[med-svn] [Git][med-team/microbiomeutil][master] 10 commits: chimeraslayer: Depends: ncbi-blast+-legacy

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / microbiomeutil


Commits:
3e2eb3e4 by Andreas Tille at 2019-12-11T08:42:54Z
chimeraslayer: Depends: ncbi-blast+-legacy

- - - - -
5572fd8a by Andreas Tille at 2019-12-11T08:44:20Z
nast-ier: Recommends: ncbi-blast+

- - - - -
2d9a8b93 by Andreas Tille at 2019-12-11T08:46:27Z
routine-update: debhelper-compat 12

- - - - -
51a049f4 by Andreas Tille at 2019-12-11T08:46:33Z
routine-update: Standards-Version: 4.4.1

- - - - -
053ee09c by Andreas Tille at 2019-12-11T08:46:34Z
routine-update: Secure URI in copyright format

- - - - -
e345447e by Andreas Tille at 2019-12-11T08:46:34Z
R-U: Trailing whitespace in debian/changelog

- - - - -
947f9c71 by Andreas Tille at 2019-12-11T08:46:34Z
R-U: Trailing whitespace in debian/control

- - - - -
dbc45034 by Andreas Tille at 2019-12-11T08:46:34Z
R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

- - - - -
b6de9d53 by Andreas Tille at 2019-12-11T08:49:59Z
Fix also Build-Depends

- - - - -
68a8d68e by Andreas Tille at 2019-12-11T08:56:34Z
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+microbiomeutil (20101212+dfsg1-3) unstable; urgency=medium
+
+  * chimeraslyer: Depends: ncbi-blast+-legacy
+    Closes: #946537
+  * nast-ier: Recommends: ncbi-blast+
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/control
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+
+ -- Andreas Tille <tille at debian.org>  Wed, 11 Dec 2019 09:50:55 +0100
+
 microbiomeutil (20101212+dfsg1-2) unstable; urgency=low
 
   [ Steffen Moeller ]
@@ -42,7 +56,7 @@ microbiomeutil (20101212+dfsg-1) unstable; urgency=low
 
 microbiomeutil (20101212-1ubuntu8) precise; urgency=low
 
-  * Bio-Linux rebuild with Andreas' fixes  
+  * Bio-Linux rebuild with Andreas' fixes
   * ChimeraSlayer run from QIIME was not working.  Need to pre-compute
     index files and add them to RESOURCES directory
   * Also added missing direct dep on blast2
@@ -80,7 +94,7 @@ microbiomeutil (20101212-2) unstable; urgency=low
 microbiomeutil (20101212-1ubuntu6) lucid; urgency=low
 
   * Another patch needed to Perl code due to inappropriate use of
-    FindBin 
+    FindBin
   * Move to /usr/lib rather than /usr/share as per Lintian warnings.
   * Set --with quilt on dh.  (Possibly not needed now?)
   * Added better descriptions in debian/control


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,10 +4,10 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cdbfasta,
-               blast2
-Standards-Version: 4.1.4
+               ncbi-blast+-legacy
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil
 Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git
 Homepage: http://microbiomeutil.sourceforge.net/
@@ -32,7 +32,7 @@ Architecture: all
 Depends: ${misc:Depends},
          microbiomeutil-data,
          cdbfasta,
-         blast2
+         ncbi-blast+-legacy
 Recommends: nast-ier
 Description: detects likely chimeras in PCR amplified DNA
  ChimeraSlayer is a chimeric sequence detection utility, compatible with
@@ -64,11 +64,12 @@ Depends: ${misc:Depends},
          ${shlibs:Depends},
          microbiomeutil-data,
          cdbfasta
+Recommends: ncbi-blast+
 Description: NAST-based DNA alignment tool
- The NAST-iEr alignment utility aligns a single raw nucleotide sequence 
+ The NAST-iEr alignment utility aligns a single raw nucleotide sequence
  against one or more NAST formatted sequences.
  .
- The alignment algorithm involves global dynamic programming profile 
+ The alignment algorithm involves global dynamic programming profile
  alignment to fixed (NAST-formatted) multiply aligned template sequences
  without any end-gap penalty.
  .


=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Contact: Brian J. Haas <bhaas at broadinstitute.org>
 Source: http://microbiomeutil.sourceforge.net/
 Files-Excluded:


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,10 +1,10 @@
 #!/bin/sh -e
 
 pkg=microbiomeutil-data
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 cp -a /usr/share/doc/${pkg}/examples/* .
 find . -name "*.gz" -exec gunzip \{\} \;
 for runtest in `find . -mindepth 1 -maxdepth 1 -type d` ; do



View it on GitLab: https://salsa.debian.org/med-team/microbiomeutil/compare/f456ada47a6e308830b35fd6f7cea8539b57d789...68a8d68ef50c798979fffcac34cb8347775a4283

-- 
View it on GitLab: https://salsa.debian.org/med-team/microbiomeutil/compare/f456ada47a6e308830b35fd6f7cea8539b57d789...68a8d68ef50c798979fffcac34cb8347775a4283
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