[med-svn] [Git][med-team/ncbi-tools6][master] ncbi-tools6 6.1.20170106+dfsg1-3: More UniVec rm fixups (#935424)

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6


Commits:
03d0f82a by Aaron M. Ucko at 2019-08-26T01:04:55Z
ncbi-tools6 6.1.20170106+dfsg1-3: More UniVec rm fixups (#935424)

* 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.
  (Closes: #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+dfsg1-3) unstable; 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.
+    (Closes: #935424.)
+
+ -- Aaron M. Ucko <ucko at debian.org>  Sun, 25 Aug 2019 21:03:24 -0400
+
 ncbi-tools6 (6.1.20170106+dfsg1-2) unstable; urgency=medium
 
   * debian/test/run-unit-test: Substitute UniVec_Core for UniVec (removed


=====================================
debian/ncbi-data.NEWS
=====================================
@@ -0,0 +1,17 @@
+ncbi-tools6 (6.1.20170106+dfsg1-3) unstable; urgency=medium
+
+    As of version 6.1.20170106+dfsg1-1 (and corresponding -0deb* 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 <ucko at debian.org>  Sun, 25 Aug 2019 21:03:22 -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/03d0f82a53df3e2c569d6b7504ea4c2e00f6ca82

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/03d0f82a53df3e2c569d6b7504ea4c2e00f6ca82
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