Michael R. Crusoe pushed to branch master at Debian Med / diamond-aligner
Commits: 11111f9b by Michael R. Crusoe at 2021-09-14T12:19:35+02:00 Autopkgtest: ignore warnings about the C2 sequences looking like DNA - - - - - 2191758d by Michael R. Crusoe at 2021-09-14T12:20:33+02:00 routine-update: Ready to upload to unstable - - - - - 2 changed files: - debian/changelog - debian/tests/diamond-calls Changes: ===================================== debian/changelog ===================================== @@ -1,10 +1,17 @@ -diamond-aligner (2.0.11-1) UNRELEASED; urgency=medium +diamond-aligner (2.0.11-1) unstable; urgency=medium + * Team upload. + + [ Andreas Tille ] * Fix watchfile to detect new versions on github (routine-update) * New upstream version * Standards-Version: 4.6.0 (routine-update) - -- Andreas Tille <[email protected]> Wed, 01 Sep 2021 06:46:50 +0200 + [ Michael R. Crusoe ] + * Autopkgtest: pass "--ignore-warnings" when needed due to a protein sequence + that looks like a DNA sequence + + -- Michael R. Crusoe <[email protected]> Tue, 14 Sep 2021 12:20:33 +0200 diamond-aligner (2.0.7-1) unstable; urgency=medium ===================================== debian/tests/diamond-calls ===================================== @@ -1,48 +1,50 @@ #!/bin/sh set -e set -x -# Test sxcript obtained from proteinortho (see bug #9580909 +# Test sxcript obtained from proteinortho (see bug #958090 TESTDIR=`mktemp -d` -#TODO: 10 DONE: 0 Running: 4 -> 14 -diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# ./proteinortho6.pl -debug -force -project=test_diamond -p=diamond test/*.faa -cpus=1 -verbose=2 -#TODO: 10 DONE: 1 Running: 3 -> 12 -diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 0 Running: 1 -> 11 +diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive -#TODO: 10 DONE: 1 Running: 3 -> 12 -diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 1 Running: 0 -> 9 +diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 1 Running: 3 -> 12 -diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 2 Running: 0 -> 8 +diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 1 Running: 3 -> 12 -diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 3 Running: 0 -> 7 +diamond blastp --ignore-warnings --threads 1 --db 'test/C.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 2 Running: 3 -> 11 -diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 4 Running: 0 -> 6 +diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 3 Running: 3 -> 10 -diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 5 Running: 0 -> 5 +diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 4 Running: 3 -> 9 -diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 6 Running: 0 -> 4 +diamond blastp --ignore-warnings --threads 1 --db 'test/E.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive -# TODO: 10 DONE: 5 Running: 3 -> 8 -diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 7 Running: 0 -> 3 +diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive -#TODO: 10 DONE: 6 Running: 3 -> 7 -diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null -diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null +# DONE: 8 Running: 0 -> 2 +diamond blastp --ignore-warnings --threads 1 --db 'test/L.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive + +# DONE: 9 Running: 0 -> 1 +diamond blastp --ignore-warnings --threads 1 --db 'test/M.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive +diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive rm -rf $TESTDIR View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/97ab99e8662381954b090b8eba75410b629f9392...2191758da105d2093f10337b9db2b1fb0ea9c57c -- View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/97ab99e8662381954b090b8eba75410b629f9392...2191758da105d2093f10337b9db2b1fb0ea9c57c You're receiving this email because of your account on salsa.debian.org.
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