diff options
| -rw-r--r-- | academic/archeopteryx/README | 6 | ||||
| -rw-r--r-- | academic/archeopteryx/_aptx_configuration_file.txt | 502 | ||||
| -rw-r--r-- | academic/archeopteryx/archeopteryx.SlackBuild | 8 | ||||
| -rw-r--r-- | academic/archeopteryx/archeopteryx.info | 6 | ||||
| -rw-r--r-- | academic/archeopteryx/slack-desc | 2 |
5 files changed, 515 insertions, 9 deletions
diff --git a/academic/archeopteryx/README b/academic/archeopteryx/README index f5940b6f7f..ed8730cfab 100644 --- a/academic/archeopteryx/README +++ b/academic/archeopteryx/README @@ -1,8 +1,8 @@ -Archaeopteryx: visualise, analyse and edit phylogenetic trees +Archeopteryx: visualise, analyse and edit phylogenetic trees -Archaeopteryx is a software tool for the visualization, analysis, and +Archeopteryx 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 +Archeopteryx (the successor to ATV) is entirely written in the Java programming language and is based on the forester libraries. Please cite: diff --git a/academic/archeopteryx/_aptx_configuration_file.txt b/academic/archeopteryx/_aptx_configuration_file.txt new file mode 100644 index 0000000000..a7230a4272 --- /dev/null +++ b/academic/archeopteryx/_aptx_configuration_file.txt @@ -0,0 +1,502 @@ +# 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 index bc74f234cd..c7041a1f24 100644 --- a/academic/archeopteryx/archeopteryx.SlackBuild +++ b/academic/archeopteryx/archeopteryx.SlackBuild @@ -23,12 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=archeopteryx -VERSION=${VERSION:-0.9901_beta} +VERSION=${VERSION:-0.9917_beta} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} SRCNAM=forester -SRCVER=1038 +SRCVER=1044 ARCH=noarch CWD=$(pwd) @@ -47,6 +47,10 @@ 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 archeopteryx... mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications diff --git a/academic/archeopteryx/archeopteryx.info b/academic/archeopteryx/archeopteryx.info index 6c45f20adc..61071b1cd4 100644 --- a/academic/archeopteryx/archeopteryx.info +++ b/academic/archeopteryx/archeopteryx.info @@ -1,8 +1,8 @@ PRGNAM="archeopteryx" -VERSION="0.9901_beta" +VERSION="0.9917_beta" HOMEPAGE="https://sites.google.com/site/cmzmasek/home/software/archaeopteryx" -DOWNLOAD="https://googledrive.com/host/0BxMokdxOh-JRM1d2azFoRnF3bGM/download/forester_1038.jar" -MD5SUM="e101cba9a22f6df63e9bcd8fa199c029" +DOWNLOAD="https://dl.dropboxusercontent.com/u/14456265/forester/download/forester_1044.jar" +MD5SUM="1e55a5eee563e39e0a66b836faf09897" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/archeopteryx/slack-desc b/academic/archeopteryx/slack-desc index 387deab9c7..84df0deffa 100644 --- a/academic/archeopteryx/slack-desc +++ b/academic/archeopteryx/slack-desc @@ -8,7 +8,7 @@ |-----handy-ruler------------------------------------------------------| archeopteryx: archeopteryx (Visualise, analyse and edit phylogenetic trees) archeopteryx: -archeopteryx: Archaeopteryx is a software tool for the visualization, analysis, +archeopteryx: Archeopteryx is a software tool for the visualization, analysis, archeopteryx: and editing of potentially large and highly annotated phylogenetic archeopteryx: trees. archeopteryx: |