From 47875e48df4d4a9e0ec0bd87c4d39d28c55c8825 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 3 Sep 2011 09:31:47 -0300 Subject: academic/gp2fasta: Added (Convert gp files to fasta) Signed-off-by: Niels Horn --- academic/gp2fasta/README | 3 ++ academic/gp2fasta/doinst.sh | 3 ++ academic/gp2fasta/gp2fasta.SlackBuild | 96 ++++++++++++++++++++++++++++++++++ academic/gp2fasta/gp2fasta.desktop | 7 +++ academic/gp2fasta/gp2fasta.info | 10 ++++ academic/gp2fasta/gp2fasta.png | Bin 0 -> 3410 bytes academic/gp2fasta/slack-desc | 19 +++++++ 7 files changed, 138 insertions(+) create mode 100644 academic/gp2fasta/README create mode 100644 academic/gp2fasta/doinst.sh create mode 100644 academic/gp2fasta/gp2fasta.SlackBuild create mode 100644 academic/gp2fasta/gp2fasta.desktop create mode 100644 academic/gp2fasta/gp2fasta.info create mode 100644 academic/gp2fasta/gp2fasta.png create mode 100644 academic/gp2fasta/slack-desc (limited to 'academic/gp2fasta') 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, 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 Binary files /dev/null and b/academic/gp2fasta/gp2fasta.png 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 -- cgit v1.2.3