Nilesh Patra pushed to branch master at Debian Med / seqkit
Commits: abd67fc5 by Nilesh Patra at 2020-08-03T15:46:36+00:00 Add autopkgtests - - - - - ae9eb5c8 by Nilesh Patra at 2020-08-03T15:46:55+00:00 Add missing sources for repack bam files - - - - - 91a69c40 by Nilesh Patra at 2020-08-03T15:47:34+00:00 Convert to bam files during install - - - - - c1f42c1b by Nilesh Patra at 2020-08-03T15:48:15+00:00 Add new binary: seqkit-examples - - - - - 620e9103 by Nilesh Patra at 2020-08-03T21:22:40+05:30 Add myself to uploaders - - - - - 11 changed files: - debian/control - − debian/install - + debian/missing-sources/pcs109_5k.sam - + debian/missing-sources/pcs109_5k_prim.sam - + debian/missing-sources/pcs109_5k_spliced.sam - debian/rules - + debian/seqkit-examples.docs - + debian/seqkit.install - debian/links → debian/seqkit.links - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/control ===================================== @@ -1,8 +1,7 @@ Source: seqkit Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, Nilesh Patra <[email protected]> Section: science -Testsuite: autopkgtest-pkg-go Priority: optional Build-Depends: debhelper-compat (= 13), dh-golang, @@ -22,7 +21,8 @@ Build-Depends: debhelper-compat (= 13), golang-github-op-go-logging-dev, golang-github-logrusorgru-aurora-dev, golang-github-tatsushid-go-prettytable-dev, - golang-github-bsipos-thist-dev + golang-github-bsipos-thist-dev, + samtools Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/seqkit Vcs-Git: https://salsa.debian.org/med-team/seqkit.git @@ -43,3 +43,19 @@ Description: cross-platform and ultrafast toolkit for FASTA/Q file manipulation demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. + +Package: seqkit-examples +Architecture: all +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: examples for seqkit: cross-platform and ultrafast toolkit for FASTA/Q file manipulation + SeqKit describes a cross-platform ultrafast comprehensive toolkit for + FASTA/Q processing. SeqKit provides executable binary files for all + major operating systems, including Windows, Linux, and Mac OS X, and can + be directly used without any dependencies or pre-configurations. SeqKit + demonstrates competitive performance in execution time and memory usage + compared to similar tools. The efficiency and usability of SeqKit enable + researchers to rapidly accomplish common FASTA/Q file manipulations. + . + This package contains a test data set as well as sample scripts + running some test suite provided by Debian also as autopkgtest. ===================================== debian/install deleted ===================================== @@ -1,2 +0,0 @@ -build/bin/seqkit usr/bin -build/bin/benchmark usr/lib/seqkit ===================================== debian/missing-sources/pcs109_5k.sam ===================================== The diff for this file was not included because it is too large. ===================================== debian/missing-sources/pcs109_5k_prim.sam ===================================== The diff for this file was not included because it is too large. ===================================== debian/missing-sources/pcs109_5k_spliced.sam ===================================== The diff for this file was not included because it is too large. ===================================== debian/rules ===================================== @@ -9,4 +9,13 @@ include /usr/share/dpkg/default.mk override_dh_auto_install: dh_auto_install -- --no-source - rm debian/seqkit/usr/bin/benchmark + +override_dh_installdocs: + # Regenerate bam and bam index files + cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam + cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam + cat debian/missing-sources/pcs109_5k_spliced.sam | samtools view -Sb - > tests/pcs109_5k_spliced.bam + samtools index tests/pcs109_5k_prim.bam tests/pcs109_5k_prim.bam.bai + samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai + samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai + dh_installdocs ===================================== debian/seqkit-examples.docs ===================================== @@ -0,0 +1,3 @@ +tests +debian/missing-sources/* +debian/tests/run-unit-test ===================================== debian/seqkit.install ===================================== @@ -0,0 +1,2 @@ +debian/tmp/usr/bin/seqkit usr/bin +debian/tmp/usr/bin/benchmark usr/lib/seqkit ===================================== debian/links → debian/seqkit.links ===================================== ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,36 @@ +#!/bin/bash +set -e + +pkg=seqkit + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -Rf /usr/share/doc/${pkg}-examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * +file=tests/hairpin.fa + +seqkit seq -w 60 $file > testfile + +echo "Test 1" +filegrep=`grep -c '^>' $file` +testfilegrep=`grep -c '^>' $file` +if [ "$filegrep" != "$testfilegrep" ] +then + exit 1 +fi +echo "PASS" + +cksumfile=`cat $file | md5sum | cut -d" " -f 1` +cksumtestfile=`cat testfile | md5sum | cut -d' ' -f 1` +echo "Test 2" +if [ "$cksumfile" != "$cksumtestfile" ] +then + exit 1 +fi +echo "PASS" + View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466 -- View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466 You're receiving this email because of your account on salsa.debian.org.
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