[med-svn] [Git][med-team/unicycler][master] Provide upstream sample_data in a separate package

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / unicycler


Commits:
a3b90a3a by Liubov Chuprikova at 2018-09-27T10:51:32Z
Provide upstream sample_data in a separate package

- - - - -


3 changed files:

- debian/control
- debian/rules
- + debian/unicycler-data.install


Changes:

=====================================
debian/control
=====================================
@@ -27,17 +27,30 @@ Architecture: any
 Depends: ${python3:Depends},
          ${shlibs:Depends},
          ${misc:Depends},
+         python3-setuptools,
          default-jre,
          bowtie2,
-         freebayes,
          ncbi-blast+,
          pilon,
          racon,
          samtools,
          spades
+Recommends: unicycler-data
 Description: hybrid assembly pipeline for bacterial genomes
  Unicycler is an assembly pipeline for bacterial genomes. It can assemble
  Illumina-only read sets where it functions as a SPAdes-optimiser. It can
  also assembly long-read-only sets (PacBio or Nanopore) where it runs a
  miniasm+Racon pipeline. For the best possible assemblies, give it both
  Illumina reads and long reads, and it will conduct a hybrid assembly.
+
+Package: unicycler-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: hybrid assembly pipeline for bacterial genomes (data package)
+ Unicycler is an assembly pipeline for bacterial genomes. It can assemble
+ Illumina-only read sets where it functions as a SPAdes-optimiser. It can
+ also assembly long-read-only sets (PacBio or Nanopore) where it runs a
+ miniasm+Racon pipeline. For the best possible assemblies, give it both
+ Illumina reads and long reads, and it will conduct a hybrid assembly.
+ .
+ This package contains architecture independent data for unicycler.


=====================================
debian/rules
=====================================
@@ -2,20 +2,16 @@
 
 # DH_VERBOSE := 1
 
-
-# Build time tests are flaky
-# export DH_BUILD_MAINT_OPTIONS=nocheck
-# But rather run the tests and ignore errors than no tests at all.
-# Thus we might have a look into build-logs to see what is failing
-
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 include /usr/share/dpkg/default.mk
 
+export PYBUILD_NAME=unicycler
+
 # copy all nacessary data before testing and make clean after the testing
 export PYBUILD_BEFORE_TEST=cp -a unicycler-runner.py {build_dir}; \
 	cp -a unicycler/cpp_functions.so {build_dir}/unicycler; \
-	cp -r sample_data {build_dir}
+	cp -a sample_data {build_dir}
 export PYBUILD_AFTER_TEST=rm {build_dir}/unicycler-runner.py; \
 	rm -r {build_dir}/sample_data; \
 	rm -r {build_dir}/unicycler/__pycache__
@@ -33,3 +29,9 @@ override_dh_auto_clean:
 override_dh_auto_build:
 	make
 	dh_auto_build
+
+override_dh_auto_install:
+	dh_auto_install --destdir=debian/$(PYBUILD_NAME)
+
+override_dh_python3:
+	dh_python3 --no-ext-rename


=====================================
debian/unicycler-data.install
=====================================
@@ -0,0 +1 @@
+sample_data /usr/share/unicycler-data



View it on GitLab: https://salsa.debian.org/med-team/unicycler/commit/a3b90a3a5c00e9b83a48c7746b4aa598202c8642

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View it on GitLab: https://salsa.debian.org/med-team/unicycler/commit/a3b90a3a5c00e9b83a48c7746b4aa598202c8642
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