[med-svn] r6029 - in trunk/packages/transtermhp/trunk: . debian debian/patches debian/source
Alexandre Mestiashvili
malex-guest at alioth.debian.org
Sat Feb 19 15:14:06 UTC 2011
Author: malex-guest
Date: 2011-02-19 15:14:02 +0000 (Sat, 19 Feb 2011)
New Revision: 6029
Added:
trunk/packages/transtermhp/trunk/debian/
trunk/packages/transtermhp/trunk/debian/README.Debian
trunk/packages/transtermhp/trunk/debian/README.source
trunk/packages/transtermhp/trunk/debian/changelog
trunk/packages/transtermhp/trunk/debian/compat
trunk/packages/transtermhp/trunk/debian/control
trunk/packages/transtermhp/trunk/debian/copyright
trunk/packages/transtermhp/trunk/debian/docs
trunk/packages/transtermhp/trunk/debian/patches/
trunk/packages/transtermhp/trunk/debian/patches/missing_headers
trunk/packages/transtermhp/trunk/debian/patches/series
trunk/packages/transtermhp/trunk/debian/rules
trunk/packages/transtermhp/trunk/debian/source/
trunk/packages/transtermhp/trunk/debian/source/format
trunk/packages/transtermhp/trunk/debian/transtermhp.dirs
trunk/packages/transtermhp/trunk/debian/transtermhp.install
trunk/packages/transtermhp/trunk/debian/watch
Log:
Added: trunk/packages/transtermhp/trunk/debian/README.Debian
===================================================================
--- trunk/packages/transtermhp/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/README.Debian 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,387 @@
+transtermhp for Debian
+----------------------
+TransTermHP Version 2.07
+
+CONTENTS
+ 0. LICENSE & CREDITS
+ 1. INSTALLATION
+ 2. TRANSTERM USAGE
+ 3. FORMAT OF THE TRANSTERM OUTPUT
+ 4. TRANSTERM COMMAND LINE OPTIONS
+ 5. RECALIBRATING USING DIFFERENT PARAMETERS
+ 6. FORMAT OF THE EXPTERMS.DAT FILE
+ 7. PORTING NOTES
+ 8. 2NDSCORE PROGRAM
+ 9. FORMAT OF .BAG FILES
+ 10. USING TRANSTERM WITHOUT GENOME ANNOTATIONS
+
+0. LICENSE & CREDITS
+
+TransTermHP v. 2.0 is a complete rewrite by Carl Kingsford of TransTerm v. 1.0,
+originally written by Maria D. Ermolaeva. The first TransTermHP was described in
+the paper:
+
+ [1] Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and
+ Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial
+ Genomes. J Mol Biol 301, (1), 27-33 (2000)
+
+TransTermHP v 2.0 is free software and is distributed under the GNU Public
+License. See the file LICENSE.txt included with TransTermHP for complete
+details.
+
+
+1. INSTALLATION
+
+At present, TransTermHP has only been tested on UNIX-like systems with the
+GCC/G++ compiler. To compile TransTermHP on such a system, "cd" into the
+TransTermHP src directory, and type:
+
+ make clean transterm
+
+If there are no errors reported, there should be a "transterm" executable file
+in the same directory. You can move this executable anyplace that is
+convenient. To save space, you can type:
+
+ make no_obj
+
+to remove all the .o files that were created during compilation.
+
+If you want to use TransTermHP on a non-UNIX-like system, see 'PORTING NOTES'
+below for some tips.
+
+
+2. TRANSTERM USAGE
+
+The standard usage of TransTermHP is:
+
+ transterm -p expterm.dat seq.fasta annotation.ptt > output.tt
+
+Any number of fasta and annotation files can be listed but fasta files should
+come before annotation files. The type of the file is determined by the
+extension:
+
+ .ptt a GenBank ptt annotation file
+ .coords or .crd a simple annotation file
+
+Each line of a .coords or .crd file has the format:
+
+ gene_name start end chrom_id
+
+The chrom_id specifies which sequence the annotation should apply to. For a
+.ptt file, the chrom_id is taken to be the filename with the path and
+extension removed. A filename with any other extension is assumed to be a
+fasta file.
+
+When processing an annotation for a chromosom with id = ID, the first word of
+the '>' lines of the input sequences are searched for ID. Because there is no
+good standard for how the '>' line is formated, several heuristics are tried
+to find ID in the '>' line. In the order tried, they are:
+
+ >ID
+ >junk|cmr:ID|junk or junk|ID|junk
+ >junk|gi|ID|junk or >junk|gi|ID.junk|junk
+ >junk:ID
+
+The option '-p expterm.dat' uses the newest confidence scheme, where
+expterm.dat is the path to the file of that name supplied with TransTermHP. If
+'-p expterm.dat' is omited, the version 1.0 confidence scheme is used. See
+section 'COMMAND LINE OPTIONS' for more detail.
+
+
+3. FORMAT OF THE TRANSTERM OUTPUT
+
+The organism's genes are listed sorted by their end coordinate and terminators
+are output between them. A terminator entry looks like this:
+
+ TERM 19 15310 - 15327 - F 99 -12.7 -4.0 |bidir
+ (name) (start - end) (sense)(loc) (conf) (hp) (tail) (notes)
+
+where 'conf' is the overall confidence score, 'hp' is the hairpin score, and
+'tail' is the tail score. 'Conf' (which ranges from 0 to 100) is what you
+probably want to use to assess the quality of a terminator. Higher is better.
+The confidence, hp score, and tail scores are described in the paper cited
+above. 'Loc' gives type of region the terminator is in:
+
+ 'G' = in the interior of a gene (at least 50bp from an end),
+ 'F' = between two +strand genes,
+ 'R' = between two -strand genes,
+ 'T' = between the ends of a +strand gene and a -strand gene,
+ 'H' = between the starts of a +strand gene and a -strand gene,
+ 'N' = none of the above (for the start and end of the DNA)
+
+Because of how overlapping genes are handled, these designations are not
+exclusive. 'G', 'F', or 'R' can also be given in lowercase, indicating that
+the terminator is on the opposite strand as the region. Unless the
+--all-context option is given, only candidate terminators that appear to be in
+an appropriate genome context (e.g. T, F, R) are output.
+
+Following the TERM line is the sequence of the hairpin and the 5' and 3'
+tails, always written 5' to 3'.
+
+
+4. TRANSTERM COMMAND LINE OPTIONS
+
+You can also set how large a hairpin must be to be considered:
+
+ --min-stem=n Stem must be n nucleotides long
+ --min-loop=n Loop portion of the hairpin must be at least n long
+
+You can also set the maximum size of the hairpin that will be found:
+
+ --max-len=n Total extent of hairpin <= n NT long
+ --max-loop=n The loop portion can be no longer than n
+
+The maximum length is the total length for the hairpin portion (2 stems, 1
+loop) and does not include the U-tail. It's measured in nuceotides in the
+input sequence, so because of gaps, the actual structure may be longer than
+max-len. Max-len must be less than the compiled-in constant REALLY_MAX_UP
+(which by default is 1000). To increase the size of structures found recompile
+after increasing this constant.
+
+TransTermHP assigns a score to the hairpin and tail portions of potential
+terminators. Lower scores are considered better. Many of the constants used in
+scoring hairpins can be set from the command line:
+
+ --gc=f Score of a G-C pair
+ --au=f Score of an A-U pair
+ --gu=f Score of a G-U pair
+ --mm=f Score of any other pair
+ --gap=f Score of a gap in the hairpin
+
+The cost of loops of various lengths can be set using:
+
+ --loop-penalty=f1,f2,f3,f4,f5,...fn
+
+where f1 is the cost of a loop of length --min-loop, f2 is the cost of a loop
+of length --min-loop+1, as so on. If there are too few terms to cover up to
+max-loop, the last term is repeated. Thus --loop-penalty=0,2 would assign cost
+0 to any loop of length min-loop, and 2 to any longer loop (up to max-loop,
+after which longer loops are given infinite scores). Extra terms are ignored.
+
+Note that if you are using the --pval-conf confidence scheme (see below), you
+must regenerate the expterm.dat file if you change any of the above constants.
+
+To weed out any potential terminator with tail or hairpin scores that are too
+large, you can use the following options:
+
+ --max-hp-score=f Maximum allowable hairpin score
+ --max-tail-score=f Maximum allowable tail score
+
+Terminator hairpins must be adjacent to a "U-rich" region. You can adjust the
+constants the define what constitutes a U-rich region. Using the options:
+
+ --uwin-size=s
+ --uwin-require=r
+
+requires that there are at least r 'U' nucleotides in the s-nucleotide-long
+window adjacent to the hairpin. Again, if you change these constants, you
+should regenerate expterms.dat.
+
+Before the main output, TransTermHP will output the values of the above options
+in a format suitable to be used on the command line.
+
+In addition to the tail and hairpin scores, each possible terminator is
+assigned a confidence --- a value between 0 and 100 that indicates how likely
+it is that the sequence is a terminator. The scoring scheme needs a background
+file (supplied with TransTermHP) that is specified using:
+
+ --pval-conf expterms.dat
+
+This will use the distribution in the file expterms.dat as the background. (You can
+abreivate this as "-p expterms.dat".) Though the supplied expterms.dat file is
+derived from random sequences, any background distribution can be used by
+supplying your own expterms.dat file. See below for the format of
+expterms.dat. The values in expterms.dat depend on the scoring constants,
+definition of u-rich regions, and the maximum allowed tail and hp scores.
+Thus, if you change any of these constants using the options above, you should
+regenerate expterms.dat.
+
+The main output of TransTermHP is a list of terminators interleaved between a
+listing of the gene annotations that were provided as input. This output can
+be customized in a few ways:
+
+ -S Don't output the terminator sequences
+ --min-conf=n Only output terminators with confidence >= n (can
+ abbreviate this as -c n; default is 76.)
+
+Additional analysis output can be obtained with the following options:
+
+ --bag-output file.bag Output the Best terminator After Gene
+ --t2t-perf file.t2t Output a summary of which tail-to-tail regions
+ have good terminators
+
+
+5. RECALIBRATING USING DIFFERENT PARAMETERS
+
+As mentioned above, if you change any of the basic scoring function and search
+parameters and are using the version 2.0 confidence scheme (recommended) then
+you have to recompute the values in the expterm.dat file. If you have python
+installed this is easy (though perhaps time consuming). You can issue the
+command:
+
+ % calibrate.sh newexpterms.dat [OPTIONS TO TRANSTERM]
+
+where "[OPTIONS TO TRANSTERM]" are TransTermHP options (discussed above) that
+set the parameters to what you want them to be. After calibrate.sh finishes,
+newexpterms.dat will be in the current directory and can serve as an argument
+to -p when using the same parameters you passed to calibrate.sh.
+
+Note that for the newexpterms.dat to be valid, you must supply the same basic
+parameters to TransTermHP on subsequent runs. TransTerm (or newexpterms.dat)
+will not remember these parameters for you. The best way to handle this is to
+make a shell script wrapper around transterm that always passes in your new
+parameters.
+
+Output formating parameters do not require regeneration of expterms.dat ---
+see discussion above for which parameters expterm.dat depends on.
+
+
+6. FORMAT OF THE EXPTERMS.DAT FILE
+
+The 'pval-conf' confidence scheme, selected with the option "--pval-conf
+expterms.dat" (or '-p expterms.dat') computes the confidence of a terminator
+with HP energy E and tail energy T as follows. First, the ranges of HP
+energies and tail energies are evenly divided into bins, and the appropriate
+bins e and t are found for E and T. Then the confidence is computed as
+described in [2].
+
+The first line of expterms.dat contains 6 numbers:
+
+ seqlen num_bins
+
+The (low_hp, high_hp) and (low_tail, high_tail) ranges give the bounds on the
+hairpin and tail scores. The integer num_bins gives the number of
+equally-sized bins into which those ranges are divided. Seqlen gives the
+length of the random sequence that was used to generate the data in the rest
+of the file.
+
+Following this line are any number of (at, R, M) triples, where 'at' is the AT
+content, R is a 4-tuple (low_hp, high_hp, low_tail, high_tail) giving the
+range of the HP and tail scores observed in random sequences of this AT
+content, and M is the distribution matrix. These (at, R, M) triples are
+formated as follows:
+
+ at low_hp high_hp low_tail high_tail
+ n11 n12 n13 n14 ... n1,num_bins
+ n21 ...
+ ...
+ n_num_bins,1 ...
+
+The mu_r(e,t) term is computed by selecting the matrix with the at value
+closest to the computed %AT of the region r. If the total length of region r
+sequence is L_r, then
+
+ mu_r(e,t) = n_t_e * L_r/seqlen
+
+where n_t_e is the entry in the t-th row and e-th column of the selected
+matrix, and seqlen is the first number in the first line of the file.
+
+
+7. PORTING NOTES
+
+If you want to run TransTermHP on a non-UNIX-like system, you should take note
+of the following:
+
+* gene-reader.cc assumes that the filename extension separators is "." and the
+ path separator is "/".
+
+* getopt_long() is used to process the command line arguments.
+
+
+8. 2NDSCORE PROGRAM
+
+The package also comes with a program '2ndscore' which will find the best
+hairpin anchored at each position. The basic usage is:
+
+ 2ndscore in.fasta > out.hairpins
+
+For every position in the sequence this will output a line:
+
+ -0.6 52 .. 62 TTCCTAAAGGTTCCA GCG CAAAA TGC CATAAGCACCACATT
+ (score) (start .. end) (left context) (hairpin) (right contenxt)
+
+For positions near the ends of the sequences, the context may be padded with
+'x' characters. If no hairpin can be found, the score will be 'None'.
+
+Multiple fasta files can be given and multiple sequences can be in each fasta
+file. The output for each sequence will be separated by a line starting with
+'>' and containing the FASTA description of the sequence.
+
+Because the hairpin scores of the plus-strand and minus-strand may differ (due
+to GU binding in RNA), by default 2ndscore outputs two sets of hairpins for
+every sequence: the FORWARD hairpins and the REVERSE hairpins. All the forward
+hairpins are output first, and are identified by having the word 'FORWARD' at
+the end of the '>' line preceding them. Similarly, the REVERSE hairpins are
+listed after a '>' line ending with 'REVERSE'. If you want to search only one
+or the other strand, you can use:
+
+ --no-fwd Don't print the FORWARD hairpins
+ --no-rvs Don't print the REVERSE hairpins
+
+You can set the energy function used, just as with transterm with the --gc,
+--au, --gu, --mm, --gap options. The --min-loop, --max-loop, and --max-len
+options are also supported.
+
+9. FORMAT OF THE .BAG FILES
+
+The columns for the .bag files are, in order:
+
+ 1. gene_name
+ 2. terminator_start
+ 3. terminator_end
+ 4. hairpin_score
+ 5. tail_score
+ 6. terminator_sequence
+
+ 7. terminator_confidence: a combination of the hairpin and tail score that
+ takes into account how likely such scores are in a random sequence. This
+ is the main "score" for the terminator and is computed as described in
+ the paper.
+
+ 8. APPROXIMATE_distance_from_end_of_gene: The *approximate* number of base
+ pairs between the end of the gene and the start of the terminator. This
+ is approximate in several ways: First, (and most important) TransTermHP
+ doesn't always use the real gene ends. Depending on the options you give
+ it may trim some off the ends of genes to handle terminators that
+ partially overlap with genes. Second, where the terminator "begins"
+ isn't that well defined. This field is intended only for a sanity check
+ (terminators reported to be the best near the ends of genes shouldn't be
+ _too far_ from the end of the gene).
+
+
+10. USING TRANSTERM WITHOUT GENOME ANNOTATIONS
+
+TransTermHP uses known gene information for only 3 things: (1) tagging the
+putative terminators as either "inside genes" or "intergenic," (2) choosing the
+background GC-content percentage to compute the scores, because genes often
+have different GC content than the intergenic regions, and (3) producing
+slightly more readable output. Items (1) and (3) are not really necessary, and
+(2) has no effect if your genes have about the same GC-content as your
+intergenic regions.
+
+Unfortunately, TransTermHP doesn't yet have a simple option to run without an
+annotation file (either .ptt or .coords), and requires at least 2 genes to be
+present. The solution is to create fake, small genes that flank each
+chromosome. To do this, make a fake.coords file that contains only these two
+lines:
+
+ fakegene1 1 2 chome_id
+ fakegene2 L-1 L chrom_id
+
+where L is the length of the input sequence and L-1 is 1 less than the length
+of the input sequence. "chrom_id" should be the word directly following the ">"
+in the .fasta file containing your sequence. (If, for example, your .fasta file
+began with ">seq1", then chrom_id = seq1).
+
+This creates a "fake" annotation with two 1-base-long genes flanking the
+sequence in a tail-to-tail arrangement: --> <--. TransTermHP can then be run
+with:
+
+ transterm -p expterm.dat sequence.fasta fake.coords
+
+If the G/C content of your intergenic regions is about the same as your genes,
+then this won't have too much of an effect on the scores terminators receive.
+On the other hand, this use of TransTermHP hasn't been tested much at all, so
+it's hard to vouch for its accuracy.
+
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Sat, 19 Feb 2011 12:36:10 +0000
Added: trunk/packages/transtermhp/trunk/debian/README.source
===================================================================
--- trunk/packages/transtermhp/trunk/debian/README.source (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/README.source 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,8 @@
+transtermhp for Debian
+----------------------
+
+test target is broken .
+
+
+
+
Added: trunk/packages/transtermhp/trunk/debian/changelog
===================================================================
--- trunk/packages/transtermhp/trunk/debian/changelog (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/changelog 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,5 @@
+transtermhp (2.0.7-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Sat, 19 Feb 2011 12:36:10 +0000
Added: trunk/packages/transtermhp/trunk/debian/compat
===================================================================
--- trunk/packages/transtermhp/trunk/debian/compat (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/compat 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1 @@
+7
Added: trunk/packages/transtermhp/trunk/debian/control
===================================================================
--- trunk/packages/transtermhp/trunk/debian/control (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/control 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,21 @@
+Source: transtermhp
+Section: science
+Priority: optional
+Maintainer: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Build-Depends: debhelper (>= 7.0.50~), quilt (>= 0.47)
+Standards-Version: 3.9.1
+Homepage: http://transterm.cbcb.umd.edu/index.php
+#Vcs-Git: git://git.debian.org/collab-maint/transtermhp.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/transtermhp.git;a=summary
+
+Package: transtermhp
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Finds rho-independent transcription terminators in bacterial genomes.
+ TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is
+ assigned a confidence value that estimates its probability of being a true terminator. TransTermHP is described in:
+ C. Kingsford, K. Ayanbule and S.L. Salzberg. Rapid, accurate, computational discovery of Rho-independent
+ transcription terminators illuminates their relationship to DNA uptake. Genome Biology 8:R22 (2007).
+ A predecessor system, TransTerm, that used very different search and scoring algorithms is described in:
+ Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription
+ Terminators in Bacterial Genomes. J Mol Biol 301, (1), 27-33 (2000)
Added: trunk/packages/transtermhp/trunk/debian/copyright
===================================================================
--- trunk/packages/transtermhp/trunk/debian/copyright (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/copyright 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,28 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: transterm_hp
+Source: http://transterm.cbcb.umd.edu/index.php
+
+Files: *
+Copyright: Steven Salzberg salzberg at umiacs.umd.edu
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ 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".
Added: trunk/packages/transtermhp/trunk/debian/docs
===================================================================
--- trunk/packages/transtermhp/trunk/debian/docs (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/docs 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,3 @@
+LICENSE.txt
+RELEASE-NOTES.txt
+USAGE.txt
Added: trunk/packages/transtermhp/trunk/debian/patches/missing_headers
===================================================================
--- trunk/packages/transtermhp/trunk/debian/patches/missing_headers (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/patches/missing_headers 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,46 @@
+Description: fixed missing headers in the source .
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-02-19
+--- transtermhp-2.0.7.orig/seq.cc
++++ transtermhp-2.0.7/seq.cc
+@@ -5,6 +5,10 @@
+ #include <cctype>
+ #include <vector>
+ #include <iomanip>
++#include <cstdlib>
++#include <string.h>
++#include <algorithm>
++#include <cstdio>
+
+ #include "seq.h"
+ #include "util.h"
+--- transtermhp-2.0.7.orig/seq.h
++++ transtermhp-2.0.7/seq.h
+@@ -4,6 +4,7 @@
+ #ifndef SEQ_H
+ #define SEQ_H
+ #include <string>
++#include <cstdlib>
+ #include <vector>
+ #include <list>
+
+--- transtermhp-2.0.7.orig/search.cc
++++ transtermhp-2.0.7/search.cc
+@@ -10,6 +10,7 @@
+ #include "seq.h"
+ #include "ermolaeva-score.h"
+ #include "util.h"
++#include <algorithm>
+
+ int UWINDOW_SIZE = 6;
+ int UWINDOW_REQUIRE = 3;
+--- transtermhp-2.0.7.orig/analysis.cc
++++ transtermhp-2.0.7/analysis.cc
+@@ -6,6 +6,7 @@
+ #include <vector>
+ #include <sstream>
+ #include <cassert>
++#include <algorithm>
+ #include "map-output.h"
+ #include "conf.h"
+ #include "seq.h"
Added: trunk/packages/transtermhp/trunk/debian/patches/series
===================================================================
--- trunk/packages/transtermhp/trunk/debian/patches/series (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/patches/series 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1 @@
+missing_headers
Added: trunk/packages/transtermhp/trunk/debian/rules
===================================================================
--- trunk/packages/transtermhp/trunk/debian/rules (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/rules 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+#
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets by Bill Allombert 2001
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+
+%:
+ dh $@
+
+# test: target in Makefile is broken.
+# don't forget to notify upstream .
+override_dh_auto_test:
Property changes on: trunk/packages/transtermhp/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/transtermhp/trunk/debian/source/format
===================================================================
--- trunk/packages/transtermhp/trunk/debian/source/format (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/source/format 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/transtermhp/trunk/debian/transtermhp.dirs
===================================================================
--- trunk/packages/transtermhp/trunk/debian/transtermhp.dirs (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/transtermhp.dirs 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1 @@
+/usr/share/transtermhp
Added: trunk/packages/transtermhp/trunk/debian/transtermhp.install
===================================================================
--- trunk/packages/transtermhp/trunk/debian/transtermhp.install (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/transtermhp.install 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,4 @@
+transterm /usr/bin
+2ndscore /usr/bin
+calibrate.sh /usr/share/transtermhp
+make_expterm.py /usr/share/transtermhp
Added: trunk/packages/transtermhp/trunk/debian/watch
===================================================================
--- trunk/packages/transtermhp/trunk/debian/watch (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/watch 2011-02-19 15:14:02 UTC (rev 6029)
@@ -0,0 +1,10 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+http://transterm.cbcb.umd.edu/transterm_hp_v(.*)\.zip
+
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