[med-svn] [Git][med-team/allelecount][master] 2 commits: Add Conda ID

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / allelecount


Commits:
a346e745 by Andreas Tille at 2020-05-12T11:20:10+02:00
Add Conda ID

- - - - -
e3f44a9c by Andreas Tille at 2020-05-12T11:30:33+02:00
Provide separate Perl module package

- - - - -


6 changed files:

- + debian/allelecount.install
- debian/control
- + debian/liballelecount-perl.install
- + debian/liballelecount-perl.lintian-overrides
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/allelecount.install
=====================================
@@ -0,0 +1 @@
+c/bin/alleleCounter	usr/bin


=====================================
debian/control
=====================================
@@ -3,6 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
+Testsuite: autopkgtest-pkg-perl
 Build-Depends: debhelper-compat (= 12),
                libhts-dev,
                libbz2-dev,
@@ -23,7 +24,19 @@ Homepage: https://github.com/cancerit/alleleCount
 Package: allelecount
 Architecture: any
 Depends: ${shlibs:Depends},
-         ${misc:Depends},
+         ${misc:Depends}
+Description: NGS copy number algorithms
+ Support code for NGS copy number algorithms. Takes a file of locations
+ and a [cr|b]am file and generates a count of coverage of each allele
+ [ACGT] at that location (given any filter settings).
+ .
+ The alleleCount package primarily exists to prevent code duplication
+ between some other projects, specifically AscatNGS and Battenberg.
+
+Package: liballelecount-perl
+Architecture: all
+Section: perl
+Depends: ${misc:Depends},
          ${perl:Depends},
          libconst-fast-perl,
          libdevel-cover-perl,
@@ -33,10 +46,13 @@ Depends: ${shlibs:Depends},
          libpod-coverage-perl,
          libtest-fatal-perl (>= 0.013),
          libtry-tiny-perl
-Description: NGS copy number algorithms
+Description: Perl interface to NGS copy number algorithms
  Support code for NGS copy number algorithms. Takes a file of locations
  and a [cr|b]am file and generates a count of coverage of each allele
  [ACGT] at that location (given any filter settings).
  .
  The alleleCount package primarily exists to prevent code duplication
  between some other projects, specifically AscatNGS and Battenberg.
+ .
+ This package provided the Perl interface to alleleCounter providing
+ Sanger::CGP::AlleleCount::Genotype.


=====================================
debian/liballelecount-perl.install
=====================================
@@ -0,0 +1 @@
+debian/tmp/usr


=====================================
debian/liballelecount-perl.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+libalelecounter-perl: script-with-language-extension usr/bin/*.*


=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ include /usr/share/dpkg/default.mk
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --sourcedirectory=c
+	dh $@
 
 override_dh_auto_clean:
 	dh_auto_clean --sourcedirectory=c


=====================================
debian/upstream/metadata
=====================================
@@ -1,12 +1,3 @@
-Reference:
-  Author: 
-  Title: 
-  Journal: 
-  Year: 
-  Volume: 
-  Number: 
-  Pages: 
-  DOI: 
-  PMID:
-  URL: 
-  eprint: 
+Registry:
+ - Name: conda:bioconda
+   Entry: cancerit-allelecount



View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52

-- 
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52
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