[med-svn] [prank] 01/01: Autopkgtest Added
Büşra Selin Pekişçi
busraselinpekisci-guest at moszumanska.debian.org
Wed Mar 22 22:44:54 UTC 2017
This is an automated email from the git hooks/post-receive script.
busraselinpekisci-guest pushed a commit to branch master
in repository prank.
commit ce693c59af05546c306d320f02220bc9e75781f0
Author: Büşra Selin Pekişçi <busra.pekisci at gmail.com>
Date: Thu Mar 23 01:43:32 2017 +0300
Autopkgtest Added
---
debian/changelog | 6 +++-
debian/prank-examples/sample.cdna.fasta | 20 +++++++++++
debian/prank/DEBIAN/control | 37 +++++++++++++++++++++
debian/prank/DEBIAN/md5sums | 6 ++++
debian/prank/usr/bin/prank | Bin 0 -> 1096080 bytes
.../prank/usr/share/doc/prank/changelog.Debian.gz | Bin 0 -> 584 bytes
debian/prank/usr/share/doc/prank/changelog.gz | Bin 0 -> 1433 bytes
debian/prank/usr/share/doc/prank/copyright | 31 +++++++++++++++++
.../share/doc/prank/examples/sample.cdna.fasta.gz | Bin 0 -> 5527 bytes
debian/prank/usr/share/man/man1/prank.1.gz | Bin 0 -> 2904 bytes
debian/tests/control | 3 ++
debian/tests/run-unit-test | 22 ++++++++++++
12 files changed, 124 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index c9a1ffa..40c721a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
prank (0.0.150803-3) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Move packaging from SVN to Git
- -- Andreas Tille <tille at debian.org> Tue, 21 Mar 2017 08:57:07 +0100
+ [ Büşra Selin Pekişçi ]
+ * Autopkgtest Added
+
+ -- Büşra Selin Pekişçi <busra.pekisci at gmail.com> Thu, 23 Mar 2017 01:32:50 +0300
prank (0.0.150803-2) unstable; urgency=medium
diff --git a/debian/prank-examples/sample.cdna.fasta b/debian/prank-examples/sample.cdna.fasta
new file mode 100644
index 0000000..25883e4
--- /dev/null
+++ b/debian/prank-examples/sample.cdna.fasta
@@ -0,0 +1,20 @@
+>gi|74316016|ref|NM_026831.1| Mus musculus myosin binding protein H-like (Mybphl), mRNA
+GTGACCCCAGGGAGACCAGCCTGGACAGCAGGTGCACAGCCCCTCCCTCACCAGCAACAAAGAAAATTTTCAGCTAGACCCCAGGCATGGAGACAGCCACCACACTGGAGATAGCCTCATGCTCCCAGCGGCAGGTAGAAGCAGCTGCTGACCCAGCGGATGCTAAAGGACCCCGGACTTCACATCAACAGGAGGCAGGCAGCCCTTCTCTGCAGCTCCTGCCCTCTATTGAAGAGCACCCCAAGATCTGGCTACCTCGGGCCCTGAAGCAGACTTACATCCGGAAGGCTGGGGAGACAGTGAATCTACTAATCCCGATCCAGGGTAAGCCCAAACCTCAAACCACCTGGACTCACAATGGCTGTGCCCTGGACAGCAGCCGTGTCAGCGTGCGGAATGGGGAGCATGACTCTATTCTTTTCATCAGAGAGGCCCAACGCACTGACTCAGGATGCTACCAACTCTGTGTGCAGCTCGGTGGGCTGCAGGCCA [...]
+>gi|33859764|ref|NM_080469.2| Mus musculus prion protein interacting protein 1 (Prnpip1), mRNA
+GCTGCCGTCAACTGCCCGGAGCGTCTGCTGAGGCCGAGGGAGACGCCGGGGCCTGCACCTGGAGAGAGCCTGCCGTGCTGGCCCGGAGGAGGGGGCGTTGCCATGGCGACAGCCTCTCCGGCAGCTGACGGGGGGCGGGGGCGGCCCTGGGAAGGAGGGCTGGTCTCCTGGCCCCCTGCCCCTCCCCTTACGCTTCCCTGGACCTGGATGGGCCCGAGCTGGGGGCAACACCCTGGGCATTGGGGCTTTCCAGCTCTCACAGACCCTTCAGCATCTCCAGCTGCCAGTCTTGGCATCTTCGAAGTAAGGAGAGTTTTAGATGCCTCTGGATGTTCAATGCTAGCGCCGTTACAGACGGGAGCGGCTCGGTTCTCTTCATATTTACTTTCAAGAGCAAGAAAAGTGCTGGGCTCCCACTTGTTATCTCCCTGTGGCGTTCCGGAGCTCTGTTCCATATCCACCAGAAAGCTGGCGGCCCACGGCTTTGGCGCG [...]
+>gi|115334670|ref|NM_019993.3| Mus musculus aldehyde dehydrogenase 9, subfamily A1 (Aldh9a1), mRNA
+GACTGTCCCTTCCTCCCAGTGGGCTCTACTGGGCTCTCCTTGAGGGCCCCGGGTCTTCACACTCACGGTCCACACCTCCCCGAGGTCCTGTTCCCTAGTGGTCCACCCCTGCCCAGCCAGGGTCGCCTCTTTCCATGGGCCACGCCCCAGAGATTCCGCCCCTCGCCACTCCCTCCTCGTTACCGCGCTATCTCCCCCTCCAGTAGTAATCTGCTGGGGCTTCCGGACGCTTTGCACGCGTAGCAGATGATCCTCGGTGCAGTCGGTTCTGTGCTGACCTCGCTCCTCCGCATTCACCGGGCTGCAGCAGTCGCCGCCATGAGTACTGGCACCTTCGTCGTGTCGCAGCCGCTCAACTACCGCGGCGGGGCCCGTGTGGAGCCGGTGGATGCTTCCGGCACGGAGAAAGCGTTCGAGCCAGCCACCGGCCGAGTGATTGCCACTTTCGCGTGTTCAGGAGAAAAGGAAGTAAACTTGGCCGTTGAGAATGCA [...]
+>gi|6754317|ref|NM_010548.1| Mus musculus interleukin 10 (Il10), mRNA
+GGGGGGGGGGATTTAGAGACTTGCTCTTGCACTACCAAAGCCACAAAGCAGCCTTGCAGAAAAGAGAGCTCCATCATGCCTGGCTCAGCACTGCTATGCTGCCTGCTCTTACTGACTGGCATGAGGATCAGCAGGGGCCAGTACAGCCGGGAAGACAATAACTGCACCCACTTCCCAGTCGGCCAGAGCCACATGCTCCTAGAGCTGCGGACTGCCTTCAGCCAGGTGAAGACTTTCTTTCAAACAAAGGACCAGCTGGACAACATACTGCTAACCGACTCCTTAATGCAGGACTTTAAGGGTTACTTGGGTTGCCAAGCCTTATCGGAAATGATCCAGTTTTACCTGGTAGAAGTGATGCCCCAGGCAGAGAAGCATGGCCCAGAAATCAAGGAGCATTTGAATTCCCTGGGTGAGAAGCTGAAGACCCTCAGGATGCGGCTGAGGCGCTGTCATCGATTTCTCCCCTGTGAAAATAAGAGCAAGGCAGTG [...]
+>gi|27883843|ref|NM_009227.1| Mus musculus small nuclear ribonucleoprotein E (Snrpe), mRNA
+GTTTCCGAGGCGGCCTTCCTACTCGTGTGGTCTTTGTGACTTCCACCATGGCGTACCGCGGCCAGGGCCAAAAGGTGCAGAAGGTGATGGTGCAGCCCATCAACCTTATCTTCAGATACTTGCAAAATAGATCTCGAATTCAGGTGTGGCTGTATGAACAAGTGAATATGCGGATAGAAGGTTGTATTATTGGCTTTGATGAGTACATGAACCTCGTATTAGATGATGCAGAAGAGATTCATTCTAAAACAAAGTCAAGAAAACAACTGGGTCGGATCATGCTAAAAGGAGATAATATTACTCTGCTCCAAAGTGTTTCCAACTAGCAGTGAATGGTGAAGTCTGTAGGATGTTGAGAAGACCCCTTGAGCGTGTTTAAAGATGTCTGCTGCAACCTGCATTTACTCAACTTGTTTTACTTGCACATTATTATTAGGTGACAATAAATGCTGTAGGAAGTTTTTGC
+>gi|31982203|ref|NM_008546.2| Mus musculus microfibrillar-associated protein 2 (Mfap2), mRNA
+AGCGCAGAGGCCCCAACAGCTGTCCTCAACGCCACCACCGCCTCCTCACTCCATGGCCATGAGAGCCGCCTGCCTCTTCCTGCTGTTCATGCCTGGCCTGCTGGCTCAGGGCCAATATGACCTGGATCCTCTCCCCCCATTCCCGGACCATGTCCAGTACAACCACTATGGCGACCAGATTGACAACGCAGACTACTATGACTACCAAGAAGTGAGTCCTCGGACCCCTGAAGAGCAGTTCCAGTCCCAGCAGCAAGTTCAACAGGAAGTCATCCCAGCCCCTACCCCAGAACCAGCAGCTGCAGGGGACCTGGAGACTGAGCCTACCGAGCCTGGCCCTCTTGACTGCCGCGAAGAACAGTACCCGTGTACCCGCCTCTACTCCATCCACAAGCCTTGCAAACAGTGTCTCAACGAGGTCTGCTTCTACAGCCTCCGCCGAGTGTATGTGGTCAACAAGGAAATATGTGTCCGCACTGTCTGTGCCCACGA [...]
+>gi|21314853|ref|NM_139304.1| Mus musculus GATA zinc finger domain containing 2B (Gatad2b), mRNA
+AACGCCAGGATGGATAGAATGACAGAAGATGCTCTGCGCCTGAATCTTTTGAAGAGGAGTTTGGACCCAGCAGATGAGCGAGATGATGTTCTGGCAAAACGACTGAAAATGGAGGGGCATGAGGCCATGGAACGGCTGAAAATGTTAGCACTGCTCAAAAGGAAAGATTTGGCAAATCTTGAGGTGCCGCATGAGTTACCTACTAAGCAAGATGGCAGTGGTGTCAAGGGTTATGAAGAGAAACTTAATGGAAATCTCAGGCCTCATGGAGACAACAACAGGACTGCTGGAAGGCCCGGCAAAGAAAACATCAATGATGAGCCTGTGGATATGAGTGCTAGACGGAGTGAGCCAGACCGAGGAAGGCTAACTCCTTCCCCAGACATAATTGTTTTGTCTGATAATGAGGCCTCCAGTCCCCGATCCAGCTCCCGGATGGAAGAGAGACTCAAAGCAGCCAACCTAGAGATGTTTAAGGGGAAAGGCATGGAG [...]
+>gi|31981052|ref|NM_019777.2| Mus musculus inhibitor of kappaB kinase epsilon (Ikbke), mRNA
+GGAGGAAGTATGATAGTTAAGAGCCTGGGACTGGGTACCCCACTGCTCTCAGAGAGGCAGGAAAGAGACCTTCAGGCTCAAGACCATCACCTGCTTTGCCTGTGGATCCTGGGGGGCCCCATAGCTACCAGGATCTTCTAGGCACTGCCCAGGATTGACTTCAAGGCCTGAATCCCTGGGGGTGCCACCCAGTTCCACAAGTCTGCATTGCCCTGCAACTGAGATAGGAGATGGGCTCAGCTCCTGGACTTGCCCCAGACAGAAAGCAAAACACACACTTGCCAGGGAGAGTCTTTGCCTGATTCTGAGCCACTTGGAGTGCAGGAAGAAGATAGCCAAGCCCAGGAGATGCAGAGTACCACTAACTACCTGTGGCATACTGATGACCTGCTAGGGCAGGGGGCCACTGCCAGTGTGTACAAGGCCCGAAACAAGAAATCCGGGGAGGTGGTTGCTGTAAAGGTCTTCAACTCAGCCAGCTATCGGCGACCT [...]
+>gi|31982176|ref|NM_175259.3| Mus musculus transmembrane protein 58 (Tmem58), mRNA
+GCGGGCTGGGCGGTGCTGCAGCTCCCGCCGGCCGGCTTCGTCCAGCTTTGTCCTGCGGCCCCTTTTCCAGGCCGTCCTGGCCGCGCCCAGCCCCCTCTCGCCATGCCGCCCGCCGGGCCCCGCGGGACCGCGCCGCTCGCAGCCGTCGTCCTGCTGGTGCTTGGGGCTCCTCTGGCGCTGGCGAGTGAGGACTGCTTGTGGTATCTGGACCGGAATGGCTCCTGGCATCCGGGATTTGACTGCGAGTTCTTCACCTTCTGCTGCGGGACCTGCTACCAGCGGTACTGCTGCAGGGACCTGACCTTACTCATCACCGAGAGACAGCAGAAACACTGCCTGGCCTTCAGTCCCAAGACCATAGCAGGCATCGCCTCTGCTGTAATCCTCTTTGTTGCTGTGGTTGCCACCACCATCTGCTGCTTCCTCTGTTCCTGTTGTTACCTATACCGAAGGCGCCAGCAGCTCCAGAGCACGTTTGAAGGCCAGGAGATT [...]
+>gi|23956081|ref|NM_016980.1| Mus musculus ribosomal protein L5 (Rpl5), mRNA
+GGCCGACTCTGCAGGTCTGCGTGGAGCCGCGGTTGCGGGTCTCTATTCCGCAGGATGGGGTTTGTGAAAGTTGTCAAGAATAAGGCCTACTTTAAAAGATACCAAGTGAGATTTCGAAGGCGGCGAGAGGGTAAAACTGACTACTATGCTCGAAAACGATTGGTGATCCAGGACAAGAATAAGTACAACACACCCAAATATAGGATGATAGTTCGTGTAACTAACAGAGATATCATCTGCCAGATTGCATATGCCCGTATAGAAGGGGATATGATCGTCTGTGCAGCATATGCACATGAACTTCCAAAATATGGTGTGAAAGTTGGCCTGACAAATTATGCTGCAGCCTATTGCACTGGCCTGCTGCTGGCCCGCAGGCTTCTGAATAGGTTTGGCATGGACAAGATCTATGAAGGCCAAGTGGAGGTGAATGGAGGTGAATACAATGTGGAAAGCATTGACGGTCAGCCTGGTGCCTTCACTTGCTATCTG [...]
diff --git a/debian/prank/DEBIAN/control b/debian/prank/DEBIAN/control
new file mode 100644
index 0000000..6faa3a6
--- /dev/null
+++ b/debian/prank/DEBIAN/control
@@ -0,0 +1,37 @@
+Package: prank
+Version: 0.0.150803-3
+Architecture: amd64
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Installed-Size: 1095
+Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2)
+Enhances: t-coffee
+Section: science
+Priority: optional
+Homepage: http://wasabiapp.org/software/prank/
+Description: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
+ PRANK is a probabilistic multiple alignment program for DNA, codon
+ and amino-acid sequences. It's based on a novel algorithm that treats
+ insertions correctly and avoids over-estimation of the number of
+ deletion events. In addition, PRANK borrows ideas from maximum
+ likelihood methods used in phylogenetics and correctly takes into
+ account the evolutionary distances between sequences. Lastly, PRANK
+ allows for defining a potential structure for sequences to be aligned
+ and then, simultaneously with the alignment, predicts the locations
+ of structural units in the sequences.
+ .
+ PRANK is a command-line program for UNIX-style environments but the
+ same sequence alignment engine is implemented in the graphical
+ program PRANKSTER. In addition to providing a user-friendly interface
+ to those not familiar with Unix systems, PRANKSTER is an alignment
+ browser for alignments saved in the HSAML format. The novel format
+ allows for storing all the information generated by the aligner and
+ the alignment browser is a convenient way to analyse and manipulate
+ the data.
+ .
+ PRANK aims at an evolutionarily correct sequence alignment and often
+ the result looks different from ones generated with other alignment
+ methods. There are, however, cases where the different look is caused
+ by violations of the method's assumptions. To understand why things
+ may go wrong and how to avoid that, read this explanation of
+ differences between PRANK and traditional progressive alignment
+ methods.
diff --git a/debian/prank/DEBIAN/md5sums b/debian/prank/DEBIAN/md5sums
new file mode 100644
index 0000000..dae6d3f
--- /dev/null
+++ b/debian/prank/DEBIAN/md5sums
@@ -0,0 +1,6 @@
+19078c1ddb652f9b2782fd1fb9f51b73 usr/bin/prank
+f3fa5d58a2a22150837c2af2ffb2b6c7 usr/share/doc/prank/changelog.Debian.gz
+ffa55dc2daaa63a0765e2eec6e592ca5 usr/share/doc/prank/changelog.gz
+3fb9292c389f6d47f7f504b4cb2b91fa usr/share/doc/prank/copyright
+75096cf535ca4ec17f9b8b9453d1647d usr/share/doc/prank/examples/sample.cdna.fasta.gz
+81d59a693bd0a0c65550bca83e40f26f usr/share/man/man1/prank.1.gz
diff --git a/debian/prank/usr/bin/prank b/debian/prank/usr/bin/prank
new file mode 100755
index 0000000..a62bb60
Binary files /dev/null and b/debian/prank/usr/bin/prank differ
diff --git a/debian/prank/usr/share/doc/prank/changelog.Debian.gz b/debian/prank/usr/share/doc/prank/changelog.Debian.gz
new file mode 100644
index 0000000..437c4e9
Binary files /dev/null and b/debian/prank/usr/share/doc/prank/changelog.Debian.gz differ
diff --git a/debian/prank/usr/share/doc/prank/changelog.gz b/debian/prank/usr/share/doc/prank/changelog.gz
new file mode 100644
index 0000000..e19ca23
Binary files /dev/null and b/debian/prank/usr/share/doc/prank/changelog.gz differ
diff --git a/debian/prank/usr/share/doc/prank/copyright b/debian/prank/usr/share/doc/prank/copyright
new file mode 100644
index 0000000..53d7a0b
--- /dev/null
+++ b/debian/prank/usr/share/doc/prank/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: prank-msa
+Upstream-Contact: Ari Loytynoja <ari.loytynoja at helsinki.fi>
+Source: http://wasabiapp.org/download/prank/
+
+Files: *
+Copyright: © 2005-2015 Ari Loytynoja <ari.loytynoja at gmail.com>
+License: GPL-2+
+
+Files: debian/*
+Copyright: © 2011 Manuel Prinz <manuel at debian.org>
+ © 2013-2016 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+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 you can find a copy of the GPL-v2 license
+ at /usr/share/common-licenses/GPL-2.
diff --git a/debian/prank/usr/share/doc/prank/examples/sample.cdna.fasta.gz b/debian/prank/usr/share/doc/prank/examples/sample.cdna.fasta.gz
new file mode 100644
index 0000000..fd49d7e
Binary files /dev/null and b/debian/prank/usr/share/doc/prank/examples/sample.cdna.fasta.gz differ
diff --git a/debian/prank/usr/share/man/man1/prank.1.gz b/debian/prank/usr/share/man/man1/prank.1.gz
new file mode 100644
index 0000000..fecf7ca
Binary files /dev/null and b/debian/prank/usr/share/man/man1/prank.1.gz differ
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..e8aa21d
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,22 @@
+#!/bin/bash
+set -e
+
+pkg="prank"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+gunzip *.gz
+
+echo "TEST START"
+
+/usr/bin/prank sample.cdna.fasta
+
+cat output.best.fas
+
+echo "PASS"
--
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