[med-svn] [amap-align] 01/01: Autopkgtest added
Canberk Koç
cbk-guest at moszumanska.debian.org
Thu Aug 4 22:44:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
cbk-guest pushed a commit to branch master
in repository amap-align.
commit 14a53d0d7c5b59dc7f07d8f513908d3fcf2ed520
Author: cbk-guest <cbk-guests at scm.alioth.debian.org>
Date: Fri Aug 5 01:44:06 2016 +0300
Autopkgtest added
---
debian/amap-align/DEBIAN/control | 19 ++++
debian/amap-align/DEBIAN/md5sums | 10 ++
debian/amap-align/usr/bin/amap | Bin 0 -> 242384 bytes
.../usr/share/doc/amap-align/NEWS.Debian.gz | Bin 0 -> 381 bytes
.../usr/share/doc/amap-align/PROBCONS.README | 102 +++++++++++++++++++++
debian/amap-align/usr/share/doc/amap-align/README | 39 ++++++++
.../usr/share/doc/amap-align/README.Debian | 16 ++++
.../usr/share/doc/amap-align/changelog.Debian.gz | Bin 0 -> 1639 bytes
.../amap-align/usr/share/doc/amap-align/copyright | 55 +++++++++++
.../usr/share/doc/amap-align/examples/BB12020.tfa | 16 ++++
.../doc/amap-align/examples/BB12020.tfa.out.gz | Bin 0 -> 21548 bytes
debian/amap-align/usr/share/man/man1/amap.1.gz | Bin 0 -> 2898 bytes
debian/changelog | 6 +-
debian/tests/control | 3 +
debian/tests/run-unit-test | 24 +++++
15 files changed, 289 insertions(+), 1 deletion(-)
diff --git a/debian/amap-align/DEBIAN/control b/debian/amap-align/DEBIAN/control
new file mode 100644
index 0000000..64e18d5
--- /dev/null
+++ b/debian/amap-align/DEBIAN/control
@@ -0,0 +1,19 @@
+Package: amap-align
+Version: 2.2-5
+Architecture: amd64
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Installed-Size: 286
+Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2)
+Section: science
+Priority: optional
+Homepage: http://code.google.com/p/amap-align/
+Description: Protein multiple alignment by sequence annealing
+ AMAP is a command line tool to perform multiple alignment of peptidic
+ sequences. It utilizes posterior decoding, and a sequence-annealing
+ alignment, instead of the traditional progressive alignment method. It is
+ the only alignment program that allows one to control the sensitivity /
+ specificity tradeoff. It is based on the ProbCons source code, but
+ uses alignment metric accuracy and eliminates the consistency
+ transformation.
+ .
+ The java visualisation tool of AMAP 2.2 is not yet packaged in Debian.
diff --git a/debian/amap-align/DEBIAN/md5sums b/debian/amap-align/DEBIAN/md5sums
new file mode 100644
index 0000000..eb643f5
--- /dev/null
+++ b/debian/amap-align/DEBIAN/md5sums
@@ -0,0 +1,10 @@
+aac4ee8ce681dbf64eddb28dbace3576 usr/bin/amap
+700d016e862d09692f569a2375817ef2 usr/share/doc/amap-align/NEWS.Debian.gz
+c06c1a4c550038626184ff7ea9982333 usr/share/doc/amap-align/PROBCONS.README
+0a6e235bf1e4602b1a11c259dd48c559 usr/share/doc/amap-align/README
+a9355edee70f81e338a7841f3cf9d624 usr/share/doc/amap-align/README.Debian
+189c90495f0aaaf2e0da2bf209c304c5 usr/share/doc/amap-align/changelog.Debian.gz
+aaa2261775f4587839f2f5ba9aa3a3d3 usr/share/doc/amap-align/copyright
+81603e893b72c98ca63f37ede7015cd8 usr/share/doc/amap-align/examples/BB12020.tfa
+52f07075b64ed6bdfdda5badff671c0b usr/share/doc/amap-align/examples/BB12020.tfa.out.gz
+19e6e2207f064b3202447ff367213722 usr/share/man/man1/amap.1.gz
diff --git a/debian/amap-align/usr/bin/amap b/debian/amap-align/usr/bin/amap
new file mode 100755
index 0000000..3581bfa
Binary files /dev/null and b/debian/amap-align/usr/bin/amap differ
diff --git a/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz b/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz
new file mode 100644
index 0000000..3fe8268
Binary files /dev/null and b/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz differ
diff --git a/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README b/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README
new file mode 100644
index 0000000..76d566c
--- /dev/null
+++ b/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README
@@ -0,0 +1,102 @@
+
+ PROBCONS
+ ~~~~~~~~
+
+ Probabilistic consistency-based multiple sequence alignment
+
+-----------------------------------------------------------------
+
+PROBCONS is a novel tool for generating multiple alignments
+of protein sequences. Using a combination of probabilistic
+modeling and consistency-based alignment techniques, PROBCONS
+has achieved the highest accuracy of all alignment methods to
+date.
+
+PROBCONS was developed by Chuong B. Do in collaboration with
+Michael Brudno in the research group of Serafim Batzoglou,
+Department of Computer Science, Stanford University.
+
+For more information on the algorithms, please see
+
+ Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
+ Probabilistic Consistency-based Multiple Alignment of
+ Amino Acid Sequences. 12th International Conference on
+ Intelligent Systems for Molecular Biology. In press.
+
+and
+
+ Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
+ Probabilistic Consistency-based Multiple Alignment of
+ Amino Acid Sequences. The 19th National Conference on
+ Artificial Intelligence (AAAI-04). In press.
+
+-----------------------------------------------------------------
+
+PROBCONS has been made freely available as PUBLIC DOMAIN
+software and hence is not subject to copyright in the United
+States. This system and/or any portion of the source code
+may be used, modified, or redistributed without restrictions.
+PROBCONS is distributed WITHOUT WARRANTY, express or implied.
+The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
+loss due to reliance on the program.
+
+-----------------------------------------------------------------
+
+Version History
+
+1.0, 3/23/2004 (Chuong Do)
+ -- initial release
+
+1.01, 3/25/2004 (Chuong Do)
+ -- fixed error in training procedure
+ -- retrained default parameters for 1 and 2 pairs of insert
+ states
+
+1.02, 4/17/2004 (Chuong Do)
+ -- replaced LOG_ADD and EXP routines
+ -- added support for reading MSF format files
+ -- added two extra utilities for scoring PROBCONS alignments
+ (for benchmarking purposes)
+ -- added the "compare" program for scoring alignments
+ according to a reference alignment with respect to
+ sum-of-pairs and column scores
+ -- added the "fixref" program for adjusting PREFAB
+ alignments to contain all letters of the input
+ sequences; basically the main program for PROBCONS
+ "hacked" to get the job done
+
+1.03, 5/3/2004 (Chuong Do)
+ -- added option to do all-pairs pairwise alignments instead
+ of constructing a full multiple alignment
+ -- added support for reading DIALIGN style files
+ -- enabled support for using BAliBASE annotations for scoring
+ BAliBASE alignments
+ -- several minor bug fixes thanks to Bob Edgar
+ -- added "project" program to project multiple alignment to
+ pairwise alignments
+
+1.04, 5/9/2004 (Chuong Do)
+ -- switched over to default of one-insert state pair
+ -- retrained default parameters
+ -- added annotation scores
+ -- small changes to model topology to make end gaps symmetrical
+ -- added makegnuplot utility to plot annotation scores
+
+1.05, 5/26/2004 (Chuong Do)
+ -- added cutoff filtering for posterior scores
+ -- made small corrections to recurrences for computing alignments
+ -- added CLUSTALW output support
+
+1.06, 7/13/2004 (Chuong Do)
+ -- ProbCons is now PUBLIC DOMAIN software.
+
+1.07, 8/30/2004 (Chuong Do)
+ -- Fixed CLUSTALW output for sequence names (thanks to John Calley
+ for pointing this out)
+
+1.08, 8/31/2004 (Chuong Do)
+ -- Added option for alignment order output (-a).
+
+1.09, 9/1/2004 (Chuong Do)
+ -- PROBCONS now allows input files with existing gaps -- these are
+ automatically stripped before alignment.
diff --git a/debian/amap-align/usr/share/doc/amap-align/README b/debian/amap-align/usr/share/doc/amap-align/README
new file mode 100644
index 0000000..f9ec8cb
--- /dev/null
+++ b/debian/amap-align/usr/share/doc/amap-align/README
@@ -0,0 +1,39 @@
+
+See http://baboon.math.berkeley.edu/amap/ for more information.
+
+INSTALL
+=======
+
+To build the AMAP alignment code change to the 'align' directory and type:
+
+ % make
+
+
+This distribution includes the compiled AmapDisplay.jar file.
+In case you want to build the AmapDisplay from the source code,
+you'll need ant (http://ant.apache.org) installed.
+Once ant is installed change to the 'display' directory, and type:
+
+ % ant all
+
+USE
+===
+To run AMAP with the default options change to the 'align' directory and type:
+ % amap <multi-fasta-file-name>
+
+If no file name is provided the list of options are printed.
+
+In order to use the AMAP Display run AMAP with the -gui option, and save the output to a file,
+then use the file as the input to AmapDisplay. For example, type:
+
+ % align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out
+ % java -jar display/AmapDisplay.jar examples/BB12020.tfa.out
+
+
+LICENSE
+=======
+
+The various bits of AMAP code are distributed under the GPL. Please see the license
+in the license directory for details.
+
+
diff --git a/debian/amap-align/usr/share/doc/amap-align/README.Debian b/debian/amap-align/usr/share/doc/amap-align/README.Debian
new file mode 100644
index 0000000..ee56b8c
--- /dev/null
+++ b/debian/amap-align/usr/share/doc/amap-align/README.Debian
@@ -0,0 +1,16 @@
+amap for Debian
+===============
+
+Please note that the previous upstream homepage
+ http://bio.math.berkeley.edu/amap/
+vanished and there is no information left about further updates
+of this program.
+
+The version hosted at
+ http://code.google.com/p/amap-align/
+is older than the Debian packaged version.
+
+If you have any knowledge about new location of the code, please
+drop a note to the address below.
+
+ -- Andreas Tille <tille at debian.org> Thu, 13 Jan 2011 13:50:30 +0100
diff --git a/debian/amap-align/usr/share/doc/amap-align/changelog.Debian.gz b/debian/amap-align/usr/share/doc/amap-align/changelog.Debian.gz
new file mode 100644
index 0000000..b8d55a1
Binary files /dev/null and b/debian/amap-align/usr/share/doc/amap-align/changelog.Debian.gz differ
diff --git a/debian/amap-align/usr/share/doc/amap-align/copyright b/debian/amap-align/usr/share/doc/amap-align/copyright
new file mode 100644
index 0000000..8f9fccc
--- /dev/null
+++ b/debian/amap-align/usr/share/doc/amap-align/copyright
@@ -0,0 +1,55 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Author: Ariel Schwartz <sariel at cs.berkeley.edu>
+Source: http://bio.math.berkeley.edu/amap/download
+ This download area as well as the homepage vanished
+
+Files: *
+Copyright: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
+License: PD
+
+Files: display/*
+Copyright: © 2007 Michael E. Smoot
+License: GPL-2+
+ This program 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 program 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, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL'.
+
+License: PD
+ The current version of AMAP uses the PROBCONS 1.09 code base for some of the
+ input/output procedures, and for the calculation of posterior probabilities
+ (see PROBCONS.README).
+ .
+ AMAP has been made freely available as PUBLIC DOMAIN software and hence is
+ not subject to copyright in the United States. This system and/or any portion
+ of the source code may be used, modified, or redistributed without
+ restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The
+ authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
+ the program.
+ .
+ PROBCONS is copyright © 2004 Chuong Do <chuongdo at cs.stanford.edu>
+ .
+ PROBCONS has been made freely available as PUBLIC DOMAIN software and
+ hence is not subject to copyright in the United States. This system and/or
+ any portion of the source code may be used, modified, or redistributed
+ without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or
+ implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
+ due to reliance on the program.
+
+Files: debian/*
+Copyright: © 2007 David Paleino <d.paleino at gmail.com>
+ © 2006—2008 Charles Plessy <chalres-debian-nospam at plessy.org>
+ © 2011-2013 Andreas Tille <tille at debian.org>
+License: PD
diff --git a/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa
new file mode 100644
index 0000000..801fc17
--- /dev/null
+++ b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa
@@ -0,0 +1,16 @@
+>1vvc_
+VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEW
+SDPPTCQIVKCPHPTISNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSS
+STCSPGNTWKPELPKCVR
+>1ghq_B
+AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKD
+KVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACK
+TNFSMNGNKSVWCQANNMWGPTRLPTCVS
+>1ckl_A
+CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNH
+TWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGYYLI
+GEEILYCELKGSVAIWSGKPPICEKV
+>1nwv_A
+FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLT
+CLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGY
+KLFGSTSSFCLISGSSVQWSDPLPECREH
diff --git a/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa.out.gz b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa.out.gz
new file mode 100644
index 0000000..77d8d37
Binary files /dev/null and b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa.out.gz differ
diff --git a/debian/amap-align/usr/share/man/man1/amap.1.gz b/debian/amap-align/usr/share/man/man1/amap.1.gz
new file mode 100644
index 0000000..f0727a5
Binary files /dev/null and b/debian/amap-align/usr/share/man/man1/amap.1.gz differ
diff --git a/debian/changelog b/debian/changelog
index 5ad2ef9..71ceebc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,15 @@
amap-align (2.2-6) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Add README.source
* Moved packaging from SVN to Git
* hardening=+all
* Add lintian override for false positive
- -- Andreas Tille <tille at debian.org> Wed, 03 Aug 2016 08:23:14 +0200
+ [ Canberk Koç ]
+ * Autopkgtest added
+
+ -- Canberk Koç <canberkkoc at gmail.com> Fri, 05 Aug 2016 01:43:15 +0300
amap-align (2.2-5) unstable; urgency=medium
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..d1326d4
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,24 @@
+#!/bin/bash
+set -e
+
+pkg="amap-align"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+find . -name "*.gz" -exec gunzip \{\} \;
+
+/usr/bin/amap BB12020.tfa > 1.out
+/usr/bin/amap -clustalw BB12020.tfa > 2.out
+/usr/bin/amap -viterbi BB12020.tfa > 3.out
+/usr/bin/amap -pairs BB12020.tfa > 4.out
+/usr/bin/amap -prog BB12020.tfa > 5.out
+/usr/bin/amap -noreorder BB12020.tfa > 6.out
+/usr/bin/amap -gui BB12020.tfa > 7.out
+
+echo "PASS"
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/amap-align.git
More information about the debian-med-commit
mailing list