Pranav Ballaney pushed to branch master at Debian Med / transrate-tools
Commits: 301682c2 by Pranav Ballaney at 2020-05-25T01:32:04+05:30 Add test data - - - - - 4cbfbb68 by Pranav Ballaney at 2020-05-25T01:32:41+05:30 Add autopkgtests - - - - - ca01cffc by Pranav Ballaney at 2020-05-25T01:36:31+05:30 Install docs and update changelog - - - - - 11 changed files: - + debian/README.test - debian/changelog - + debian/docs - + debian/examples - + debian/tests/control - + debian/tests/data/README.test-data - + debian/tests/data/SRR11728627.bam - + debian/tests/data/SRR11728641.bam - + debian/tests/data/SRR11828387.bam - + debian/tests/data/SRR11828399.bam - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +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. ===================================== debian/changelog ===================================== @@ -1,3 +1,18 @@ +transrate-tools (1.0.0-3) UNRELEASED; urgency=medium + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Steffen Möller ] + * Update metadata with ref to conda + + [ Pranav Ballaney ] + * Add test data + * Add autopkgtests + * Install docs + + -- Pranav Ballaney <ballaneypra...@gmail.com> Mon, 25 May 2020 01:33:02 +0530 + transrate-tools (1.0.0-2) unstable; urgency=medium * Team upload. ===================================== debian/docs ===================================== @@ -0,0 +1,4 @@ +README.md +debian/README.test +debian/tests/run-unit-test +debian/tests/data/README.test-data \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/data/* \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data/README.test-data ===================================== @@ -0,0 +1,18 @@ +The files used for testing were obtained by downloading the following: +* NC_045512.2.fasta from https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta +* SRR11728627.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728627 +* SRR11728641.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728641 +* SRR11828387.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11828387 +* SRR11828399.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11828399 + +And applying the following operations: + +bowtie2-build NC_045512.2.fasta sars-cov-2 +bowtie2 -x sars-cov-2 SRR11728627.fq -S SRR11728627.sam +bowtie2 -x sars-cov-2 SRR11728641.fq -S SRR11728641.sam +bowtie2 -x sars-cov-2 SRR11828387.fq -S SRR11828387.sam +bowtie2 -x sars-cov-2 SRR11828399.fq -S SRR11828399.sam +samtools view -b SRR11728627.sam > SRR11728627.bam +samtools view -b SRR11728641.sam > SRR11728641.bam +samtools view -b SRR11828387.sam > SRR11828387.bam +samtools view -b SRR11828399.sam > SRR11828399.bam \ No newline at end of file ===================================== debian/tests/data/SRR11728627.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11728627.bam differ ===================================== debian/tests/data/SRR11728641.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11728641.bam differ ===================================== debian/tests/data/SRR11828387.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11828387.bam differ ===================================== debian/tests/data/SRR11828399.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11828399.bam differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,44 @@ +#!/bin/bash +set -e + +pkg=transrate-tools + +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 * +#do_stuff_to_test_package# + +echo -e "\e[93m\e[1mTest 1\e[0m" +bam-read SRR11828387.bam SRR11828387.csv +cat SRR11828387.csv +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 2\e[0m" +bam-read SRR11828399.bam SRR11828399.csv +cat SRR11828399.csv +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 3\e[0m" +bam-read SRR11728641.bam SRR11728641.csv +cat SRR11728641.csv +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 4\e[0m" +bam-read SRR11728627.bam SRR11728627.csv +cat SRR11728627.csv +echo -e "\e[92m\e[1mPassed\e[0m" +echo View it on GitLab: https://salsa.debian.org/med-team/transrate-tools/-/compare/cd29d81b6aad93a465c22e01ef2976645ae4db66...ca01cffcaf8f5b52c05c6e5702a387e7ef360eef -- View it on GitLab: https://salsa.debian.org/med-team/transrate-tools/-/compare/cd29d81b6aad93a465c22e01ef2976645ae4db66...ca01cffcaf8f5b52c05c6e5702a387e7ef360eef You're receiving this email because of your account on salsa.debian.org.
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