academic/gp2fasta: Added (Convert gp files to fasta)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

7 files changed, 138 insertions, 0 deletions

diff --git a/academic/gp2fasta/README b/academic/gp2fasta/README
new file mode 100644
index 000000000000..47c071396ff2
--- /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 000000000000..5fb28930db0b
--- /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 000000000000..971f9861b79e
--- /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 000000000000..5e0c73e123db
--- /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 000000000000..f00775136db3
--- /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 000000000000..9878dedd306e
--- /dev/null
+++ b/academic/gp2fasta/gp2fasta.png
diff --git a/academic/gp2fasta/slack-desc b/academic/gp2fasta/slack-desc
new file mode 100644
index 000000000000..a3d4b921705f
--- /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