[med-svn] r18720 - in trunk/packages/macsyfinder/trunk: . debian debian/source
Néron Bertrand
bneron-guest at moszumanska.debian.org
Sun Feb 1 15:50:39 UTC 2015
Author: bneron-guest
Date: 2015-02-01 15:50:38 +0000 (Sun, 01 Feb 2015)
New Revision: 18720
Added:
trunk/packages/macsyfinder/trunk/debian/
trunk/packages/macsyfinder/trunk/debian/changelog
trunk/packages/macsyfinder/trunk/debian/compat
trunk/packages/macsyfinder/trunk/debian/control
trunk/packages/macsyfinder/trunk/debian/copyright
trunk/packages/macsyfinder/trunk/debian/macsyfinder.1
trunk/packages/macsyfinder/trunk/debian/macsyfinder.doc-base
trunk/packages/macsyfinder/trunk/debian/macsyfinder.links
trunk/packages/macsyfinder/trunk/debian/macsyfinder.manpages
trunk/packages/macsyfinder/trunk/debian/rules
trunk/packages/macsyfinder/trunk/debian/source/
trunk/packages/macsyfinder/trunk/debian/source/format
trunk/packages/macsyfinder/trunk/debian/substvars
trunk/packages/macsyfinder/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (1.0.2-1) to trunk
Property changes on: trunk/packages/macsyfinder/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/macsyfinder/trunk/debian/changelog
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/changelog (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/changelog 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,6 @@
+macsyfinder (1.0.2-1) UNRELEASED; urgency=medium
+
+ * first package import (Closes: #776722).
+
+ -- bertrand Neron <bneron at pasteur.fr> Sat, 31 Jan 2015 15:31:23 +0100
+
Added: trunk/packages/macsyfinder/trunk/debian/compat
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/compat (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/compat 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1 @@
+9
Added: trunk/packages/macsyfinder/trunk/debian/control
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/control (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/control 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,27 @@
+Source: macsyfinder
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Bertrand Neron <bneron at pasteur.fr>
+Build-Depends: debhelper (>= 9), python (>= 2.7),
+ python-sphinx,
+ texlive-latex-recommended, texlive-latex-extra, texlive-fonts-recommended
+Standards-Version: 3.9.6
+#Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava3/trunk/
+#Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava3/trunk/
+Homepage: https://github.com/gem-pasteur/macsyfinder
+
+Package: macsyfinder
+Architecture: all
+Depends: ${python:Depends}, ${misc:Depends},
+ hmmer, ncbi-blast+
+Description: Detection of macromolecular systems in protein datasets.
+ MacSyFinder is a program to model and detect macromolecular systems,
+ genetic pathways... in protein datasets. In prokaryotes, these systems
+ have often evolutionarily conserved properties: they are made of conserved
+ components, and are encoded in compact loci (conserved genetic architecture).
+ The user models these systems with MacSyFinder to reflect these conserved
+ features, and to allow their efficient detection
+ .
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
Added: trunk/packages/macsyfinder/trunk/debian/copyright
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/copyright (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/copyright 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: macsyfinder
+Source: https://github.com/gem-pasteur/macsyfinder
+
+Files: *
+Copyright: 2014 Institut Pasteur (Paris) and CNRS.
+License: GPL-3
+
+Files: debian/*
+Copyright: 2015 Institut Pasteur (Paris)
+License: GPL-3
+
+License: GPL-3
+ The source code of MacSyFinder and MacSyView is distributed
+ under the terms of the GNU GeneralPublic License.
+ See the file COPYING for details.
+ These programs are free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation version 3 of the License.
+ These programs are distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ A copy of the GNU General Public License is in the file COPYING. You
+ may also obtain a copy from <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
Added: trunk/packages/macsyfinder/trunk/debian/macsyfinder.1
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/macsyfinder.1 (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/macsyfinder.1 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,202 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
+.TH MACSYFINDER "1" "January 2015" "macsyfinder 1.0.2" "User Commands"
+.SH NAME
+macsyfinder \- manual page for macsyfinder 1.0.2
+.SH DESCRIPTION
+usage: macsyfinder [\-h] [\-\-sequence\-db SEQUENCE_DB]
+.IP
+[\-\-db\-type {unordered_replicon,ordered_replicon,gembase,unordered}]
+[\-\-replicon\-topology {linear,circular}]
+[\-\-topology\-file TOPOLOGY_FILE] [\-\-idx]
+[\-\-inter\-gene\-max\-space INTER_GENE_MAX_SPACE INTER_GENE_MAX_SPACE]
+[\-\-min\-mandatory\-genes\-required MIN_MANDATORY_GENES_REQUIRED MIN_MANDATORY_GENES_REQUIRED]
+[\-\-min\-genes\-required MIN_GENES_REQUIRED MIN_GENES_REQUIRED]
+[\-\-max\-nb\-genes MAX_NB_GENES MAX_NB_GENES]
+[\-\-multi\-loci MULTI_LOCI] [\-\-hmmer HMMER_EXE]
+[\-\-index\-db INDEX_DB_EXE] [\-\-e\-value\-search E_VALUE_RES]
+[\-\-i\-evalue\-select I_EVALUE_SEL]
+[\-\-coverage\-profile COVERAGE_PROFILE] [\-d DEF_DIR]
+[\-o OUT_DIR] [\-r RES_SEARCH_DIR]
+[\-\-res\-search\-suffix RES_SEARCH_SUFFIX]
+[\-\-res\-extract\-suffix RES_EXTRACT_SUFFIX] [\-p PROFILE_DIR]
+[\-\-profile\-suffix PROFILE_SUFFIX] [\-w WORKER_NB] [\-v]
+[\-\-log LOG_FILE] [\-\-config CFG_FILE]
+[\-\-previous\-run PREVIOUS_RUN]
+systems [systems ...]
+.PP
+MacSyFinder is a tool for the detection of protein secretion systems
+of diderm bacteria from a protein dataset.
+.SS "positional arguments:"
+.TP
+systems
+The systems to detect. This is an obligatory option
+with no keyword associated to it. To detect all the
+protein secretion systems and related appendages: set
+to "all" (case insensitive). Otherwise, a single or
+multiple systems can be specified. For example: "T2SS
+T4P".
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "Input dataset options:"
+.TP
+\fB\-\-sequence\-db\fR SEQUENCE_DB
+Path to the sequence dataset in fasta format.
+.TP
+\fB\-\-db\-type\fR {unordered_replicon,ordered_replicon,gembase,unordered}
+The type of dataset to deal with. "unordered_replicon"
+corresponds to a non\-assembled genome, "unordered" to
+a metagenomic dataset, "ordered_replicon" to an
+assembled genome, and "gembase" to a set of replicons
+where sequence identifiers follow this convention:
+">RepliconName SequenceID".
+.TP
+\fB\-\-replicon\-topology\fR {linear,circular}
+The topology of the replicons (this option is
+meaningful only if the db_type is 'ordered_replicon'
+or 'gembase'.
+.TP
+\fB\-\-topology\-file\fR TOPOLOGY_FILE
+Topology file path. The topology file allows one to
+specify a topology (linear or circular) for each
+replicon (this option is meaningful only if the
+db_type is 'ordered_replicon' or 'gembase'. A topology
+file is a tabular file with two columns: the 1st is
+the replicon name, and the 2nd the corresponding
+topology: "RepliconA linear"
+.TP
+\fB\-\-idx\fR
+Forces to build the indexes for the sequence dataset
+even if they were presviously computed and present at
+the dataset location (default = False)
+.SS "Systems detection options:"
+.TP
+\fB\-\-inter\-gene\-max\-space\fR INTER_GENE_MAX_SPACE INTER_GENE_MAX_SPACE
+Co\-localization criterion: maximum number of
+components non\-matched by a profile allowed between
+two matched components for them to be considered
+contiguous. Option only meaningful for 'ordered'
+datasets. The first value must match to a system, the
+second to a number of components. This option can be
+repeated several times: "\-\-inter\-gene\-max\-space T2SS
+12 \fB\-\-inter\-gene\-max\-space\fR Flagellum 20"
+.TP
+\fB\-\-min\-mandatory\-genes\-required\fR MIN_MANDATORY_GENES_REQUIRED MIN_MANDATORY_GENES_REQUIRED
+The minimal number of mandatory genes required for
+system assessment. The first value must correspond to
+a system name, the second value to an integer. This
+option can be repeated several times: "\-\-minmandatory\-genes\-required T2SS 15 \fB\-\-min\-mandatorygenes\-required\fR Flagellum 10"
+.TP
+\fB\-\-min\-genes\-required\fR MIN_GENES_REQUIRED MIN_GENES_REQUIRED
+The minimal number of genes required for system
+assessment (includes both 'mandatory' and 'accessory'
+components). The first value must correspond to a
+system name, the second value to an integer. This
+option can be repeated several times: "\-\-min\-genesrequired T2SS 15 \fB\-\-min\-genes\-required\fR Flagellum 10"
+.TP
+\fB\-\-max\-nb\-genes\fR MAX_NB_GENES MAX_NB_GENES
+The maximal number of genes required for system
+assessment. The first value must correspond to a
+system name, the second value to an integer. This
+option can be repeated several times: "\-\-max\-nb\-genes
+T2SS 5 \fB\-\-max\-nb\-genes\fR Flagellum 10
+.TP
+\fB\-\-multi\-loci\fR MULTI_LOCI
+Allow the storage of multi\-loci systems for the
+specified systems. The systems are specified as a
+comma separated list (\fB\-\-multi\-loci\fR sys1,sys2) default
+is False
+.SS "Options for Hmmer execution and hits filtering:"
+.TP
+\fB\-\-hmmer\fR HMMER_EXE
+Path to the Hmmer program.
+.TP
+\fB\-\-index\-db\fR INDEX_DB_EXE
+The indexer to be used for Hmmer. The value can be
+either 'makeblastdb' or 'formatdb' or the path to one
+of these binary (default = makeblastb)
+.TP
+\fB\-\-e\-value\-search\fR E_VALUE_RES
+Maximal e\-value for hits to be reported during Hmmer
+search. (default = 1)
+.TP
+\fB\-\-i\-evalue\-select\fR I_EVALUE_SEL
+Maximal independent e\-value for Hmmer hits to be
+selected for system detection. (default = 0.001)
+.TP
+\fB\-\-coverage\-profile\fR COVERAGE_PROFILE
+Minimal profile coverage required in the hit alignment
+to allow the hit selection for system detection.
+(default = 0.5)
+.SS "Path options:"
+.TP
+\fB\-d\fR DEF_DIR, \fB\-\-def\fR DEF_DIR
+Path to the systems definition files.
+.TP
+\fB\-o\fR OUT_DIR, \fB\-\-out\-dir\fR OUT_DIR
+Path to the directory where to store results. if outdir is specified res\-search\-dir will be ignored.
+.TP
+\fB\-r\fR RES_SEARCH_DIR, \fB\-\-res\-search\-dir\fR RES_SEARCH_DIR
+Path to the directory where to store MacSyFinder
+search results directories (default current working
+directory).
+.TP
+\fB\-\-res\-search\-suffix\fR RES_SEARCH_SUFFIX
+The suffix to give to Hmmer raw output files.
+.TP
+\fB\-\-res\-extract\-suffix\fR RES_EXTRACT_SUFFIX
+The suffix to give to filtered hits output files.
+.TP
+\fB\-p\fR PROFILE_DIR, \fB\-\-profile\-dir\fR PROFILE_DIR
+Path to the profiles directory.
+.TP
+\fB\-\-profile\-suffix\fR PROFILE_SUFFIX
+The suffix of profile files. For each 'Gene' element,
+the corresponding profile is searched in the
+\&'profile_dir', in a file which name is based on the
+Gene name + the profile suffix. For instance, if the
+Gene is named 'gspG' and the suffix is '.hmm3', then
+the profile should be placed at the specified location
+and be named 'gspG.hmm3'
+.SS "General options:"
+.TP
+\fB\-w\fR WORKER_NB, \fB\-\-worker\fR WORKER_NB
+Number of workers to be used by MacSyFinder. In the
+case the user wants to run MacSyFinder in a multithread mode. (0 mean all cores will be used, default
+1)
+.TP
+\fB\-v\fR, \fB\-\-verbosity\fR
+Increases the verbosity level. There are 4 levels:
+Error messages (default), Warning (\fB\-v\fR), Info (\fB\-vv\fR) and
+Debug.(\fB\-vvv\fR)
+.TP
+\fB\-\-log\fR LOG_FILE
+Path to the directory where to store the
+\&'macsyfinder.log' log file.
+.TP
+\fB\-\-config\fR CFG_FILE
+Path to a putative MacSyFinder configuration file to
+be used.
+.TP
+\fB\-\-previous\-run\fR PREVIOUS_RUN
+Path to a previous MacSyFinder run directory. It
+allows one to skip the Hmmer search step on same dataset,
+as it uses previous run results and thus parameters
+regarding Hmmer detection. The configuration file from
+this previous run will be used. (conflict with options
+\fB\-\-config\fR, \fB\-\-sequence\-db\fR, \fB\-\-profile\-suffix\fR, \fB\-\-resextract\-suffix\fR, \fB\-\-e\-value\-res\fR, \fB\-\-db\-type\fR, \fB\-\-hmmer\fR)
+.PP
+For more details, visit the MacSyFinder website and see the MacSyFinder documentation.
+.SH "SEE ALSO"
+The full documentation for
+.B macsyfinder
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B macsyfinder
+programs are properly installed at your site, the command
+.IP
+.B info macsyfinder
+.PP
+should give you access to the complete manual.
Added: trunk/packages/macsyfinder/trunk/debian/macsyfinder.doc-base
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/macsyfinder.doc-base (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/macsyfinder.doc-base 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,19 @@
+Document: macsyfinder
+Title: MacSyFinder
+Author: Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC
+Abstract: MacSyFinder - Detection of macromolecular systems in protein datasets.
+ MacSyFinder is a program to model and detect macromolecular systems,
+ genetic pathways... in protein dataset using systems modelling and similarity
+ search. In prokaryotes, these systems have often evolutionarily conserved
+ properties: they are made of conserved components, and are encoded in
+ compact loci (conserved genetic architecture).
+ The user models these systems with MacSyFinder to reflect these conserved
+ features, and to allow their efficient detection.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/macsyfinder/html/*
+Index: /usr/share/doc/macsyfinder/html/index.html
+
+Format:pdf
+Files: /usr/share/doc/macsyfinder/pdf/Macsyfinder.pdf.gz
Added: trunk/packages/macsyfinder/trunk/debian/macsyfinder.links
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/macsyfinder.links (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/macsyfinder.links 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,3 @@
+usr/share/javascript/jquery/jquery.js usr/share/doc/macsyfinder/html/_static/jquery.js
+usr/share/javascript/underscore/undscore.js usr/share/doc/macsyfinder/html/_static/underscore.js
+
Added: trunk/packages/macsyfinder/trunk/debian/macsyfinder.manpages
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/macsyfinder.manpages (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/macsyfinder.manpages 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/macsyfinder/trunk/debian/rules
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/rules (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/rules 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with python2
+
+override_dh_auto_install:
+ cd doc && make html
+ cd doc && make latexpdf
+ python setup.py install --prefix=debian/macsyfinder/usr/ --install-conf=debian/macsyfinder/etc/ --no-viewer
+ mv debian/macsyfinder/etc/macsyfinder/macsyfinder.conf.new debian/macsyfinder/etc/macsyfinder/macsyfinder.conf
+ rm debian/macsyfinder/usr/share/doc/macsyfinder/html/_static/jquery.js
+ rm debian/macsyfinder/usr/share/doc/macsyfinder/html/_static/underscore.js
+ rm -Rf debian/macsyfinder/usr/share/macsyfinder/macsyview
+
+override_dh_clean:
+ rm -Rf doc/_build
+ rm -f uninstall.cfg
+ rm -f uninstall_files
+ dh_clean
Property changes on: trunk/packages/macsyfinder/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/macsyfinder/trunk/debian/source/format
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/source/format (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/source/format 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/macsyfinder/trunk/debian/substvars
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/substvars (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/substvars 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1 @@
+misc:Depends=
Added: trunk/packages/macsyfinder/trunk/debian/watch
===================================================================
--- trunk/packages/macsyfinder/trunk/debian/watch (rev 0)
+++ trunk/packages/macsyfinder/trunk/debian/watch 2015-02-01 15:50:38 UTC (rev 18720)
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/gem-pasteur/macsyfinder/tags .*/macsyfinder-?(\d\S*)\.tar\.gz
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