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 <[email protected]> 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 <[email protected]> -Uploaders: Michael R. Crusoe <[email protected]> +Uploaders: Michael R. Crusoe <[email protected]>, + Pranav Ballaney <[email protected]> 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 @@ +@HD VN:1.4 SO:unsorted +@RG ID:FASTQ PL:Illumina PU:pu LB:lb SM:sm +@PG ID:SNAP PN:SNAP CL:single datatest datatest.fq -o output.sam VN:1.0beta.18 +@SQ SN:ref1 LN:202 +read1 0 ref1 1 70 101M * 0 0 GTCACAAATGCCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGG -@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$78:974?C>382;A?=:83;96:AB1>=D@4A;C=AD+<E9=;CBC$<EB2@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.
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