9241e254855a55169074 /biology
parent90132438eb5da4a8fccce91c84189da8489de51b (diff)
downloadports-21d58ada2303ef006025b0daee9bac1ec4190010.tar.gz
ports-21d58ada2303ef006025b0daee9bac1ec4190010.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/tRNAscan-SE/Makefile26
-rw-r--r--biology/tRNAscan-SE/files/patch-aa35
-rw-r--r--biology/tRNAscan-SE/pkg-descr2
-rw-r--r--biology/tRNAscan-SE/pkg-plist44
4 files changed, 46 insertions, 61 deletions
diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile
index 1ffeebff9282..da7e62619150 100644
--- a/biology/tRNAscan-SE/Makefile
+++ b/biology/tRNAscan-SE/Makefile
@@ -7,22 +7,42 @@
PORTNAME= tRNAscan-SE
PORTVERSION= 1.23
+PORTREVISION= 1
CATEGORIES= biology
-MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/software/
+MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/
EXTRACT_SUFX= .tar.Z
MAINTAINER= ports@FreeBSD.org
COMMENT= An improved tool for transfer RNA detection
+USE_PERL5= yes
+MAKE_ARGS= BINDIR="${PREFIX}/bin" \
+ LIBDIR="${DATADIR}" \
+ CC="${CC}" \
+ CFLAGS="${CFLAGS}"
+
MAN1= tRNAscan-SE.1
-USE_PERL5= yes
+post-patch:
+ @${REINPLACE_CMD} -e 's|tRNAscanSE setpaths|tRNAscanSE|g ; \
+ s|if tRNAscan-SE|if ./tRNAscan-SE|g' ${WRKSRC}/Makefile
+
+do-install:
+.for f in covels-SE coves-SE eufindtRNA trnascan-1.4
+ ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
+.endfor
+ ${INSTALL_SCRIPT} ${WRKSRC}/tRNAscan-SE ${PREFIX}/bin
+ ${INSTALL_MAN} ${WRKSRC}/tRNAscan-SE.man ${MANPREFIX}/man/man1/tRNAscan-SE.1
+ @${MKDIR} ${DATADIR}
+.for f in TPCsignal Dsignal *.cm gcode.*
+ ${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}
+.endfor
#
# have to install before testing as path to data files is hardcoded
#
post-install:
- @ cd ${WRKSRC} && $(MAKE) testrun
+ @ cd ${WRKSRC} && $(MAKE) testrun
.if !defined(NOPORTDOCS)
@${MKDIR} ${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/Manual.ps ${DOCSDIR}
diff --git a/biology/tRNAscan-SE/files/patch-aa b/biology/tRNAscan-SE/files/patch-aa
deleted file mode 100644
index 82f9a3b420a0..000000000000
--- a/biology/tRNAscan-SE/files/patch-aa
+++ /dev/null
@@ -1,35 +0,0 @@
---- Makefile.orig Sat Oct 7 00:16:41 2000
-+++ Makefile Thu Dec 20 17:26:37 2001
-@@ -19,10 +19,11 @@
- ## (this could be 'perl5' or otherwise on some systems)
- PERLBIN = perl
-
-+prefix = ${PREFIX}
- ## where you want things installed
--BINDIR = $(HOME)/bin
--LIBDIR = $(HOME)/lib/tRNAscan-SE
--MANDIR = $(HOME)/man
-+BINDIR = $(prefix)/bin
-+LIBDIR = $(prefix)/share/tRNAscan-SE
-+MANDIR = $(prefix)/man
-
- ## NOTE !! If you later manually move the location of
- ## binaries or data files in the BINDIR or LIBDIR directories,
-@@ -106,7 +107,7 @@
-
- MPOBJ = mpviterbi.o mp-dbviterbi.o
-
--all: $(PROGS) tRNAscanSE setpaths
-+all: $(PROGS) tRNAscanSE
-
- covels-SE: $(OBJ) scan_main.o
- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
-@@ -178,7 +179,7 @@
- @echo ""
- @rm -f testrun.out
- @echo "tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa"
-- @if tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \
-+ @if ./tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \
- then echo ""; \
- else echo "tRNAscan-SE did NOT complete properly."; fi
- @if diff testrun.out testrun.ref; \
diff --git a/biology/tRNAscan-SE/pkg-descr b/biology/tRNAscan-SE/pkg-descr
index 008e02d08a16..288f622a4c1c 100644
--- a/biology/tRNAscan-SE/pkg-descr
+++ b/biology/tRNAscan-SE/pkg-descr
@@ -7,4 +7,4 @@ the flow of information between them, performing a limited amount of
post-processing, and outputting the results in one of several
formats.
-WWW: http://www.genetics.wustl.edu/eddy/software/
+WWW: http://selab.janelia.org/software.html
diff --git a/biology/tRNAscan-SE/pkg-plist b/biology/tRNAscan-SE/pkg-plist
index 3ebf814cc5c0..086d2cf6325b 100644
--- a/biology/tRNAscan-SE/pkg-plist
+++ b/biology/tRNAscan-SE/pkg-plist
@@ -1,26 +1,26 @@
-bin/tRNAscan-SE
-bin/eufindtRNA
-bin/coves-SE
bin/covels-SE
+bin/coves-SE
+bin/eufindtRNA
+bin/tRNAscan-SE
bin/trnascan-1.4
-share/tRNAscan-SE/TPCsignal
-share/tRNAscan-SE/gcode.vertmito
-share/tRNAscan-SE/gcode.othmito
-share/tRNAscan-SE/gcode.invmito
-share/tRNAscan-SE/gcode.echdmito
-share/tRNAscan-SE/gcode.cilnuc
-share/tRNAscan-SE/TRNA2ns.cm
-share/tRNAscan-SE/TRNA2.cm
-share/tRNAscan-SE/TRNA2-eukns.cm
-share/tRNAscan-SE/TRNA2-euk.cm
-share/tRNAscan-SE/TRNA2-bactns.cm
-share/tRNAscan-SE/TRNA2-bact.cm
-share/tRNAscan-SE/TRNA2-archns.cm
-share/tRNAscan-SE/TRNA2-arch.cm
-share/tRNAscan-SE/PSELC.cm
-share/tRNAscan-SE/ESELC.cm
-share/tRNAscan-SE/Dsignal
-share/tRNAscan-SE/gcode.ystmito
-@dirrm share/tRNAscan-SE
%%PORTDOCS%%%%DOCSDIR%%/Manual.ps
+%%DATADIR%%/TPCsignal
+%%DATADIR%%/gcode.vertmito
+%%DATADIR%%/gcode.othmito
+%%DATADIR%%/gcode.invmito
+%%DATADIR%%/gcode.echdmito
+%%DATADIR%%/gcode.cilnuc
+%%DATADIR%%/TRNA2ns.cm
+%%DATADIR%%/TRNA2.cm
+%%DATADIR%%/TRNA2-eukns.cm
+%%DATADIR%%/TRNA2-euk.cm
+%%DATADIR%%/TRNA2-bactns.cm
+%%DATADIR%%/TRNA2-bact.cm
+%%DATADIR%%/TRNA2-archns.cm
+%%DATADIR%%/TRNA2-arch.cm
+%%DATADIR%%/PSELC.cm
+%%DATADIR%%/ESELC.cm
+%%DATADIR%%/Dsignal
+%%DATADIR%%/gcode.ystmito
+@dirrm %%DATADIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%