summaryrefslogtreecommitdiff
path: root/biology
diff options
context:
space:
mode:
authoragc <agc@pkgsrc.org>2004-01-20 12:07:06 +0000
committeragc <agc@pkgsrc.org>2004-01-20 12:07:06 +0000
commitdc52048e014fdad9bb69ef9db159835a61c8dd4d (patch)
tree28fc431efa48feea798736cefee933a6529a5c91 /biology
parent46eceba7253d40f1643bc06f73cc7fd2148c2e8e (diff)
downloadpkgsrc-dc52048e014fdad9bb69ef9db159835a61c8dd4d.tar.gz
Move WRKSRC definition away from the first paragraph in a Makefile.
Diffstat (limited to 'biology')
-rw-r--r--biology/clustalw/Makefile4
-rw-r--r--biology/coalesce/Makefile4
-rw-r--r--biology/fastDNAml/Makefile5
-rw-r--r--biology/fluctuate/Makefile4
-rw-r--r--biology/genesplicer/Makefile4
-rw-r--r--biology/glimmer/Makefile4
-rw-r--r--biology/hmmer/Makefile4
-rw-r--r--biology/mummer/Makefile4
-rw-r--r--biology/pdbalign/Makefile5
-rw-r--r--biology/phylip/Makefile5
-rw-r--r--biology/profit/Makefile4
-rw-r--r--biology/rasmol/Makefile4
-rw-r--r--biology/sewer/Makefile4
-rw-r--r--biology/stride/Makefile4
-rw-r--r--biology/xylem/Makefile4
15 files changed, 33 insertions, 30 deletions
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index e8edcb33d37..f225d91d010 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2001/02/16 13:41:28 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2004/01/20 12:08:40 agc Exp $
DISTNAME= clustalw1.8.UNIX
PKGNAME= clustalw-1.8
-WRKSRC= ${WRKDIR}/clustalw1.8
CATEGORIES= biology
MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \
ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
@@ -13,6 +12,7 @@ COMMENT= General purpose multiple alignment program for DNA or proteins
MAKEFILE= makefile
ALL_TARGET= clustalw
+WRKSRC= ${WRKDIR}/clustalw1.8
post-patch:
@${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \
diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile
index 1c46cde2dd1..e8835d1618a 100644
--- a/biology/coalesce/Makefile
+++ b/biology/coalesce/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= coalesce1.5b
PKGNAME= coalesce-1.5.0.2
-WRKSRC= ${WRKDIR}/coalesce1.5beta
CATEGORIES= biology
MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/coalesce/
@@ -11,6 +10,7 @@ MAINTAINER= brook@nmsu.edu
HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/coalesce.html
COMMENT= Estimates effective population size and mutation rate
+WRKSRC= ${WRKDIR}/coalesce1.5beta
USE_BUILDLINK2= YES
ALL_TARGET= coalesce
diff --git a/biology/fastDNAml/Makefile b/biology/fastDNAml/Makefile
index 90ff1fabc62..8503dc2dc1e 100644
--- a/biology/fastDNAml/Makefile
+++ b/biology/fastDNAml/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.3 2001/02/16 13:41:29 wiz Exp $
+# $NetBSD: Makefile,v 1.4 2004/01/20 12:08:40 agc Exp $
DISTNAME= fastDNAml_1.2.1
PKGNAME= fastDNAml-1.2.1
-WRKSRC= ${WRKDIR}/${DISTNAME}
CATEGORIES= biology
MASTER_SITES= http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
@@ -14,6 +13,8 @@ RESTRICTED= "No commercial distribution without a royalty agreement with the aut
NO_SRC_ON_CDROM= ${RESTRICTED}
NO_BIN_ON_CDROM= ${RESTRICTED}
+WRKSRC= ${WRKDIR}/${DISTNAME}
+
do-build :
@ cd ${WRKSRC}/source && ${MAKE} LDFLAGS=-lm fastDNAml
diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile
index 99c8a1cd405..5fcdfbfc7b4 100644
--- a/biology/fluctuate/Makefile
+++ b/biology/fluctuate/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= fluctuate1.4.src.doc
PKGNAME= fluctuate-1.4
-WRKSRC= ${WRKDIR}/fluctuate1.4
CATEGORIES= biology
MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/fluctuate/
@@ -11,6 +10,7 @@ MAINTAINER= brook@nmsu.edu
HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/fluctuate.html
COMMENT= Estimation of population growth rate
+WRKSRC= ${WRKDIR}/fluctuate1.4
USE_BUILDLINK2= YES
ALL_TARGET= fluctuate
diff --git a/biology/genesplicer/Makefile b/biology/genesplicer/Makefile
index 04175e10d3e..cb98cb2f814 100644
--- a/biology/genesplicer/Makefile
+++ b/biology/genesplicer/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:57:08 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= GeneSplicer
PKGNAME= genesplicer-20030403
-WRKSRC= ${WRKDIR}/GeneSplicer/sources
CATEGORIES= biology
MASTER_SITES= ftp://ftp.tigr.org/pub/software/GeneSplicer/
@@ -16,6 +15,7 @@ EXAMPLES= arabidopsis drosophila malaria pyoelii human rice \
training_data_sets/Arabidopsis \
training_data_sets/Human
MAKEFILE= makefile
+WRKSRC= ${WRKDIR}/GeneSplicer/sources
USE_BUILDLINK2= yes
do-install:
diff --git a/biology/glimmer/Makefile b/biology/glimmer/Makefile
index 4483ae0da18..d53ffdfecc9 100644
--- a/biology/glimmer/Makefile
+++ b/biology/glimmer/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.2 2003/10/07 18:20:15 jschauma Exp $
+# $NetBSD: Makefile,v 1.3 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= glimmer212
PKGNAME= glimmer-2.12
-WRKSRC= ${WRKDIR}/glimmer2.12
CATEGORIES= biology
MASTER_SITES= ftp://ftp.tigr.org/pub/software/Glimmer/
@@ -12,6 +11,7 @@ HOMEPAGE= ftp://ftp.tigr.org/pub/software/Glimmer/
COMMENT= System for finding genes in microbial DNA
USE_BUILDLINK2= yes
+WRKSRC= ${WRKDIR}/glimmer2.12
do-install:
.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists \
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index f13cb9ab0d8..f626eb4de5e 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2003/09/26 05:21:04 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= hmmer-2.3.1
-WRKSRC= ${WRKDIR}/hmmer-2.3.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.1/
@@ -10,6 +9,7 @@ MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://hmmer.wustl.edu/
COMMENT= Implementation of profile HMM software for protein sequence analysis
+WRKSRC= ${WRKDIR}/hmmer-2.3.1
USE_BUILDLINK2= yes
GNU_CONFIGURE= yes
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index af83ff789c7..9655eb6a6f5 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 22:24:56 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= MUMmer3.04
PKGNAME= mummer-3.04
-WRKSRC= ${WRKDIR}/${DISTNAME}
CATEGORIES= biology
MASTER_SITES= ftp://ftp.tigr.org/pub/software/MUMmer/
@@ -11,6 +10,7 @@ MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://www.tigr.org/software/mummer/
COMMENT= System for aligning whole genome sequences
+WRKSRC= ${WRKDIR}/${DISTNAME}
USE_BUILDLINK2= YES
USE_GNU_TOOLS+= make
diff --git a/biology/pdbalign/Makefile b/biology/pdbalign/Makefile
index 0cba27571cd..e91b270d53c 100644
--- a/biology/pdbalign/Makefile
+++ b/biology/pdbalign/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:15:28 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= pdbalign
PKGNAME= pdbalign-20030812
-WRKSRC= ${WRKDIR}
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/pdbalign/
@@ -11,6 +10,8 @@ MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= #empty
COMMENT= Prediction of Protein Secondary Structure and Active Sites
+WRKSRC= ${WRKDIR}
+
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/pdbalign ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/distalign ${PREFIX}/bin
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index 1418f923908..912ba1e7415 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.5 2003/03/29 12:40:14 jmmv Exp $
+# $NetBSD: Makefile,v 1.6 2004/01/20 12:08:40 agc Exp $
DISTNAME= phylip
PKGNAME= phylip-3.573c
-WRKSRC= ${WRKDIR}
CATEGORIES= biology
MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ \
ftp://ftp.bioss.sari.ac.uk/pub/phylogeny/phylip/
@@ -16,6 +15,8 @@ RESTRICTED= "No commercial distribution without a royalty agreement with the au
NO_SRC_ON_CDROM= ${RESTRICTED}
NO_BIN_ON_CDROM= ${RESTRICTED}
+WRKSRC= ${WRKDIR}
+
do-install:
${INSTALL_DATA_DIR} ${PREFIX}/share/doc/phylip
.for DOC in main.doc \
diff --git a/biology/profit/Makefile b/biology/profit/Makefile
index 08ac873321a..7e76d0f7140 100644
--- a/biology/profit/Makefile
+++ b/biology/profit/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 23:18:26 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= profit
PKGNAME= profit-2.2
-WRKSRC= ${WRKDIR}/ProFitV2.2/src
CATEGORIES= biology
MASTER_SITES= http://www.rubic.rdg.ac.uk/~andrew/bioinf.org/software/profit/235216/
@@ -13,6 +12,7 @@ COMMENT= Performs least squares fits of two protein structures
ALL_TARGET= ${DISTNAME}
USE_BUILDLINK2= YES
+WRKSRC= ${WRKDIR}/ProFitV2.2/src
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/profit ${PREFIX}/bin
diff --git a/biology/rasmol/Makefile b/biology/rasmol/Makefile
index b888c5bc8d7..64f05f8e095 100644
--- a/biology/rasmol/Makefile
+++ b/biology/rasmol/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.14 2003/09/17 19:40:00 grant Exp $
+# $NetBSD: Makefile,v 1.15 2004/01/20 12:08:40 agc Exp $
DISTNAME= RasMol_2.7.1
PKGNAME= rasmol-2.7.1
PKGREVISION= 1
-WRKSRC= ${WRKDIR}/${DISTNAME}/src
CATEGORIES= biology
MASTER_SITES= ftp://ftp.bernstein-plus-sons.com/software/
@@ -11,6 +10,7 @@ MAINTAINER= tech-pkg@NetBSD.org
HOMEPAGE= http://www.bernstein-plus-sons.com/software/rasmol/
COMMENT= Molecular Graphics Visualisation Tool
+WRKSRC= ${WRKDIR}/${DISTNAME}/src
USE_BUILDLINK2= YES
USE_IMAKE= YES
diff --git a/biology/sewer/Makefile b/biology/sewer/Makefile
index fc3b97736bc..e5a05c1dbcc 100644
--- a/biology/sewer/Makefile
+++ b/biology/sewer/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 23:36:34 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
DISTNAME= sewer
PKGNAME= sewer-2.6
-WRKSRC= ${WRKDIR}
CATEGORIES= biology
MASTER_SITES= ftp://iubio.bio.indiana.edu/molbio/analyze/
EXTRACT_SUFX= .zip
@@ -14,6 +13,7 @@ COMMENT= SEquence Analysis using WEb Resources
NO_CONFIGURE= YES
NO_BUILD= YES
+WRKSRC= ${WRKDIR}
USE_BUILDLINK2= YES
pre-install:
diff --git a/biology/stride/Makefile b/biology/stride/Makefile
index 9a9b15275b2..946fb093705 100644
--- a/biology/stride/Makefile
+++ b/biology/stride/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 23:46:55 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= stride
PKGNAME= stride-20030804
-WRKSRC= ${WRKDIR}
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/
@@ -11,6 +10,7 @@ MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/stride/stride_info.html
COMMENT= Protein secondary structure assignment from atomic coordinates
+WRKSRC= ${WRKDIR}
USE_BUILDLINK2= YES
do-install:
diff --git a/biology/xylem/Makefile b/biology/xylem/Makefile
index 81560ebe373..c3d096ffa86 100644
--- a/biology/xylem/Makefile
+++ b/biology/xylem/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/10/04 19:13:28 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2004/01/20 12:08:40 agc Exp $
#
DISTNAME= xylem.1.8.7
PKGNAME= xylem-1.8.7
-WRKSRC= ${WRKDIR}/xylem/src.c
CATEGORIES= biology
MASTER_SITES= ftp://ftp.cc.umanitoba.ca/psgendb/
EXTRACT_SUFX= .tar.Z
@@ -12,6 +11,7 @@ MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://home.cc.umanitoba.ca/~psgendb/XYLEM.html
COMMENT= Tools for manipulation of genetic databases
+WRKSRC= ${WRKDIR}/xylem/src.c
USE_BUILDLINK2= YES
do-configure:
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-16 12:16:44 +0000