[med-svn] [Git][med-team/resfinder][master] Package only Python version, provide example data in examples package

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / resfinder


Commits:
5982f45b by Andreas Tille at 2019-11-15T09:17:47Z
Package only Python version, provide example data in examples package

- - - - -


8 changed files:

- + debian/README.Debian
- debian/changelog
- debian/control
- − debian/install
- debian/lintian-overrides
- + debian/resfinder-example.install
- + debian/resfinder.install
- + debian/resfinder.links


Changes:

=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,21 @@
+resfinder for Debian
+====================
+
+Quoting the resfinder doc:
+
+    The ResFinder service contains one perl script *resfinder.pl* which is the
+    script of the latest version of the ResFinder service. ResFinder identifies
+    acquired antimicrobial resistance genes in total or partial sequenced isolates
+    of bacteria.
+
+    This repository also contains a python script *resfinder.py* which is  a new version
+    of ResFinder, but not yet running on the CGE server. This program was added because
+    it uses a newer version of blastn,  which, in contrary from the blastall version
+    that the perl script uses, is avail to download.
+
+The user who requested this package is just interested in the Python version of
+redfinder thus only this script is packaged.
+
+
+ -- Andreas Tille <tille at debian.org>  Thu, 07 Nov 2019 12:41:11 +0100
+


=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
 resfinder (3.2-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
-  TODO: Clarify relation between *.pl and *.py
 
  -- Andreas Tille <tille at debian.org>  Thu, 07 Nov 2019 12:41:11 +0100


=====================================
debian/control
=====================================
@@ -4,16 +4,16 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
-               dh-python
+               dh-python,
+               python3
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/resfinder
 Vcs-Git: https://salsa.debian.org/med-team/resfinder.git
 Homepage: https://bitbucket.org/genomicepidemiology/resfinder
 
 Package: resfinder
-Architecture: any
-Depends: ${perl:Depends},
-         ${python3:Depends},
+Architecture: all
+Depends: ${python3:Depends},
          ${misc:Depends},
          bioperl,
          ncbi-blast+-legacy
@@ -27,3 +27,20 @@ Description: identifies acquired antimicrobial resistance genes
  from four different sequencing platforms. The method was evaluated on
  1862 GenBank files containing 1411 different resistance genes, as well
  as on 23 de-novo-sequenced isolates.
+
+Package: resfinder-example
+Architecture: all
+Depends: ${misc:Depends},
+Recommends: resfinder
+Description: identifies acquired antimicrobial resistance genes (example data)
+ ResFinder identifies acquired antimicrobial resistance genes in total or
+ partial sequenced isolates of bacteria.
+ .
+ ResFinder that uses BLAST for identification of acquired antimicrobial
+ resistance genes in whole-genome data. As input, the method can use both
+ pre-assembled, complete or partial genomes, and short sequence reads
+ from four different sequencing platforms. The method was evaluated on
+ 1862 GenBank files containing 1411 different resistance genes, as well
+ as on 23 de-novo-sequenced isolates.
+ .
+ This package contains example data to test resfinder.


=====================================
debian/install deleted
=====================================
@@ -1,2 +0,0 @@
-*.py	/usr/bin
-*.pl	/usr/bin


=====================================
debian/lintian-overrides
=====================================
@@ -1,4 +1,4 @@
 # see discussion on Debian Med mailing list
 #   https://lists.debian.org/debian-med/2018/06/msg00042.html
 # and following mails in thread
-resfinder: script-with-language-extension usr/bin/resfinder.pl
+resfinder: script-with-language-extension usr/bin/resfinder.py


=====================================
debian/resfinder-example.install
=====================================
@@ -0,0 +1 @@
+test.fsa	usr/share/doc/resfinder/examples


=====================================
debian/resfinder.install
=====================================
@@ -0,0 +1 @@
+*.py	usr/share/resfinder


=====================================
debian/resfinder.links
=====================================
@@ -0,0 +1 @@
+usr/share/resfinder/resfinder.py	usr/bin/resfinder.py



View it on GitLab: https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6

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