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authorPetar Petrov <ppetrov@paju.oulu.fi>2012-09-11 22:47:57 +0300
committerRobby Workman <rworkman@slackbuilds.org>2012-09-11 23:53:42 -0500
commitdea576fec344061d75fce02c9b07ee7d14596a32 (patch)
tree73ec8570b07375d41184e22e8d0aa389a97e6d08 /academic
parent4be8b0406fe27b22b7fd2725009bf6bcb495f65a (diff)
downloadslackbuilds-dea576fec344061d75fce02c9b07ee7d14596a32.tar.gz
academic/staden: Build fixes for Slackware 14.0
Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/staden/README4
-rwxr-xr-x[-rw-r--r--]academic/staden/staden.SlackBuild12
-rw-r--r--academic/staden/staden.info8
3 files changed, 15 insertions, 9 deletions
diff --git a/academic/staden/README b/academic/staden/README
index 1dcc9f0dca..09f23ced67 100644
--- a/academic/staden/README
+++ b/academic/staden/README
@@ -1,5 +1,5 @@
-The programs part of the Staden package provide a fully developed set
-of DNA sequence assembly, editing, analysis and more.
+The programs part of the Staden package provide an excellent and fully
+developed set of DNA sequence assembly, editing, analysis and more.
Some of its features include:
GAP4 - Performs assembly, contig joining, assembly checking, repeat
diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild
index 707e9007de..17f236fdb6 100644..100755
--- a/academic/staden/staden.SlackBuild
+++ b/academic/staden/staden.SlackBuild
@@ -24,7 +24,7 @@
PRGNAM=staden
VERSION=${VERSION:-2.0.0b9}
-BUILD=${BUILD:-2}
+BUILD=${BUILD:-3}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
@@ -35,8 +35,8 @@ if [ -z "$ARCH" ]; then
esac
fi
-SLKTCL=tcl8.5.9 # Slackware 13.37 sources for TCL
-SLKTK=tk8.5.9 # Slackware 13.37 sources for TK
+SLKTCL=tcl8.5.11 # Slackware 14.0 sources for TCL
+SLKTK=tk8.5.11 # Slackware 14.0 sources for TK
TKLIB=tklib0.5 # Folder name of TKLIB
CWD=$(pwd)
@@ -86,6 +86,7 @@ find $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src \
-exec chmod 644 {} \;
cd $PRGNAM-$VERSION-src
+
# On Slackware64, the components of staden (like GAP4, GAP5, PREGAP4,
# SPIN, TREV) will not run, as they still expect their libraries to be
# in /usr/lib not /usr/lib64. Let's correct the libraries path.
@@ -103,6 +104,11 @@ sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
# Correct the path where staden components look for their manual.
sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config
+# These fixes are from Arch linux AUR
+# http://aur.archlinux.org/packages/st/staden/PKGBUILD
+sed -i 's:-DSVN_VERSION=$(SVNVERS)::' system.mk.in
+sed -i "s/gzFile\ \*gz/gzFile\ gz/" gap5/zfio.h
+
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
diff --git a/academic/staden/staden.info b/academic/staden/staden.info
index 8c80e9c884..b4475719a9 100644
--- a/academic/staden/staden.info
+++ b/academic/staden/staden.info
@@ -3,12 +3,12 @@ VERSION="2.0.0b9"
HOMEPAGE="http://staden.sourceforge.net/"
DOWNLOAD="http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden-2.0.0b9-src.tar.gz \
http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden_doc-2.0.0b9-src.tar.gz \
- http://slackware.osuosl.org/slackware-13.37/source/tcl/tcl/tcl8.5.9-src.tar.xz \
- http://slackware.osuosl.org/slackware-13.37/source/tcl/tk/tk8.5.9-src.tar.xz"
+ http://slackware.osuosl.org/slackware-14.0/source/tcl/tcl/tcl8.5.11-src.tar.xz \
+ http://slackware.osuosl.org/slackware-14.0/source/tcl/tk/tk8.5.11-src.tar.xz"
MD5SUM="94dc304b00d18b95f783136c9ffd934f \
730b433d8344624925b662ec37ac0804 \
- c1e4eea4afdd9a8f8888d5b7c481122d \
- 78b59df55904095af40d64a0cd08c50d"
+ 304a8ecc61d5db9e41f3653161997712 \
+ fd5a5fabaf946568b4bb8d5213b7a92c"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="io_lib tklib"