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author Petar Petrov2011-09-03 14:31:47 +0200
committer Niels Horn2011-09-03 14:31:47 +0200
commit47875e48df4d4a9e0ec0bd87c4d39d28c55c8825 (patch)
treeec8d3c8fd9712ae75f6983de12e16aa89016d53b /academic
parentd4353e6dec3841394462e0c35de336b52e63d3b5 (diff)
downloadslackbuilds-47875e48df4d4a9e0ec0bd87c4d39d28c55c8825.tar.gz
academic/gp2fasta: Added (Convert gp files to fasta)
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/gp2fasta/README3
-rw-r--r--academic/gp2fasta/doinst.sh3
-rw-r--r--academic/gp2fasta/gp2fasta.SlackBuild96
-rw-r--r--academic/gp2fasta/gp2fasta.desktop7
-rw-r--r--academic/gp2fasta/gp2fasta.info10
-rw-r--r--academic/gp2fasta/gp2fasta.pngbin0 -> 3410 bytes
-rw-r--r--academic/gp2fasta/slack-desc19
7 files changed, 138 insertions, 0 deletions
diff --git a/academic/gp2fasta/README b/academic/gp2fasta/README
new file mode 100644
index 0000000000..47c071396f
--- /dev/null
+++ b/academic/gp2fasta/README
@@ -0,0 +1,3 @@
+gp2fasta can convert gp files from NCBI GenPept or GenBank to fasta
+format. Its main purpose is to create fasta files with short, but
+accurate headers for sequence.
diff --git a/academic/gp2fasta/doinst.sh b/academic/gp2fasta/doinst.sh
new file mode 100644
index 0000000000..5fb28930db
--- /dev/null
+++ b/academic/gp2fasta/doinst.sh
@@ -0,0 +1,3 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+ /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
diff --git a/academic/gp2fasta/gp2fasta.SlackBuild b/academic/gp2fasta/gp2fasta.SlackBuild
new file mode 100644
index 0000000000..971f9861b7
--- /dev/null
+++ b/academic/gp2fasta/gp2fasta.SlackBuild
@@ -0,0 +1,96 @@
+#!/bin/sh
+
+# Slackware build script for gp2fasta
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
+# hereby submitted to the public domain
+
+# The icon used by the gp2fasta.desktop file is taken from
+# http://kde-look.org/content/show.php/Fasta+icons?content=54012
+# Author is Luis-Miguel Rodriguez. Thank you!
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=gp2fasta
+VERSION=${VERSION:-0.2}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+ case "$( uname -m )" in
+ i?86) ARCH=i486 ;;
+ arm*) ARCH=arm ;;
+ *) ARCH=$( uname -m ) ;;
+ esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+ SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+ LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+ SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+ LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+ SLKCFLAGS="-O2 -fPIC"
+ LIBDIRSUFFIX="64"
+else
+ SLKCFLAGS="-O2"
+ LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM
+unzip $CWD/$PRGNAM.zip
+cd $PRGNAM
+# Remove the precompiled binary just in case
+rm gp2fasta
+
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+qmake -project
+qmake
+
+# Use our CFLAGS
+sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+ make
+
+install -D -m755 gp2fasta $PKG/usr/bin/gp2fasta
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+ example.gp README \
+ $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+# Menu item and icon
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications/
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps/
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/gp2fasta/gp2fasta.desktop b/academic/gp2fasta/gp2fasta.desktop
new file mode 100644
index 0000000000..5e0c73e123
--- /dev/null
+++ b/academic/gp2fasta/gp2fasta.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=gp2fasta
+Icon=gp2fasta.png
+Name=GP2Fasta
+StartupNotify=false
+Type=Application
diff --git a/academic/gp2fasta/gp2fasta.info b/academic/gp2fasta/gp2fasta.info
new file mode 100644
index 0000000000..f00775136d
--- /dev/null
+++ b/academic/gp2fasta/gp2fasta.info
@@ -0,0 +1,10 @@
+PRGNAM="gp2fasta"
+VERSION="0.2"
+HOMEPAGE="http://gp2fasta.ovh.org/"
+DOWNLOAD="http://gp2fasta.ovh.org/gp2fasta.zip"
+MD5SUM="f1124fb098c531154f4e6dcf7c9d174d"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/gp2fasta/gp2fasta.png b/academic/gp2fasta/gp2fasta.png
new file mode 100644
index 0000000000..9878dedd30
--- /dev/null
+++ b/academic/gp2fasta/gp2fasta.png
Binary files differ
diff --git a/academic/gp2fasta/slack-desc b/academic/gp2fasta/slack-desc
new file mode 100644
index 0000000000..a3d4b92170
--- /dev/null
+++ b/academic/gp2fasta/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description. Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in. You must
+# make exactly 11 lines for the formatting to be correct. It's also
+# customary to leave one space after the ':'.
+
+ |-----handy-ruler------------------------------------------------------|
+gp2fasta: gp2fasta (Convert gp files to fasta)
+gp2fasta:
+gp2fasta: GP2fasta is a QT application converting gp files from NCBI GenPept
+gp2fasta: format to fasta. Its main purpose is to create fasta files with
+gp2fasta: short, but still accurate headers for sequence.
+gp2fasta:
+gp2fasta:
+gp2fasta:
+gp2fasta:
+gp2fasta:
+gp2fasta: Home: http://gp2fasta.ovh.org