[med-svn] [Git][med-team/prokka][master] 7 commits: routine-update: New upstream version

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / prokka


Commits:
9cc48b04 by Steffen Moeller at 2020-03-19T00:34:33+01:00
routine-update: New upstream version

- - - - -
ca61a788 by Steffen Moeller at 2020-03-19T00:34:34+01:00
New upstream version 1.14.6+dfsg
- - - - -
6794b3c8 by Steffen Moeller at 2020-03-19T00:35:04+01:00
Update upstream source from tag 'upstream/1.14.6+dfsg'

Update to upstream version '1.14.6+dfsg'
with Debian dir 3422117fb59546e5cab08c1f9b425a05d1524629
- - - - -
987842ed by Steffen Moeller at 2020-03-19T00:35:04+01:00
routine-update: Standards-Version: 4.5.0

- - - - -
0388d483 by Steffen Moeller at 2020-03-19T00:35:08+01:00
routine-update: Add salsa-ci file

- - - - -
68772eed by Steffen Moeller at 2020-03-19T00:35:08+01:00
routine-update: Rules-Requires-Root: no

- - - - -
211cb1e5 by Steffen Moeller at 2020-03-19T00:36:49+01:00
Set upstream metadata fields: Repository.

- - - - -


7 changed files:

- .travis.yml
- README.md
- bin/prokka
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
.travis.yml
=====================================
@@ -1,10 +1,13 @@
-language: perl
+dist: bionic
+
+addons:
+    apt:
+        packages:
+            - libdb-dev
+            - libbio-perl-perl
+            - libxml-simple-perl
 
-perl:
-    - "5.26"
-    
 install:
-    - "cpanm --quiet --notest Time::Piece XML::Simple Digest::MD5 Bio::Perl"
     - "export PATH=$PWD/bin:$PATH"
 
 script:


=====================================
README.md
=====================================
@@ -14,6 +14,13 @@ viral genomes quickly and produce standards-compliant output files.
 
 ## Installation
 
+### Bioconda
+If you use [Conda](https://conda.io/docs/install/quick.html)
+you can use the [Bioconda channel](https://bioconda.github.io/):
+```
+conda install -c conda-forge -c bioconda -c defaults prokka
+```
+
 ### Brew
 If you are using the [MacOS Brew](http://brew.sh/) 
 or [LinuxBrew](http://brew.sh/linuxbrew/) packaging system:
@@ -21,11 +28,18 @@ or [LinuxBrew](http://brew.sh/linuxbrew/) packaging system:
 brew install brewsci/bio/prokka
 ```
 
-### Bioconda
-If you use [Conda](https://conda.io/docs/install/quick.html)
-you can use the [Bioconda channel](https://bioconda.github.io/):
+### Docker
+Maintained by https://hub.docker.com/u/staphb
 ```
-conda install -c conda-forge -c bioconda -c defaults prokka
+
+docker pull staphb/prokka:latest
+docker run staphb/prokka:latest prokka -h
+```
+
+### Singularity
+```
+singularity build prokka.sif docker://staphb/prokka:latest
+singularity exec prokka.sif prokka -h
 ```
 
 ### Ubuntu/Debian/Mint


=====================================
bin/prokka
=====================================
@@ -46,7 +46,7 @@ my @CMDLINE = ($0, @ARGV);
 my $OPSYS = $^O;
 my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
 my $EXE = $FindBin::RealScript;
-my $VERSION = "1.14.5";
+my $VERSION = "1.14.6";
 my $AUTHOR = 'Torsten Seemann <torsten.seemann at gmail.com>';
 my $URL = 'https://github.com/tseemann/prokka';
 my $PROKKA_PMID = '24642063';


=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+prokka (1.14.6+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.0 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Repository.
+
+ -- Steffen Moeller <moeller at debian.org>  Thu, 19 Mar 2020 00:35:17 +0100
+
 prokka (1.14.5+dfsg-2) unstable; urgency=medium
 
   * Allow skipping the autopkgtests if not all of the dependencies are available


=====================================
debian/control
=====================================
@@ -6,10 +6,11 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                libswiss-perl
-Standards-Version: 4.4.0
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/prokka
 Vcs-Git: https://salsa.debian.org/med-team/prokka.git
 Homepage: http://www.vicbioinformatics.com/software.prokka.shtml
+Rules-Requires-Root: no
 
 Package: prokka
 Architecture: all


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -19,7 +19,7 @@ Reference:
   URL: http://bioinformatics.oxfordjournals.org/content/30/14/2068.abstract
   eprint: "http://bioinformatics.oxfordjournals.org/content/30/14/2068.full.pdf+html\n"
   Type: article
-Repository: "https://github.com/Victorian-Bioinformatics-Consortium/prokka.git\n"
+Repository: https://github.com/Victorian-Bioinformatics-Consortium/prokka.git
 Repository-Browse: "https://github.com/Victorian-Bioinformatics-Consortium/prokka\n"
 Registry:
 - Name: bio.tools



View it on GitLab: https://salsa.debian.org/med-team/prokka/-/compare/f9de58e9f3987a90c830fb5c00c544789372a954...211cb1e50e7cf6d28af993c48bda1895eb78dce5

-- 
View it on GitLab: https://salsa.debian.org/med-team/prokka/-/compare/f9de58e9f3987a90c830fb5c00c544789372a954...211cb1e50e7cf6d28af993c48bda1895eb78dce5
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