[med-svn] [emperor] 02/15: initial commit
Afif Elghraoui
afif at moszumanska.debian.org
Thu Oct 13 06:22:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository emperor.
commit f5460d9fae25de3604ca46f07cc4274bb197b5cd
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Tue Feb 25 13:59:58 2014 +0000
initial commit
---
debian/changelog | 8 ++
debian/compat | 1 +
debian/control | 33 ++++++++
debian/copyright | 161 +++++++++++++++++++++++++++++++++++++
debian/doc-base | 8 ++
debian/docs | 2 +
debian/make_emperor.1 | 218 ++++++++++++++++++++++++++++++++++++++++++++++++++
debian/manpages | 1 +
debian/rules | 33 ++++++++
debian/source/format | 1 +
debian/watch | 2 +
11 files changed, 468 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d69d199
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,8 @@
+python-emperor (0.9.3-0biolinux1) precise; urgency=low
+
+ * New package as required by QIIME 1.8
+ * Move support_files to /usr/share
+ * Make manpage for make_emperor
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 24 Feb 2014 17:47:51 +0000
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..57f7a80
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: python-emperor
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 9),
+ python (>= 2.6.6-3~)
+Standards-Version: 3.9.4
+Homepage: http://biocore.github.io/emperor/
+
+Package: emperor
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends}
+Description: tool for visualizing high-throughput microbial community data
+ Emperor is an interactive next generation tool for the analysis, visualization
+ and understanding of high throughput microbial ecology datasets.
+ .
+ Due to its tailor-made graphical user interface, delving into a new dataset to
+ elucidate the patterns hidden in the data has never been easier. Emperor brings
+ a rich set of customizations and modifications that can be integrated into any
+ QIIME compliant dataset; with lightweight data files and hardware accelerated
+ graphics, constitutes itself as the state of the art for analyzing
+ N-dimensional data using principal coordinates analysis.
+ .
+ If you use Emperor for any published research, please include the following
+ citation:
+ .
+ EMPeror: a tool for visualizing high-throughput microbial community data
+ Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
+ Gigascience. 2013 Nov 26;2(1):16.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3989d58
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,161 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: EMPeror
+Upstream-Contact: Yoshiki Vázquez Baeza <yoshiki89 at gmail.com>
+Source: https://pypi.python.org/pypi/emperor
+
+Files: *
+Copyright: © 2013, The Emperor Project
+ Antonio Gonzalez Pena <antgonza at gmail.com>
+ Meg Pirrung
+ Yoshiki Vázquez Baeza <yoshiki89 at gmail.com>
+ Rob Knight <rob at spot.colorado.edu>
+License: BSD
+ See /usr/share/common-licenses/BSD
+ .
+ Emperor makes usage of all of the following copyrighted packages:
+
+
+Files: emperor/support_files/js/Three.js
+Copyright: (c) 2010-2013 three.js authors
+License: The MIT License
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: emperor/support_files/js/jquery*
+Copyright: (c) 2013 jQuery Foundation and other contributors (http://jquery.com/)
+License: The MIT License
+ As above.
+
+Files: emperor/support_files/js/spectrum.js
+Copyright: (c) 2013, Brian Grinstead, http://briangrinstead.com
+License: The MIT License
+ As above.
+
+Files: emperor/support_files/js/jquery.colorPicker.js
+Copyright: (c) 2012 Lakshan Perera
+License: The MIT License
+ As above.
+
+Files: emperor/support_files/js/d3.parcords.*
+Copyright: (c) 2012, Kai Chang (Parallel Coordinates [v0.1.7])
+License:
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+ * The name Kai Chang may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 MICHAEL BOSTOCK 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.
+
+Files: emperor/support_files/js/d3.v3.*
+Copyright: (c) 2013, Michael Bostock (d3 v3)
+License:
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+ * The name Michael Bostock may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 MICHAEL BOSTOCK 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.
+
+Files: emperor/support_files/js/THREEx.screenshot.js
+Copyright: (c) 2011 Jerome Etienne, http://jetienne.com
+License:
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Files: emperor/support_files/js/FileSaver*.js
+Copyright: (c) 2011 [Eli Grey](http://eligrey.com).
+License:
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>,
+License: MIT
+ As above.
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..d98d819
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,8 @@
+Document: python-emperor
+Title: A tool for visualizing high-throughput microbial community data
+Author: The EMPeror Project
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/emperor/html/*
+Index: /usr/share/doc/emperor/html/index.html
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..05ceb5f
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.md
+html
diff --git a/debian/make_emperor.1 b/debian/make_emperor.1
new file mode 100644
index 0000000..d16a70e
--- /dev/null
+++ b/debian/make_emperor.1
@@ -0,0 +1,218 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH EMPEROR: "1" "February 2014" "Version: make_emperor 0.9.3" "User Commands"
+.SH NAME
+make_emperor \- Create PCoA plots to be visualised with Emperor.
+.SH SYNOPSIS
+.B make_emperor
+[\fIoptions\fR] \fI{-i/--input_coords INPUT_COORDS -m/--map_fp MAP_FP}\fR
+.SH DESCRIPTION
+[] indicates optional input (order unimportant)
+.PP
+{} indicates required input (order unimportant)
+.PP
+This script automates the creation of three\-dimensional PCoA plots to be visualized with Emperor using Google Chrome or another comaptible browser. Note the script has been renamed from make_emperor.py to make_emperor to comply with Debian guidelines.
+.PP
+Example usage:
+Print help message and exit
+.IP
+make_emperor \fB\-h\fR
+.PP
+Plot PCoA data: Visualize the a PCoA file colored using a corresponding mapping file:
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-o\fR emperor_output
+.PP
+Coloring by metadata mapping file:
+Additionally, using the supplied mapping file and a specific category or any combination of the available categories. When using the -b option, the user can specify the coloring for multiple header names, where each header is separated by a comma. The user can also combine mapping headers and color by the combined headers that are created by inserting an '&&' between the input header names. Color by 'Treatment' and by the result of concatenating the 'DOB' category and the 'Treatment' category:
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-b\fR 'Treatment&&DOB,Treatment' \fB\-o\fR emperor_colored_by
+.PP
+PCoA plot with an explicit axis: Create a PCoA plot with an axis of the plot representing the 'DOB' of the samples. This option is useful when presenting a gradient from your metadata e. g. 'Time' or 'pH':
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-a\fR DOB \fB\-o\fR pcoa_dob
+.PP
+PCoA plot with an explicit axis and using --missing_custom_axes_values: Create a PCoA plot with an axis of the plot representing the 'DOB' of the samples and define the position over the gradient of those samples missing a numeric value; in this case we are going to plot the samples in the value 20060000. You can select for each explicit axis which value you want to use for the missing values:
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map_modified.txt \fB\-a\fR DOB \fB\-o\fR pcoa_dob_with_missing_custom_axes_values \fB\-x\fR 'DOB:20060000'
+.PP
+PCoA plot with an explicit axis and using \fB\-\-missing_custom_axes_values\fR but setting different values based on another column: Create a PCoA plot with an axis of the plot representing the 'DOB' of the samples and defining the position over the gradient of those samples missing a numeric value but using as reference another column of the mapping file. In this case we are going to plot the samples that are Control on the Treatment column on 20080220 and on 20080240 those that are Fast
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map_modified.txt \fB\-a\fR DOB \fB\-o\fR pcoa_dob_with_missing_custom_axes_with_multiple_values \fB\-x\fR 'DOB:Treatment==Control=20080220' \fB\-x\fR 'DOB:Treatment==Fast=20080240'
+.PP
+Jackknifed principal coordinates analysis plot: Create a jackknifed PCoA plot (with confidence intervals for each sample) passing as the input a directory of coordinates files (where each file corresponds to a different OTU table) and use the standard deviation method to compute the dimensions of the ellipsoids surrounding each sample:
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc \fB\-m\fR Fasting_Map.txt \fB\-o\fR jackknifed_pcoa \fB\-e\fR sdev
+.PP
+Jackknifed PCoA plot with a master coordinates file: Passing a master coordinates file (--master_pcoa) will display the ellipsoids centered by the samples in this file:
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc \fB\-s\fR unweighted_unifrac_pc/pcoa_unweighted_unifrac_rarefaction_110_5.txt \fB\-m\fR Fasting_Map.txt \fB\-o\fR jackknifed_with_master
+.PP
+BiPlots: To see which taxa are the ten more prevalent in the different areas of the PCoA plot, you need to pass a summarized taxa file i. e. the output of summarize_taxa.py. Note that if the the '\-\-taxa_fp' has fewer than 10 taxa, the script will default to use all.
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-t\fR otu_table_L3.txt \fB\-o\fR biplot
+.PP
+BiPlots with extra options: To see which are the three most prevalent taxa and save the coordinates where these taxa are centered, you can use the \fB\-n\fR (number of taxa to keep) and the \fB\-\-biplot_fp\fR (output biplot file path) options.
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-t\fR otu_table_L3.txt \fB\-o\fR biplot_options \fB\-n\fR 3 \fB\-\-biplot_fp\fR biplot.txt
+.PP
+Drawing connecting lines between samples: To draw lines betwen samples within a category use the '\-\-add_vectors' option. For example to connect the lines by the 'Treatment' category.
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-o\fR vectors \fB\-\-add_vectors\fR Treatment
+.PP
+Drawing connecting lines between samples with an explicit axis: To draw lines between samples within a category of the mapping file and have them sorted by a category that's explicitly represented in the 3D plot use the '\-\-add_vectors' and the '\-a' option.
+.IP
+make_emperor \fB\-i\fR unweighted_unifrac_pc.txt \fB\-m\fR Fasting_Map.txt \fB\-\-add_vectors\fR Treatment,DOB \fB\-a\fR DOB \fB\-o\fR sorted_by_DOB
+.PP
+Compare two coordinate files: To draw replicates of the same samples like for a procustes plot.
+.IP
+make_emperor \fB\-i\fR compare \fB\-m\fR Fasting_Map.txt \fB\-\-compare_plots\fR \fB\-o\fR comparison
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Print information during execution \fB\-\-\fR useful for
+debugging [default: False]
+.TP
+\fB\-\-number_of_axes\fR=\fINUMBER_OF_AXES\fR
+Number of axes to be incorporated in the plot. Only 3
+will be displayed at any given time but this option
+modifies how many axes you can use for your
+visualization. Note that Emperor will only use the
+axes that explain more than 0.5% (this will be shown
+as 1% in the GUI)of the variability [default: 10]
+.TP
+\fB\-a\fR CUSTOM_AXES, \fB\-\-custom_axes\fR=\fICUSTOM_AXES\fR
+Comma\-separated list of metadata categories to use as
+custom axes in the plot. For instance, if there is a
+time category and you would like to see the samples
+plotted on that axis instead of PC1, PC2, etc., you
+would pass time as the value of this option. Note: if
+there is any non\-numeric data in the metadata column,
+an error will be presented [default: none]
+.TP
+\fB\-\-add_unique_columns\fR
+Add to the output categories of the mapping file the
+columns where all values are different. Note: if the
+result of one of the concatenated fields in \fB\-\-color_by\fR
+is a column where all values are unique, the resulting
+column will get removed as well [default: False]
+.TP
+\fB\-\-add_vectors\fR=\fIADD_VECTORS\fR
+Comma\-sparated category(ies) used to add connecting
+lines (vectors) between samples. The first category
+specifies the samples that will be connected by the
+vectors, whilst the second category (optionally)
+determines the order in which the samples will be
+connected. [default: [None, None]]
+.TP
+\fB\-b\fR COLOR_BY, \fB\-\-color_by\fR=\fICOLOR_BY\fR
+Comma\-separated list of metadata categories (column
+headers) to color by in the plots. The categories must
+match the name of a column header in the mapping file
+exactly. Multiple categories can be listed by comma
+separating them without spaces. The user can also
+combine columns in the mapping file by separating the
+categories by "&&" without spaces. [default=color by
+all categories except ones where all values are
+different]
+.TP
+\fB\-\-biplot_fp\fR=\fIBIPLOT_FP\fR
+Output filepath that will contain the coordinates
+where each taxonomic sphere is centered. [default:
+none]
+.TP
+\fB\-c\fR, \fB\-\-compare_plots\fR
+Passing a directory with the \fB\-i\fR (\fB\-\-input_coords\fR)
+option in combination with this flag results in a set
+of bars connecting the replicated samples across all
+the input files. [default=False]
+.TP
+\fB\-e\fR ELLIPSOID_METHOD, \fB\-\-ellipsoid_method\fR=\fIELLIPSOID_METHOD\fR
+Used only when plotting ellipsoids for jackknifed beta
+diversity (i.e. using a directory of coord files
+instead of a single coord file). Valid values are
+"IQR" (for inter\-quartile ranges) and "sdev" (for
+standard deviation). [default=IQR]
+.TP
+\fB\-\-ignore_missing_samples\fR
+This will overpass the error raised when the
+coordinates file contains samples that are not present
+in the mapping file. Be aware that this is very
+misleading as the PCoA is accounting for all the
+samples and removing some samples could lead to
+erroneous/skewed interpretations.
+.TP
+\fB\-n\fR N_TAXA_TO_KEEP, \fB\-\-n_taxa_to_keep\fR=\fIN_TAXA_TO_KEEP\fR
+Number of taxonomic groups from the "\-\-taxa_fp" file
+to display. Passing "\-1" will cause to display all the
+taxonomic groups, this option is only used when
+creating BiPlots. [default=10]
+.TP
+\fB\-s\fR MASTER_PCOA, \fB\-\-master_pcoa\fR=\fIMASTER_PCOA\fR
+Used only when the input is a directory of coordinate
+files i. e. for jackknifed beta diversity plot or for
+a coordinate comparison plot (procrustes analysis).
+The coordinates in this file will be the center of
+each ellipsoid in the case of a jackknifed PCoA plot
+or the center where the connecting arrows originate
+from for a comparison plot. [default: arbitrarily
+selected file from the input directory for a
+jackknifed plot or None for a comparison plot in this
+case one file will be connected to the next one and so
+on]
+.TP
+\fB\-t\fR TAXA_FP, \fB\-\-taxa_fp\fR=\fITAXA_FP\fR
+Path to a summarized taxa file (i. e. the output of
+summarize_taxa.py). This option is only used when
+creating BiPlots. [default=none]
+.TP
+\fB\-x\fR MISSING_CUSTOM_AXES_VALUES, \fB\-\-missing_custom_axes_values\fR=\fIMISSING_CUSTOM_AXES_VALUES\fR
+Option to override the error shown when the catergory
+used in '\-\-custom_axes' has non\-numeric values in the
+mapping file. The basic format is
+custom_axis:new_value. For example, if you want to
+plot in time 0 all the samples that do not have a
+numeric value in the column Time. you would pass \fB\-x\fR
+"Time:0". Additionally, you can pass this format custo
+m_axis:other_column==value_in_other_column=new_value,
+with this format you can specify different values
+(new_value) to use in the substitution based on other
+column (other_column) value (value_in_other_column);
+see example above. This option could be used in all
+explicit axes.
+.TP
+\fB\-o\fR OUTPUT_DIR, \fB\-\-output_dir\fR=\fIOUTPUT_DIR\fR
+path to the output directory that will contain the
+PCoA plot. [default: emperor]
+.TP
+\fB\-\-number_of_segments\fR=\fINUMBER_OF_SEGMENTS\fR
+the number of segments to generate any spheres, this
+includes the samples, the taxa (biplots), and the
+confidence intervals (jackknifing). Higher values will
+result in better quality but can make the plots less
+responsive, also it will make the resulting SVG images
+bigger. The value should be between 4 and 14.
+[default: 8]
+.IP
+REQUIRED options:
+.IP
+The following options must be provided under all circumstances.
+.TP
+\fB\-i\fR INPUT_COORDS, \fB\-\-input_coords\fR=\fIINPUT_COORDS\fR
+Depending on the plot to be generated, can be one of
+the following: (1) Filepath of a coordinates file to
+create a PCoA plot. (2) Directory path to a folder
+containing coordinates files to create a jackknifed
+PCoA plot. (3) Directory path to a folder containing
+coordinates files to compare the coordinates there
+contained when \fB\-\-compare_plots\fR is enabled (useful for
+procustes analysis plots). For directories: hidden
+files, sub\-directories and files suffixed as
+\&'_procrustes_results.txt' [REQUIRED]
+.TP
+\fB\-m\fR MAP_FP, \fB\-\-map_fp\fR=\fIMAP_FP\fR
+path to a metadata mapping file [REQUIRED]
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..d2cbf45
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/make_emperor.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..bce2b97
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+#Allowing this to be overridden by environemnt helps with backports
+DEB_PYTHON_SUPPORT?=python2
+
+%:
+ dh $@ --with $(DEB_PYTHON_SUPPORT)
+
+override_dh_auto_install:
+ dh_auto_install
+ #Shunt support_files to /usr/share
+ ( cd debian/emperor/usr/lib/python*/dist-packages/emperor && \
+ mkdir -p ../../../../share/emperor ; \
+ mv support_files ../../../../share/emperor ; \
+ ln -s ../../../../share/emperor/support_files )
+ ( cd debian/emperor/usr/bin ; \
+ mv make_emperor.py make_emperor )
+
+override_dh_installdocs:
+ cp -rp doc html
+ dh_installdocs
+
+override_dh_clean:
+ dh_clean
+ rm -rf html
+
+#Don't compress .js files
+override_dh_compress:
+ dh_compress -X.js
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..3849ecf
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+https://pypi.python.org/pypi/emperor/ .*/emperor-([.0-9]+)\.(?:tgz|tar.gz|tar.bz2)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/emperor.git
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