Andreas Tille pushed to branch master at Debian Med / flye
Commits: f7951c65 by Andreas Tille at 2020-06-28T08:30:02+02:00 Create some hopefully sensible test once flye is supposed to work - - - - - deb022a0 by Andreas Tille at 2020-06-28T08:30:52+02:00 Add todo - - - - - 3 changed files: - debian/changelog - + debian/tests/data/get - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,7 +1,7 @@ flye (2.7.1+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #962292) - - Wait for https://github.com/fenderglass/Flye/issues/275 to be resolved. + TODO: See https://github.com/fenderglass/Flye/issues/275 + Wait until minimap2 patch is applied -- Andreas Tille <[email protected]> Fri, 05 Jun 2020 15:05:08 +0200 ===================================== debian/tests/data/get ===================================== @@ -0,0 +1,5 @@ +#!/bin/sh +# see docs/USAGE.md +wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta + +# FIXME: I'm hesitating to include such a big dataset here ===================================== debian/tests/run-unit-test ===================================== @@ -6,14 +6,21 @@ pkg=#PACKAGENAME# 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}" -#do_stuff_to_test_package# +if [ "${REALLYRUNTEST}" = "yes" ] ; then +# From docs/USAGE.md: + +wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta +flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --genome-size 5m --threads 4 + +wget https://zenodo.org/record/1172816/files/Loman_E.coli_MAP006-1_2D_50x.fasta +flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --genome-size 5m --threads 4 + +else + flye --help + echo 'Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test' +fi View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77 -- View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
