Aaron M. Ucko pushed to branch buster at Debian Med / ncbi-tools6
Commits: a591b502 by Aaron M. Ucko at 2019-08-26T01:15:14Z ncbi-tools6 6.1.20170106+dfsg1-0+deb10u2: More UniVec rm fixups. * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a bigger impact than anticipated. * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core. (See #935424.) - - - - - 3 changed files: - debian/changelog - + debian/ncbi-data.NEWS - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u2) buster; urgency=medium + + * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a + bigger impact than anticipated. + * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core. + (See #935424.) + + -- Aaron M. Ucko <[email protected]> Sun, 25 Aug 2019 21:15:12 -0400 + ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u1) buster; urgency=medium * Belatedly repackage without data/UniVec.*, some portions of which ===================================== debian/ncbi-data.NEWS ===================================== @@ -0,0 +1,17 @@ +ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u2) buster; urgency=medium + + As of version 6.1.20170106+dfsg1-1 (and corresponding -0+deb* stable + updates), Debian no longer distributes the full UniVec database + because it contains some non-free sequences. (Invitrogen Corporation + holds copyright on them and requires a license for commercial use.) + + The UniVec_Core database remains available for explicit use, for + instance by passing -d /usr/share/ncbi/data/UniVec_Core to vecscreen. + + Also, any user for whom this legal restriction isn't a concern can + download and use a copy of the UniVec database from + https://ftp.ncbi.nlm.nih.gov/entrez/misc/data/. + + Apologies for any resulting inconvenience. + + -- Aaron M. Ucko <[email protected]> Sun, 25 Aug 2019 21:15:11 -0400 ===================================== debian/tests/run-unit-test ===================================== @@ -139,7 +139,7 @@ fi ################################################################## echo '---vecscreen test---' ################################################################## -/usr/bin/vecscreen -f 3 < nc0225.fna > vecscreen.output +/usr/bin/vecscreen -f 3 -d UniVec_Core < nc0225.fna > vecscreen.output [ -s vecscreen.output ] last_in="$(grep ">" nc0225.fna | tail -1 | sed 's/>//' | sed 's/ .*//')" last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ .*//')" View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/a591b5029b87cd5c3ef5da58fa3f2130eed6355c -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/a591b5029b87cd5c3ef5da58fa3f2130eed6355c You're receiving this email because of your account on salsa.debian.org.
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