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commit 9213857d319f9390e6647260411f36715b67326f Author: Nadiya Sitdykova <[email protected]> Date: Mon Jun 5 18:18:31 2017 -0400 add autopkgtest test-suite --- debian/README.test | 8 +++++ debian/changelog | 9 ++++++ debian/docs | 3 ++ debian/tests/control | 3 ++ debian/tests/run-unit-test | 77 ++++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 100 insertions(+) diff --git a/debian/README.test b/debian/README.test new file mode 100644 index 0000000..973ad8a --- /dev/null +++ b/debian/README.test @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +________________________________________ + +To run the unit tests provided by the package you can do + + sh run-unit-test + +in this directory. diff --git a/debian/changelog b/debian/changelog index 6825b5c..3748466 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,12 @@ +fastx-toolkit (0.0.14-4) unstable; urgency=low + + * Team upload. + + [ Nadiya Sitdykova ] + * Add autopkgtest test-suite + + -- Nadiya Sitdykova <[email protected]> Mon, 05 Jun 2017 17:55:44 -0400 + fastx-toolkit (0.0.14-3) unstable; urgency=low [ Steffen Moeller ] diff --git a/debian/docs b/debian/docs index ffe5fe2..4e1166c 100644 --- a/debian/docs +++ b/debian/docs @@ -1,3 +1,6 @@ NEWS README THANKS +galaxy/test-data +debian/README.test +debian/tests/run-unit-test 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..93684aa --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,77 @@ +#!/bin/sh -e + +pkg=fastx-toolkit + +if [ "$ADTTMP" = "" ] ; then + ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM +fi + +cd $ADTTMP + +cp -a /usr/share/doc/${pkg}/test-data/* . +gunzip -r * + +check () { + cmp -s $1 $2 || { + echo "incorrect result" + exit 1 + } +} + +echo "testing fastq_to_fasta" +fastq_to_fasta -i fastq_to_fasta1.fastq -o out +check fastq_to_fasta1a.out out +fastq_to_fasta -i fastq_to_fasta1.fastq -r -n -o out +check fastq_to_fasta1b.out out + +echo "testing fastx_quality_stats" +fastx_quality_stats -i fastq_stats1.fastq -o out +#check fastq_stats1.out out + +echo "testing fastx_clipper" +fastx_clipper -i fastx_clipper1.fastq -a CAATTGGTTAATCCCCCTATATA -c -o out +#check fastx_clipper1a.out out + +echo "testing fastx_renamer" +fastx_renamer -i fastx_renamer1.fastq -n SEQ -o out +check fastx_renamer1.out out + +echo "testing fastx_trimmer" +fastx_trimmer -i fastx_trimmer1.fasta -f 5 -l 36 -o out +check fastx_trimmer1.out out +fastx_trimmer -i fastx_trimmer2.fastq -f 1 -l 27 -o out +check fastx_trimmer2.out out + +echo "testing fastx_collapser" +fastx_collapser -i fasta_collapser1.fasta -o out + +echo "testing fastx_artifacts_filter" +fastx_artifacts_filter -i fastx_artifacts1.fasta -o out +check fastx_artifacts1.out out +fastx_artifacts_filter -i fastx_artifacts2.fastq -o out +check fastx_artifacts2.out out + +#echo "testing fastq_quality_filter" +#fastq_quality_filter -i fastq_qual_filter1.fastq -q 33 -p 100 -o out +#check fastx_qual_filter1a.out out +#fastq_quality filter -i fastq_qual_filter1.fastq -q 20 -p 100 -o out +#check fastq_qual_filter1b.out out + +echo "testing fastx_reverse_complement" +fastx_reverse_complement -i fastx_rev_comp1.fasta -o out +check fastx_reverse_complement1.out out +fastx_reverse_complement -i fastx_rev_comp2.fastq -o out +check fastx_reverse_complement2.out out + +echo "testing fasta_formatter" +fasta_formatter -i fasta_formatter1.fasta -o out +check fasta_formatter1.out out +fasta_formatter -i fasta_formatter1.fasta -w 60 -o out +check fasta_formatter2.out out + +echo "testing fasta_nucleotide_changer" +fasta_nucleotide_changer -i fasta_nuc_changer1.fasta -r -o out +check fasta_nuc_changer1.out out +fasta_nucleotide_changer -i fasta_nuc_changer2.fasta -d -o out +check fasta_nuc_changer2.out out -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastx-toolkit.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
