[med-svn] r12326 - in trunk/packages/ltrsift/trunk/debian: . man man-src

Mon Oct 8 07:03:44 UTC 2012

Author: sascha-guest
Date: 2012-10-08 07:03:43 +0000 (Mon, 08 Oct 2012)
New Revision: 12326

Added:
   trunk/packages/ltrsift/trunk/debian/DRAFT
   trunk/packages/ltrsift/trunk/debian/ltrsift.manpages
   trunk/packages/ltrsift/trunk/debian/man-src/
   trunk/packages/ltrsift/trunk/debian/man-src/ltrsift.1.txt
   trunk/packages/ltrsift/trunk/debian/man-src/ltrsift_encode.1.txt
   trunk/packages/ltrsift/trunk/debian/man/
   trunk/packages/ltrsift/trunk/debian/man/ltrsift.1
   trunk/packages/ltrsift/trunk/debian/man/ltrsift_encode.1
Modified:
   trunk/packages/ltrsift/trunk/debian/control
   trunk/packages/ltrsift/trunk/debian/copyright
   trunk/packages/ltrsift/trunk/debian/ltrsift.docs
   trunk/packages/ltrsift/trunk/debian/ltrsift.install
Log:
add manpages


Added: trunk/packages/ltrsift/trunk/debian/DRAFT
===================================================================

--- trunk/packages/ltrsift/trunk/debian/DRAFT	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/DRAFT	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1 @@
+This is a draft for an upcoming LTRsift package.

Modified: trunk/packages/ltrsift/trunk/debian/control
===================================================================
--- trunk/packages/ltrsift/trunk/debian/control	2012-10-08 06:05:54 UTC (rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/control	2012-10-08 07:03:43 UTC (rev 12326)
@@ -13,7 +13,7 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2), libgtk2.0-0,
  libglib2.0-0, last-align, ncbi-blast+
-Description: semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations
+Description: postprocessing of LTR retrotransposons
  LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
  novo predicted LTR retrotransposon annotations, such as the ones generated by
  LTRharvest and LTRdigest. Its user-friendly interface displays LTR
@@ -26,7 +26,7 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
 Section: debug
-Description: semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations, with debug symbols
+Description: postprocessing of LTR retrotransposons, with debug symbols
  This package contains debug information stripped from LTRsift.
  You may decide to install it to help identifying issues, typically
  to help communication with upstream developers.

Modified: trunk/packages/ltrsift/trunk/debian/copyright
===================================================================
--- trunk/packages/ltrsift/trunk/debian/copyright	2012-10-08 06:05:54 UTC (rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/copyright	2012-10-08 07:03:43 UTC (rev 12326)
@@ -21,27 +21,3 @@
  .
  On Debian systems, the complete text of the GNU General
  Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# If you want to use GPL v2 or later for the /debian/* files use 
-# the following clauses, or change it to suit. Delete these two lines
-Files: debian/*
-Copyright: 2012 Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
-License: GPL-2+
- This package is 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; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is 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.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.

Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.docs
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.docs	2012-10-08 06:05:54 UTC (rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.docs	2012-10-08 07:03:43 UTC (rev 12326)
@@ -1,4 +1,2 @@
-CHANGELOG
 README
-LICENSE
 VERSION

Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.install
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.install	2012-10-08 06:05:54 UTC (rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.install	2012-10-08 07:03:43 UTC (rev 12326)
@@ -1,5 +1,9 @@
 usr/bin/ltrsift
 usr/bin/ltrsift_encode
-usr/sample_data usr/share/ltrsift
+usr/sample_data/clean_encseqs usr/share/ltrsift/sample_data/clean_encseqs
+usr/sample_data/prepare_encseqs usr/share/ltrsift/sample_data/prepare_encseqs
+usr/sample_data/dmel58.ltrd.gff3 usr/share/ltrsift/sample_data/dmel58.ltrd.gff3
+usr/sample_data/dmel-2L-chromosome-r5.8.fasta.gz usr/share/ltrsift/sample_data/dmel-2L-chromosome-r5.8.fasta.gz
+usr/sample_data/README usr/share/ltrsift/sample_data/README
 usr/filters usr/share/ltrsift
 

Added: trunk/packages/ltrsift/trunk/debian/ltrsift.manpages
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.manpages	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.manpages	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1 @@
+debian/man/*

Added: trunk/packages/ltrsift/trunk/debian/man/ltrsift.1
===================================================================
--- trunk/packages/ltrsift/trunk/debian/man/ltrsift.1	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/man/ltrsift.1	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1,45 @@
+'\" t
+.\"     Title: ltrsift
+.\"    Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 10/07/2012
+.\"    Manual: \ \&
+.\"    Source: \ \&
+.\"  Language: English
+.\"
+.TH "LTRSIFT" "1" "10/07/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ltrsift \- a graphical interface for postprocessing and classification of LTR retrotransposon candidates
+.SH "SYNOPSIS"
+.sp
+ltrsift
+.SH "DESCRIPTION"
+.sp
+LTRsift is a graphical desktop tool for semi\-automatic postprocessing of de novo predicted LTR retrotransposon annotations, such as the ones generated by LTRharvest and LTRdigest\&.
+.SH "CONFIGURATION"
+.sp
+The LAST binaries (lastal and lastdb) should be located in the system search path\&. If they are not, is it possible to specify their location using the \(lqGT_LAST_PATH" environment variable prior to running LTRsift\&. The same applies for the BLAST location\&. Use ``GT_BLAST_PATH\(rq to specify the the full path to the \(lqblastall\(rq executable\&.
+.sp
+Style files (describing how the linear diagram of the candidate features look like) can be set via the LTRSIFT_STYLE_FILE environment variable\&. A sensible default style is built into LTRsift\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <steinbiss at zbh\&.uni\-hamburg\&.de>\&.

Added: trunk/packages/ltrsift/trunk/debian/man/ltrsift_encode.1
===================================================================
--- trunk/packages/ltrsift/trunk/debian/man/ltrsift_encode.1	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/man/ltrsift_encode.1	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1,40 @@
+'\" t
+.\"     Title: ltrsift-encode
+.\"    Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 10/07/2012
+.\"    Manual: \ \&
+.\"    Source: \ \&
+.\"  Language: English
+.\"
+.TH "LTRSIFT\-ENCODE" "1" "10/07/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ltrsift_encode \- encode sequences into a LTRsift\-compatible format
+.SH "SYNOPSIS"
+.sp
+ltrsift_encode <sequence file> <indexname>
+.SH "DESCRIPTION"
+.sp
+This command creates an index with name <indexname> from the FASTA/EMBL/GenBank file <sequence file>\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <steinbiss at zbh\&.uni\-hamburg\&.de>\&.

Added: trunk/packages/ltrsift/trunk/debian/man-src/ltrsift.1.txt
===================================================================
--- trunk/packages/ltrsift/trunk/debian/man-src/ltrsift.1.txt	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/man-src/ltrsift.1.txt	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1,37 @@
+LTRSIFT(1)
+==========
+
+NAME
+----
+ltrsift - a graphical interface for postprocessing and classification of
+LTR retrotransposon candidates
+
+
+SYNOPSIS
+--------
+ltrsift
+
+
+DESCRIPTION
+-----------
+LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
+novo predicted LTR retrotransposon annotations, such as the ones generated by
+LTRharvest and LTRdigest.
+
+CONFIGURATION
+-------------
+
+The LAST binaries (lastal and lastdb) should be located in the system
+search path. If they are not, is it possible to specify their location
+using the ``GT_LAST_PATH" environment variable prior to running LTRsift.
+The same applies for the BLAST location. Use ``GT_BLAST_PATH'' to specify
+the the full path to the ``blastall'' executable.
+
+Style files (describing how the linear diagram of the candidate features
+look like) can be set via the LTRSIFT_STYLE_FILE environment variable.
+A sensible default style is built into LTRsift.
+
+
+AUTHOR
+------
+Report bugs to <steinbiss at zbh.uni-hamburg.de>.

Added: trunk/packages/ltrsift/trunk/debian/man-src/ltrsift_encode.1.txt
===================================================================
--- trunk/packages/ltrsift/trunk/debian/man-src/ltrsift_encode.1.txt	                        (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/man-src/ltrsift_encode.1.txt	2012-10-08 07:03:43 UTC (rev 12326)
@@ -0,0 +1,22 @@
+LTRSIFT-ENCODE(1)
+=================
+
+NAME
+----
+ltrsift_encode - encode sequences into a LTRsift-compatible format
+
+
+SYNOPSIS
+--------
+ltrsift_encode <sequence file> <indexname>
+
+
+DESCRIPTION
+-----------
+This command creates an index with name <indexname> from the
+FASTA/EMBL/GenBank file <sequence file>.
+
+
+AUTHOR
+------
+Report bugs to <steinbiss at zbh.uni-hamburg.de>.


