[med-svn] [Git][med-team/snap-aligner][master] 5 commits: Install example and reference data

Thu Jul 9 07:49:48 BST 2020


Pranav Ballaney pushed to branch master at Debian Med / snap-aligner


Commits:
0c3d4304 by Pranav Ballaney at 2020-07-09T11:56:07+05:30
Install example and reference data

- - - - -
020fe2da by Pranav Ballaney at 2020-07-09T12:12:25+05:30
Add autopkgtests

- - - - -
2b39be13 by Pranav Ballaney at 2020-07-09T12:12:43+05:30
Install docs

- - - - -
174b9af8 by Pranav Ballaney at 2020-07-09T12:14:24+05:30
Add Pranav Ballaney to Uploaders

- - - - -
dc5fd2ac by Pranav Ballaney at 2020-07-09T12:14:47+05:30
Update changelog

- - - - -


12 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/ref/datatest/Genome
- + debian/tests/ref/datatest/GenomeIndex
- + debian/tests/ref/datatest2/Genome
- + debian/tests/ref/datatest2/GenomeIndex
- + debian/tests/ref/output.sam
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,12 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.
+
+The input data used for testing comes with the program,
+while the reference files have been produced by running 
+the program as described in run-unit-test.
\ No newline at end of file


=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+snap-aligner (1.0~beta.18+dfsg-4) UNRELEASED; urgency=medium
+
+  [ Steffen Moeller ]
+  * d/u/metadata: yamllint
+
+  [ Pranav Ballaney ]
+  * Install example and reference data
+  * Add autopkgtests
+  * Install docs
+  * Add Pranav Ballaney to Uploaders
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Thu, 09 Jul 2020 12:14:31 +0530
+
 snap-aligner (1.0~beta.18+dfsg-3) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: snap-aligner
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
+           Pranav Ballaney <ballaneypranav at gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),


=====================================
debian/docs
=====================================
@@ -2,3 +2,5 @@ docs/Manual.pdf
 docs/QuickStart.pdf
 README.md
 import/pdclibhdfs/src/NOTICE.txt
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+tests/datatest/*
+debian/tests/ref
\ No newline at end of file


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/ref/datatest/Genome
=====================================
@@ -0,0 +1,3 @@
+1202 1
+500 ref1
+nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGTCACAAATGCCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGGCCACAGCTCTGACTCCTGCATCCTTCTCCTGTGAAGGGGAGGGAGGTGGTGCTGCAGGGGAGGGGAGGGGGCTAGGAGATGTCACTGGGAGCGGAAACGGCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
\ No newline at end of file


=====================================
debian/tests/ref/datatest/GenomeIndex
=====================================
@@ -0,0 +1 @@
+5 0 256 0 20 500 4 214016 1 4
\ No newline at end of file


=====================================
debian/tests/ref/datatest2/Genome
=====================================
@@ -0,0 +1,4 @@
+1904 2
+500 ref1
+1202 ref2
+nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGTCACAAATGCCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGGCCACAGCTCTGACTCCTGCATCCTTCTCCTGTGAAGGGGAGGGAGGTGGTGCTGCAGGGGAGGGGAGGGGGCTAGGAGATGTCACTGGGAGCGGAAACGGCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGTCACAAGGGGCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGGCCACAGCTCTGTTTTCTGCATCCTTCTCCTGTGAAGGGGAGGGAGGTGGTGCTGCAGGGGAGGGGAGGGGGCTAGGAGATGTCACTGGGAGCGGAAACGGCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
\ No newline at end of file


=====================================
debian/tests/ref/datatest2/GenomeIndex
=====================================
@@ -0,0 +1 @@
+5 0 4096 435 22 500 4 3424256 1 4
\ No newline at end of file


=====================================
debian/tests/ref/output.sam
=====================================
@@ -0,0 +1,6 @@
+ at HD	VN:1.4	SO:unsorted
+ at RG	ID:FASTQ	PL:Illumina	PU:pu	LB:lb	SM:sm
+ at PG	ID:SNAP	PN:SNAP	CL:single datatest datatest.fq -o output.sam	VN:1.0beta.18
+ at SQ	SN:ref1	LN:202
+read1	0	ref1	1	70	101M	*	0	0	GTCACAAATGCCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGG	- at 4>3.>,;$B;A>@&A<<5:@5A?<6<1,>='=7A99=<;7;61></'3+5(<&5,0)30%/=:(&(842&54-+,578)776;.*,&/538)/%$(1,-	PG:Z:SNAP	NM:i:0	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm
+read1	0	ref1	102	70	101M	*	0	0	CCACAGCTCTGACTCCTGCATCCTTCTCCTGTGAAGGGGAGGGAGGTGGTGCTGCAGGGGAGGGGAGGGGGCTAGGAGATGTCACTGGGAGCGGAAACGGC	9;6@;:>:2(5.293?+,72$78:974?C>382;A?=:83;96:AB1>=D at 4A;C=AD+<E9=;CBC$<EB2 at A;BF=EE.FA5>ECE(%FFCDBB1A??F	PG:Z:SNAP	NM:i:0	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,40 @@
+#!/bin/bash
+set -e
+
+pkg=snap-aligner
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+ls -R
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1\e[0m"
+snap-aligner index datatest.fa datatest
+diff datatest/Genome ref/datatest/Genome
+diff datatest/GenomeIndex ref/datatest/GenomeIndex
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+snap-aligner index datatest2.fa datatest2 -s 22
+diff datatest2/Genome ref/datatest2/Genome
+diff datatest2/GenomeIndex ref/datatest2/GenomeIndex
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+snap-aligner single datatest datatest.fq -o output.sam
+diff output.sam ref/output.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/snap-aligner/-/compare/6d032e189cf919ca5433e0e603158c5dfcce509f...dc5fd2ac860e6f47342dee3045947863e4519487

-- 
View it on GitLab: https://salsa.debian.org/med-team/snap-aligner/-/compare/6d032e189cf919ca5433e0e603158c5dfcce509f...dc5fd2ac860e6f47342dee3045947863e4519487
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200709/0dd4113c/attachment-0001.html>
