diff options
Diffstat (limited to 'biology/glimmer')
| -rw-r--r-- | biology/glimmer/Makefile | 12 | ||||
| -rw-r--r-- | biology/glimmer/PLIST | 4 | ||||
| -rw-r--r-- | biology/glimmer/distinfo | 7 | ||||
| -rw-r--r-- | biology/glimmer/patches/patch-ab | 25 |
4 files changed, 38 insertions, 10 deletions
diff --git a/biology/glimmer/Makefile b/biology/glimmer/Makefile index 5b9c3dbcf3f..4483ae0da18 100644 --- a/biology/glimmer/Makefile +++ b/biology/glimmer/Makefile @@ -1,9 +1,9 @@ -# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $ +# $NetBSD: Makefile,v 1.2 2003/10/07 18:20:15 jschauma Exp $ # -DISTNAME= glimmer21 -PKGNAME= glimmer-2.1 -WRKSRC= ${WRKDIR}/glimmer2.10 +DISTNAME= glimmer212 +PKGNAME= glimmer-2.12 +WRKSRC= ${WRKDIR}/glimmer2.12 CATEGORIES= biology MASTER_SITES= ftp://ftp.tigr.org/pub/software/Glimmer/ @@ -14,10 +14,12 @@ COMMENT= System for finding genes in microbial DNA USE_BUILDLINK2= yes do-install: -.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists extract \ +.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists \ generate get-len get-putative glimmer2 long-orfs ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin .endfor + # ``extract'' is also in the csound package, so rename to avoid conflict + ${INSTALL_PROGRAM} ${WRKSRC}/extract ${PREFIX}/bin/glextract ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/glimmer ${CP} ${WRKSRC}/README ${WRKSRC}/run-glimmer2.readme .for DOC in run-glimmer2.readme build-icm.readme extract.readme glimmer2.readme long-orfs.readme diff --git a/biology/glimmer/PLIST b/biology/glimmer/PLIST index f4fde8226a4..98d3a6f5b7f 100644 --- a/biology/glimmer/PLIST +++ b/biology/glimmer/PLIST @@ -1,11 +1,11 @@ -@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $ +@comment $NetBSD: PLIST,v 1.2 2003/10/07 18:20:15 jschauma Exp $ bin/adjust bin/anomaly bin/build-icm bin/check bin/codon-usage bin/compare-lists -bin/extract +bin/glextract bin/generate bin/get-len bin/get-putative diff --git a/biology/glimmer/distinfo b/biology/glimmer/distinfo index 139ebb80861..cbb0bc6924c 100644 --- a/biology/glimmer/distinfo +++ b/biology/glimmer/distinfo @@ -1,5 +1,6 @@ -$NetBSD: distinfo,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $ +$NetBSD: distinfo,v 1.2 2003/10/07 18:20:15 jschauma Exp $ -SHA1 (glimmer21.tar.gz) = 676bf2150389b4eb817ef2db7c646a332151eaf7 -Size (glimmer21.tar.gz) = 79091 bytes +SHA1 (glimmer212.tar.gz) = f2291c3b9024c56b884d6dcab032cb36f54074f6 +Size (glimmer212.tar.gz) = 79431 bytes SHA1 (patch-aa) = ceb45f887c32e91bd96b9d2c8dae39c9cc6fc658 +SHA1 (patch-ab) = e2afaa9ff8e0d4a2647a77bbf7e1ba4012d53061 diff --git a/biology/glimmer/patches/patch-ab b/biology/glimmer/patches/patch-ab new file mode 100644 index 00000000000..0ea7f46e901 --- /dev/null +++ b/biology/glimmer/patches/patch-ab @@ -0,0 +1,25 @@ +$NetBSD: patch-ab,v 1.1 2003/10/07 18:20:16 jschauma Exp $ + +--- delcher.h.orig 2003-10-07 14:07:00.000000000 -0400 ++++ delcher.h 2003-10-07 14:07:35.000000000 -0400 +@@ -18,9 +18,9 @@ + + #include <stdio.h> + #include <stdlib.h> +-#include <iostream.h> +-#include <iomanip.h> +-#include <fstream.h> ++#include <iostream> ++#include <iomanip> ++#include <fstream> + #include <math.h> + #include <string.h> + #include <ctype.h> +@@ -31,6 +31,7 @@ + #include <errno.h> + #include <unistd.h> + ++using namespace std; + + #define TRUE 1 + #define FALSE 0 |