summaryrefslogtreecommitdiffstats
path: root/academic
diff options
context:
space:
mode:
author Petar Petrov <slackalaxy@gmail.com>2017-04-16 21:17:41 +0100
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2017-04-22 08:10:38 +0700
commitd0084411ce47e94fdca9f38fad163d4018f98553 (patch)
tree7b50eb831f9c059645affde73e14bc71734a56ba /academic
parentf4dd64cc87b483d42cf00bdd8eba8bdb9081e264 (diff)
downloadslackbuilds-d0084411ce47e94fdca9f38fad163d4018f98553.tar.gz
slackbuilds-d0084411ce47e94fdca9f38fad163d4018f98553.tar.xz
academic/archeopteryx: Removed (renamed to archaeopteryx).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/archeopteryx/README11
-rw-r--r--academic/archeopteryx/References4
-rw-r--r--academic/archeopteryx/_aptx_configuration_file.txt502
-rw-r--r--academic/archeopteryx/archeopteryx.SlackBuild63
-rw-r--r--academic/archeopteryx/archeopteryx.desktop7
-rw-r--r--academic/archeopteryx/archeopteryx.info10
-rw-r--r--academic/archeopteryx/archeopteryx.pngbin39248 -> 0 bytes
-rw-r--r--academic/archeopteryx/doinst.sh3
-rw-r--r--academic/archeopteryx/slack-desc19
9 files changed, 0 insertions, 619 deletions
diff --git a/academic/archeopteryx/README b/academic/archeopteryx/README
deleted file mode 100644
index ed8730cfab..0000000000
--- a/academic/archeopteryx/README
+++ /dev/null
@@ -1,11 +0,0 @@
-Archeopteryx: visualise, analyse and edit phylogenetic trees
-
-Archeopteryx is a software tool for the visualization, analysis, and
-editing of potentially large and highly annotated phylogenetic trees.
-Archeopteryx (the successor to ATV) is entirely written in the Java
-programming language and is based on the forester libraries.
-
-Please cite:
-Han M.V. and Zmasek C.M. (2009)
-phyloXML: XML for evolutionary biology and comparative genomics
-BMC Bioinformatics, 10:356.
diff --git a/academic/archeopteryx/References b/academic/archeopteryx/References
deleted file mode 100644
index bec0a4ddb1..0000000000
--- a/academic/archeopteryx/References
+++ /dev/null
@@ -1,4 +0,0 @@
-Please cite:
-Han M.V. and Zmasek C.M. (2009)
-phyloXML: XML for evolutionary biology and comparative genomics
-BMC Bioinformatics, 10:356.
diff --git a/academic/archeopteryx/_aptx_configuration_file.txt b/academic/archeopteryx/_aptx_configuration_file.txt
deleted file mode 100644
index a7230a4272..0000000000
--- a/academic/archeopteryx/_aptx_configuration_file.txt
+++ /dev/null
@@ -1,502 +0,0 @@
-# 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
diff --git a/academic/archeopteryx/archeopteryx.SlackBuild b/academic/archeopteryx/archeopteryx.SlackBuild
deleted file mode 100644
index 3f767ddbdc..0000000000
--- a/academic/archeopteryx/archeopteryx.SlackBuild
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/sh
-
-# Slackware build script for archeopteryx
-
-# Copyright 2014-2016 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=archeopteryx
-VERSION=${VERSION:-1045}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-
-SRCNAM=forester
-ARCH=noarch
-
-CWD=$(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}_${VERSION}.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 archeopteryx...
-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/archeopteryx/archeopteryx.desktop b/academic/archeopteryx/archeopteryx.desktop
deleted file mode 100644
index df1f6b2929..0000000000
--- a/academic/archeopteryx/archeopteryx.desktop
+++ /dev/null
@@ -1,7 +0,0 @@
-[Desktop Entry]
-Categories=Education;
-Exec=java -Xmx2048m -jar /usr/bin/archeopteryx.jar
-Icon=archeopteryx
-Name=Archeopteryx
-StartupNotify=false
-Type=Application
diff --git a/academic/archeopteryx/archeopteryx.info b/academic/archeopteryx/archeopteryx.info
deleted file mode 100644
index 218b456e55..0000000000
--- a/academic/archeopteryx/archeopteryx.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="archeopteryx"
-VERSION="1045"
-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"
diff --git a/academic/archeopteryx/archeopteryx.png b/academic/archeopteryx/archeopteryx.png
deleted file mode 100644
index 5663c1b87e..0000000000
--- a/academic/archeopteryx/archeopteryx.png
+++ /dev/null
Binary files differ
diff --git a/academic/archeopteryx/doinst.sh b/academic/archeopteryx/doinst.sh
deleted file mode 100644
index 5fb28930db..0000000000
--- a/academic/archeopteryx/doinst.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-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/archeopteryx/slack-desc b/academic/archeopteryx/slack-desc
deleted file mode 100644
index 84df0deffa..0000000000
--- a/academic/archeopteryx/slack-desc
+++ /dev/null
@@ -1,19 +0,0 @@
-# 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------------------------------------------------------|
-archeopteryx: archeopteryx (Visualise, analyse and edit phylogenetic trees)
-archeopteryx:
-archeopteryx: Archeopteryx is a software tool for the visualization, analysis,
-archeopteryx: and editing of potentially large and highly annotated phylogenetic
-archeopteryx: trees.
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx: