[med-svn] [probcons] 01/01: Autopkgtest ad README.source added

[Canberk Koç]

This is an automated email from the git hooks/post-receive script.

cbk-guest pushed a commit to branch master
in repository probcons.

commit 1cab5636d2d82c31f6a793b2c70c4421ab89a480
Author: cbk-guest <cbk-guests at scm.alioth.debian.org>
Date:   Fri Jul 29 18:07:44 2016 +0300

    Autopkgtest ad README.source added
---
 debian/README.source             |  8 ++++++++
 debian/changelog                 |  8 ++++++++
 debian/probcons.examples         |  1 +
 debian/tests.probcons/example.fa | 42 ++++++++++++++++++++++++++++++++++++++++
 debian/tests/control             |  3 +++
 debian/tests/run-unit-test       | 28 +++++++++++++++++++++++++++
 6 files changed, 90 insertions(+)

diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..dc54dc3
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,8 @@
+Modifications of the Probcons sources in Debian.
+
+We added probcons.expample directory.
+
+Example.fa file is combine from Exonerate package's examples.
+(Exonerate released under the GPL version 3+)
+
+-- Canberk Koç <canberkkoc at gmail.com> Fri, 29 Jul 2016 18:01:31 +0300
diff --git a/debian/changelog b/debian/changelog
index 944d531..5374c4a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+probcons (1.12-11) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Autopkgtest added.
+  * README.source added. 
+
+ -- Canberk Koç <canberkkoc at gmail.com>  Fri, 29 Jul 2016 18:05:55 +0300
+
 probcons (1.12-10) unstable; urgency=medium
 
   * Moved debian/upstream to debian/upstream/metadata
diff --git a/debian/probcons.examples b/debian/probcons.examples
new file mode 100644
index 0000000..e664047
--- /dev/null
+++ b/debian/probcons.examples
@@ -0,0 +1 @@
+debian/tests.probcons/*
diff --git a/debian/tests.probcons/example.fa b/debian/tests.probcons/example.fa
new file mode 100644
index 0000000..ff8aa63
--- /dev/null
+++ b/debian/tests.probcons/example.fa
@@ -0,0 +1,42 @@
+>CALM_HUMAN
+MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD
+GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
+DEEVDEMIREADIDGDGQVNYEEFVQMMTAK
+>AF01595 Human telomerase reverse transcriptase (hTRT) mRNA
+MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCVP
+WDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTS
+VRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPLYQ
+LGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPK
+RPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRHS
+HPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPSL
+TGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTHC
+PLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLRRL
+VPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGCVPA
+AEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIGIR
+QHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRREK
+RAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPELYF
+VKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLT
+DLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYV
+QCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFLR
+TLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWCGLLLDTRTLEVQS
+DYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYK
+ILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAA
+GPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANP
+ALPSDFKTILD
+>P53_HUMAN
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
+DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
+SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
+RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
+SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGRDRRTEEENLRKKGEPHHELP
+PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
+GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>TUBE_DROME
+MAYGWNGCGMGVQVNGSNGAIGLSSKYSRNTELRRVEDNDIYRLAKILDENSCWRKLMS
+IIPKGMDVQACSGAGCLNFPAEIKKGFKYTAQDVFQIDEAANRLPPDQSKSQMMIDEWK
+TSGKLNERPTVGVLLQLLVQAELFSAADFVALDFLNESTPARPVDGPGALISLELLEEE
+MEVDNEGLSLKYQSSTATLGADAQGSVGLNLDNFEKDIVRRDKSVPQPSGNTPPIAPPR
+RQQRSTTNSNFATLTGTGTTSTTIPNVPNLTILNPSEQIQEPVLQPRPMNIPDLSILIS
+NSGDLRATVSDNPSNRTSSTDPPNIPRITLLIDNSGDVNSRPNHAPAKASTATTPTASS
+NNLPMISALNISKGSKETLRPESRSSSSSLSKDDDDDNDGEEDGEEEYPDAFLPNLSNS
+EQQSSNNDSSLTTVTGTSGDNSFELTNDSSSTSNDDYACNIPDLSELQQ
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..dd1915c
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -e
+
+pkg="probcons"
+
+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
+
+/usr/bin/probcons example.fa > output1
+/usr/bin/probcons -clustalw example.fa > output2.aln
+/usr/bin/probcons -c 1 example.fa > output3.mfa
+/usr/bin/probcons --consistency 1 example.fa > output4.mfa
+/usr/bin/probcons -ir 1000 example.fa > output5.mfa
+/usr/bin/probcons --iterative-refinement 1000 example.fa > output6.mfa
+/usr/bin/probcons -pre 1 example.fa > output7.mfa
+/usr/bin/probcons --pre-training 1 example.fa > output8.mfa
+/usr/bin/probcons -pairs example.fa > output9.mfa
+/usr/bin/probcons -viterbi example.fa > output10.mfa
+/usr/bin/probcons -v example.fa > output11.mfa
+/usr/bin/probcons --verbose example.fa > output12.mfa
+
+echo "PASS"

-- 
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