mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-16 19:50:19 +01:00
academic/staden: A few enhancements.
Signed-off-by: bedlam <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
26da2395a3
commit
555dbc00b3
4 changed files with 80 additions and 16 deletions
|
|
@ -1,20 +1,40 @@
|
|||
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
|
||||
search, experiment suggestion, read pair analysis and contig
|
||||
editing.
|
||||
GAP5 - The new development version of Gap4, designed to work with the
|
||||
large volumes of data attainable through the newer sequencing
|
||||
technologies.
|
||||
PREGAP4 - Provides a graphical user interface to set up the processing
|
||||
required to prepare trace data for assembly or analysis.
|
||||
SPIN - Compares pairs of sequences in many ways, often presenting its
|
||||
results graphically and has a sliding sequence window linked to
|
||||
the plots.
|
||||
TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF
|
||||
trace files.
|
||||
|
||||
* GAP4: Performs assembly, contig joining, assembly checking, repeat
|
||||
search, experiment suggestion, read pair analysis and contig editing.
|
||||
|
||||
* GAP5: The new development version of Gap4, designed to work with large
|
||||
volumes of data attainable through the newer sequencing technologies.
|
||||
|
||||
* PREGAP4: Provides a graphical user interface to set up the processing
|
||||
required to prepare trace data for assembly or analysis.
|
||||
|
||||
* SPIN: Compares pairs of sequences in many ways, often presenting its
|
||||
results graphically and has a sliding sequence window linked to the
|
||||
plots.
|
||||
|
||||
* TREV: A rapid and flexible viewer and editor for ABI, ALF or SCF trace
|
||||
files.
|
||||
|
||||
NOTE: Xfce submenus
|
||||
For XFCE, if you want to have the menu entries grouped in a submenu
|
||||
folder (multilevel menu entry), do:
|
||||
|
||||
SUBMENU="YES" ./staden.SlackBuild
|
||||
|
||||
NOTE: Staden and EMBOSS:
|
||||
Staden used to provide a GUI for (at least part of) the programs from
|
||||
EMBOSS. To give it a try, run this after install (of course you need to
|
||||
have installed EMBOSS, too):
|
||||
|
||||
create_emboss_files
|
||||
|
||||
This will create some files in:
|
||||
|
||||
/usr/share/staden/tcl/spin_emboss/acdtcl/
|
||||
|
||||
CITING
|
||||
For more information and citing, visit Staden's web page and check the
|
||||
"References" file in the documentation.
|
||||
|
|
|
|||
4
academic/staden/desktop/staden.directory
Normal file
4
academic/staden/desktop/staden.directory
Normal file
|
|
@ -0,0 +1,4 @@
|
|||
[Desktop Entry]
|
||||
Type=Directory
|
||||
Name=Staden Package
|
||||
Icon=folder
|
||||
20
academic/staden/desktop/staden.menu
Normal file
20
academic/staden/desktop/staden.menu
Normal file
|
|
@ -0,0 +1,20 @@
|
|||
<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN"
|
||||
"http://www.freedesktop.org/standards/menu-spec/menu-1.0.dtd">
|
||||
<Menu>
|
||||
<Name>Applications</Name>
|
||||
<Menu>
|
||||
<Name>Education</Name>
|
||||
<Directory>xfce4-education.directory</Directory>
|
||||
<Menu>
|
||||
<Name>Staden Package</Name>
|
||||
<Directory>staden.directory</Directory>
|
||||
<Include>
|
||||
<Filename>gap4.desktop</Filename>
|
||||
<Filename>gap5.desktop</Filename>
|
||||
<Filename>pregap4.desktop</Filename>
|
||||
<Filename>trev.desktop</Filename>
|
||||
<Filename>spin.desktop</Filename>
|
||||
</Include>
|
||||
</Menu>
|
||||
</Menu>
|
||||
</Menu>
|
||||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
# Slackware build script for staden
|
||||
|
||||
# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
|
||||
# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com
|
||||
# All rights reserved.
|
||||
#
|
||||
# Redistribution and use of this script, with or without modification, is
|
||||
|
|
@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd)
|
|||
|
||||
PRGNAM=staden
|
||||
VERSION=${VERSION:-2.0.0b11}
|
||||
BUILD=${BUILD:-1}
|
||||
BUILD=${BUILD:-2}
|
||||
TAG=${TAG:-_SBo}
|
||||
PKGTYPE=${PKGTYPE:-tgz}
|
||||
|
||||
|
|
@ -97,6 +97,11 @@ CXXFLAGS="$SLKCFLAGS" \
|
|||
--with-tklib=/usr/lib${LIBDIRSUFFIX}/$TKLIB \
|
||||
--build=$ARCH-slackware-linux
|
||||
|
||||
# Point to the right place of the EMBOSS .acd and data files. This is
|
||||
# needed if the "create_emboss_files" script is run after install.
|
||||
sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl
|
||||
sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
|
||||
|
||||
make
|
||||
make install DESTDIR=$PKG
|
||||
|
||||
|
|
@ -111,6 +116,21 @@ mkdir -p $PKG/usr/share/{applications,pixmaps}
|
|||
cp $CWD/desktop/*.desktop $PKG/usr/share/applications
|
||||
cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
|
||||
|
||||
# Do we want a submenu? For more info:
|
||||
# https://slackalaxy.com/2021/08/08/xfce-multilevel-menu/
|
||||
if [ $SUBMENU = "YES" ]; then
|
||||
# Use a separate "Staden Package" menu entry within "Education"
|
||||
mkdir -p $PKG/etc/xdg/menus/applications-merged
|
||||
cp $CWD/desktop/$PRGNAM.menu $PKG/etc/xdg/menus/applications-merged
|
||||
|
||||
# Menu directory structure
|
||||
mkdir -p $PKG/usr/share/desktop-directories
|
||||
cp $CWD/desktop/$PRGNAM.directory $PKG/usr/share/desktop-directories
|
||||
|
||||
# The category in the .desktop files is commented out to avoid duplication in menus
|
||||
sed -i "s:Categories:#Categories:" $PKG/usr/share/applications/*.desktop
|
||||
fi
|
||||
|
||||
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cp -a ChangeLog LICENCE.txt NEWS README.build \
|
||||
$PKG/usr/doc/$PRGNAM-$VERSION
|
||||
|
|
|
|||
Loading…
Reference in a new issue