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academic/archaeopteryx: Added (phylogenetic trees). 

Renamed from 'archeopteryx' and upgraded for version 0.9920_beta.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov 2017-04-16 21:34:01 +01:00 committed by Willy Sudiarto Raharjo
parent d0084411ce
commit 8cbb2a6d77
9 changed files with 623 additions and 0 deletions
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Archaeopteryx: visualise, analyse and edit phylogenetic trees
Archaeopteryx is a software tool for the visualization, analysis, and
editing of potentially large and highly annotated phylogenetic trees.
Archaeopteryx (the successor to ATV) is entirely written in the Java
programming language and is based on the forester libraries.
Check /usr/share/archaeopteryx for an example configuration file (called
'_aptx_configuration_file.txt' or get one from the program's web-site).
Please cite:
Han M.V. and Zmasek C.M. (2009)
phyloXML: XML for evolutionary biology and comparative genomics
BMC Bioinformatics, 10:356.

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Please cite:
Han M.V. and Zmasek C.M. (2009)
phyloXML: XML for evolutionary biology and comparative genomics
BMC Bioinformatics, 10:356.

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# User Interface Look and Feel
# ----------------------------
# Possible values for 'native_ui'
# 'yes' to use native (system) "look and feel"
# 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
# '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
# Archaeopteryx-style "look and feel" otherwise
native_ui: ?
# Default Values for Options
# --------------------------
# Minimal confidence value to be displayed: 'min_confidence_value':
# Example: 'min_confidence_value: 50.0' (a commonly used
# value for bootstrap support)
#
# Font family name: 'font_family':
# Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
# It is advisable to use more than one value for font_family (in
# decreasing order of preference). Font family names have to be
# comma separated (no spaces). Spaces in font names have to be
# replaced by underscores (e.g. 'Arial_Unicode_MS').
#
# Font size: 'font_size':
# Example: 'font_size: 10'
#
# Screen antialias: 'antialias_screen': values: 'yes'/'no'
#
# Show Scale: 'show_scale': values: 'yes'/'no'
#
# Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
#
# Cladogram display type: 'cladogram_type'
# Example: 'cladogram_type: non_lined_up'
# The three possible values are: lined_up
# non_lined_up
#
# Default line width for PDF export: 'pdf_export_line_wdith':
# Example: 'pdf_export_line_width: 0.5'
#
# Show overview: 'show_overview': values: 'yes'/'no'
#
# Phylogeny graphics type: 'phylogeny_graphics_type':
# Example: 'phylogeny_graphics_type: euro_style'
# The eight possible values are: rectangular
# euro_style
# rounded
# curved
# triangular
# convex
# unrooted
# circular
#
# Node label direction for circular and unrooted type: 'node_label_direction':
# Example: 'node_label_direction: horizontal'
# The two possible values are: horizontal
# radial
#
# Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
#
# Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
#
# Default node shape size: 'default_node_size'
# Example: 'default_node_size: 6'
#
# Default node shape type: 'default_node_shape'
# Example: 'default_node_shape: '
# Possible values: circle
# rectangle
#
# Default node shape fill: 'default_node_fill'
# Example: 'default_node_fill: '
# Possible values: solid
# gradient
# none
#
# To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
# Possible values: node_name
# sequence_name
# gene_name
# sequence_acc
# sequence_mol_seq_fasta
# sequence_symbol
# taxonomy_scientific_name
# taxonomy_code
# domains
# domains_collapsed
# seq_annotations
# go_term_ids
# user_selected
#
# To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
# Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
# classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
# Possible values: window (for output to window and buffer)
# console (for output to console and buffer)
# buffer_only (for output to buffer only)
#
# To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
# Example: 'list_node_data_custom_label: Get_Node_Data'
#
# Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
#
# Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
#
# Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
#
# Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
#
# Number of fraction digits for branch length values: 'branch_length_value_digits'
#
# Number of fraction digits for confidence values: 'confidence_value_digits'
#
# To turn on/off background color gradient: background_gradient
# Example: 'background_gradient: yes'
#
# To allow/not allow editing (cut, copy, and paste): allow_editing
# Example: 'allow_editing: yes'
#
# To allow/not allow thicker strokes for very small trees: allow_thick_strokes
# Example: 'allow_thick_strokes: yes'
#
# NH/NHX/Nexus file parsing
# -------------------------
# To replace underscores with spaces during NH/NHX/Nexus file parsing:
# 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
#
# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
# possible values are:
# 'no'
# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
#
# Internal node labels are confidence values during NH/NHX/Nexus file parsing:
# 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
#
# phyloXML parsing
# ----------------
# To ensure compatibility with all current and future
# phyloXML applications and to detect malformatted and
# possibly erroneous data, it is strongly recommended
# to enable validation of all phyloXML files
# against the XSD Schema (see: http://www.phyloxml.org/),
# with:
# 'validate_against_phyloxml_xsd_schema: true'
min_confidence_value: 0.0
font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
font_size: 10
font_size_min: 2
font_size_max: 20
antialias_screen: yes
show_scale: yes
cladogram_type: non_lined_up
phylogeny_graphics_type: rectangular
node_label_direction: horizontal
show_default_node_shapes_internal: no
show_default_node_shapes_external: no
show_node_shapes_for_nodes_with_vis_data: yes
default_node_size: 4
default_node_shape: rectangle
default_node_fill: solid
pdf_export_line_width: 0.5
show_overview: yes
overview_width: 120
overview_height: 120
overview_placement_type: upper_left
color_labels_same_as_branch_length_values: no
display_sequence_relations: no
show_domain_labels: yes
line_up_renderable_data: yes
right_align_domain_architectures: no
show_seq_annotation_ref_sources: yes
branch_length_value_digits: 3
confidence_value_digits: 2
background_gradient: no
allow_editing: yes
allow_thick_strokes: no
list_node_data_in: window
list_node_data_field: user_selected
list_node_data_custom_label:
# NH/NHX/Nexus file parsing:
internal_labels_are_confidence_values: no
replace_underscores_in_nh_parsing: no
taxonomy_extraction_in_nh_parsing: no
# phyloXML parsing:
validate_against_phyloxml_xsd_schema: true
# Checkbox Display Selection
# --------------------------
# This is used to select which checkboxes to display
# and what their initial values should be.
# Format: 'name: display|nodisplay yes|no'
# Note: if an option is not displayed, it will not be enabled
#
# For the following use '?' to let Archaeopteryx decide (depending on tree):
# - 'phylogram'
# - 'write_confidence_values'
# - 'write_events'
phylogram: display ?
rollover: display yes
color_according_to_sequence: display no
color_according_to_species: display no
color_according_to_annotation: display no
show_node_names: display yes
show_seq_names: display yes
show_seq_symbols: display yes
show_seq_acc: display no
show_gene_names: display yes
show_taxonomy_code: display yes
show_taxonomy_scientific_names: display yes
show_taxonomy_rank: display no
show_taxonomy_common_names: display no
show_taxonomy_images: display no
show_annotations: display no
write_confidence_values: display ?
write_branch_length_values: display no
write_events: display ?
use_visual_styles: display no
width_branches: display no
show_domain_architectures: display no
show_msa: display no
show_binary_characters: display no
show_binary_character_counts: display no
display_internal_data: display yes
dynamically_hide_data: display yes
show_relation_confidence: display no
show_properties: display no
show_vector_data: display no
# Combo-box Display Selection
# ---------------------------
# Format: 'name: display/nodisplay'
click_to: display_node_data display
click_to: collapse_uncollapse display
click_to: uncollapse_all display
click_to: reroot display
click_to: subtree display
click_to: swap display
click_to: order_subtree display
click_to: sort_descendants display
click_to: color_subtree display
click_to: change_node_font display
click_to: color_node_font display
click_to: open_seq_web display
click_to: open_pdb_web display
click_to: open_tax_web display
click_to: blast display
click_to: cut_subtree display
click_to: copy_subtree display
click_to: paste_subtree display
click_to: delete display
click_to: add_new_node display
click_to: edit_node_data display
click_to: select_nodes display
click_to: get_ext_descendents_data display
# Default click-to option (any of the above if set to "display")
default_click_to: display_node_data
# Default Tree Display Colors
# ---------------------------
display_color: background 0x000000
display_color: background_gradient_bottom 0x0000FF
display_color: sequence 0xE6E6E6
display_color: taxonomy 0xB4B4B4
display_color: confidence 0xB4B4B4
display_color: branch_length 0x8C8C8C
display_color: branch 0xFFFFFF
display_color: node_box 0xFFFFFF
display_color: collapsed 0xFFFFFF
display_color: matching_a 0x00FF00
display_color: matching_b 0xFF0000
display_color: matching_a_and_b 0xFFFF00
display_color: duplication 0xFF0000
display_color: speciation 0x00FF00
display_color: duplication_or_specation 0xFFFF00
display_color: domain_label 0xE6E6E6
display_color: domain_base 0x646464
display_color: binary_domain_combinations 0x4169FF
display_color: annotation 0xADFF2F
display_color: overview 0x828282
# GUI (graphical user interface) Colors
# -------------------------------------
#
# These are ignored if native (system) "look and feel"
# is being used ('native_ui: yes').
gui_background_color: 0x202020
gui_checkbox_text_color: 0xDCDCDC
gui_checkbox_and_button_active_color: 0xFF0000
gui_button_text_color: 0xFFFFFF
gui_button_background_color: 0x404040
gui_menu_background_color: 0x000000
gui_menu_text_color: 0xFFFFFF
gui_button_border_color: 0x000000
# Vector Data Display Colors and Sizes
# ------------------------------------
vector_data_min_color: 0x0000FF
vector_data_max_color: 0xFFFF00
vector_data_mean_color: 0x000000
vector_data_width: 120
vector_data_height: 12
# Settings Specific for Archaeopteryx Applets (E and A)
# -----------------------------------------------------
# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
midpoint_reroot: yes
# Settings Specific for ArchaeopteryxE Applets
# --------------------------------------------
# To hide controls and menus: 'hide_controls_and_menus: yes'
# To use tabbed display : 'use_tabbed_display: yes'
hide_controls_and_menus: no
use_tabbed_display: yes
# Settings For Phylogenetic Inference
# -----------------------------------
# EXPERIMENTAL: DO NOT USE!!
default_number_of_bootstrap_resamples: 100
mafft_local: /bin/mafft
fastme_local: /bin/fastme
raxml_local: /bin/raxml
# Sequence colors
# ---------------
# Format: species_color: sequencename hexcolor
sequence_color: Tubulin-alpha 0xEE0000
sequence_color: Tubulin-beta 0x00EE00
# Species colors
# --------------
# Format: species_color: speciesname hexcolor
species_color: BRAFL 0x00FFFF
species_color: SPHGR 0x9620F0
species_color: STRPU 0x9620F0
species_color: CIOIN 0xFF1CAE
species_color: CIOSA 0xFF2CAE
species_color: BOVIN 0x5C3317
species_color: CANFA 0x8B2323
species_color: HUMAN 0xFF2400
species_color: PANTR 0xCC2400
species_color: MOUSE 0xFF7F00
species_color: RAT 0xFFEF00
species_color: MONDO 0xEE9A49
species_color: ORNAN 0xCD853F
species_color: XENLA 0x6BAA23
species_color: XENTR 0x6BAA23
species_color: CHICK 0xFFC125
species_color: FUGRU 0x0000FF
species_color: BRARE 0x0000DD
species_color: DANRE 0x0000BB
species_color: TETNG 0x0000AA
species_color: ORYLA 0x000088
species_color: GASAC 0x000066
species_color: CAEEL 0x666699
species_color: CAEBR 0xB0B0B0
species_color: DROME 0x663366
species_color: DROPS 0x996699
species_color: APIME 0x7A7700
species_color: AEDAE 0x8C5900
species_color: TRICA 0x918E00
species_color: NEMVE 0x0066CC
species_color: HYDAT 0x3399FF
species_color: HYDVU 0x3399FF
species_color: LUBBA 0xF7B5CB
species_color: GEOCY 0xF5A0BD
species_color: AMPQE 0x009966
species_color: SUBDO 0xC790B9
species_color: MONBE 0xFC0FC0
species_color: DICPU 0xFFCC33
species_color: DICDI 0xFFCC00
species_color: ENTHI 0x5959AB
species_color: ARATH 0x00FF00
species_color: POPTR 0x006400
species_color: VITVI 0x00CD00
species_color: GLYMA 0x00FF7F
species_color: ORYSA 0x008B00
species_color: ORYSJ 0x008C00
species_color: SORBI 0x00EE76
species_color: SELMO 0x238E23
species_color: PHYPA 0x09F911
species_color: OSTLU 0x7FFF00
species_color: OSTTA 0x7FFF00
species_color: OSTRC 0x7FFF00
species_color: MICPU 0x66CD00
species_color: MIC99 0x66CD00
species_color: CHLRE 0xB3EE3A
species_color: VOLCA 0xC0FF3E
species_color: CHLSP 0x6B8E23
species_color: CYAME 0xD02090
species_color: YEAST 0xAAAAAA
species_color: BACFR 0xFF0000
species_color: BACTN 0xFFFF00
species_color: MYXXD 0x0000FF
species_color: STIAU 0x00FFFF
species_color: BACOV 0x8C5900
species_color: BACUN 0x66CD00
species_color: PORGI 0x918E00
# rank: Class
species_color: Mammalia 0xFF0000
species_color: mammals 0xFF0000
# rank: Phylum
species_color: Chordata 0x8470FF
species_color: Echinodermata 0x6495ED
species_color: Hemichordata 0x7EC0EE
species_color: Arthropoda 0x7AC5CD
species_color: Nematoda 0x7171C6
species_color: Tardigrada 0x388E8E
species_color: Annelida 0xC67171
species_color: Mollusca 0x00F5FF
species_color: Ctenophora 0xBBFFFF
species_color: Cnidaria 0xFF83FA
species_color: Placozoa 0xEED2EE
species_color: Porifera 0xFF3E96
species_color: Microsporidia 0x8B8378
species_color: Ascomycota 0xFF6347
species_color: Basidiomycota 0xFFD700
species_color: Chlorophyta 0x00C78C
species_color: Streptophyta 0x00C957
# rank: Kingdom
species_color: Viridiplantae 0x00FF00
species_color: plants 0x00FF00
species_color: Metazoa 0x0000FF
species_color: animals 0x0000FF
species_color: Fungi 0xFF9912
# rank: Superkingdom
species_color: Viruses 0xFFD700
species_color: Bacteria 0x00FF00
species_color: Archaea 0x0000FF
species_color: Eukaryota 0xFF0000
species_color: eukaryotes 0xFF0000
# Domain colors
# -------------
domain_color: Cofilin_ADF 0xFC0FC0
domain_color: TIR 0x900000
domain_color: NACHT 0x202020
domain_color: CARD 0xFF0000
domain_color: Peptidase_C14 0x00FF00
domain_color: Death 0x0000FF
domain_color: DED 0x00FFFF
domain_color: BIR 0xCCFF33
domain_color: PAAD_DAPIN 0x9999CC
domain_color: NB-ARC 0x500050
domain_color: WD40 0x888888
domain_color: RVT_1 0x999900
domain_color: CBM_48 0xFF0000
domain_color: Alpha-amylase 0x0000FF
domain_color: Alpha-amylase_C 0x0080FF
domain_color: CBM_48 0xFF0000
domain_color: Alpha-amylase 0x0000FF
domain_color: Alpha-amylase_C 0x0080FF
domain_color: GDE_N 0x009000
domain_color: GDE_C 0x00FF00
domain_color: hGDE_N 0x990099
domain_color: GDE_N_bis 0x007000
domain_color: hGDE_central 0xFF8000
domain_color: hGDE_amylase 0x0000EE
domain_color: hDGE_amylase 0x0000EE
# Annotation colors
# -----------------
annotation_color: dehydrogenase 0x0000FF
annotation_color: kinase 0xFF00FF
annotation_color: protease 0x009900
annotation_color: transcription 0xAAAA00
# END

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#!/bin/sh
# Slackware build script for archaeopteryx
# Copyright 2014-2017 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
# permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=archaeopteryx
VERSION=${VERSION:-0.9920_beta}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=forester
SRCVER=1045
ARCH=noarch
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
install -D -m755 $CWD/${SRCNAM}_${SRCVER}.jar $PKG/usr/bin/$PRGNAM.jar
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
# Include the example configuration file in the package. Copy it in your $HOME.
mkdir -p $PKG/usr/share/$PRGNAM
cp $CWD/_aptx_configuration_file.txt $PKG/usr/share/$PRGNAM
# I did not find an icon, so I quickly modified some picture of an archaeopteryx...
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}

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[Desktop Entry]
Categories=Education;
Exec=java -Xmx2048m -jar /usr/bin/archaeopteryx.jar
Icon=archaeopteryx
Name=Archaeopteryx
StartupNotify=false
Type=Application

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PRGNAM="archaeopteryx"
VERSION="0.9920_beta"
HOMEPAGE="https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"
DOWNLOAD="https://dl.dropboxusercontent.com/u/14456265/forester/download/forester_1045.jar"
MD5SUM="99b8bbb7a7763ca999a7056398637d8c"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="jdk"
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"

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if [ -x /usr/bin/update-desktop-database ]; then
/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
fi

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# 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 ':' except on otherwise blank lines.
|-----handy-ruler------------------------------------------------------|
archaeopteryx: archaeopteryx (Visualise, analyse and edit phylogenetic trees)
archaeopteryx:
archaeopteryx: Archaeopteryx is a software tool for the visualization, analysis,
archaeopteryx: and editing of potentially large and highly annotated phylogenetic
archaeopteryx: trees.
archaeopteryx:
archaeopteryx: Author: https://sites.google.com/site/cmzmasek/home
archaeopteryx: Refernces: /usr/doc/archaeopteryx-0.9920_beta/References
archaeopteryx:
archaeopteryx:
archaeopteryx: