[med-svn] [Git][med-team/hts-nim-tools][master] Now lintian-clean, except for missing man page

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools


Commits:
b9f81a0c by Steffen Möller at 2020-11-07T21:03:15+01:00
Now lintian-clean, except for missing man page

- - - - -


3 changed files:

- debian/control
- debian/hts-nim-tools.install
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -22,14 +22,14 @@ Package: hts-nim-tools
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: tools biological sequences: bam-filter, count-reads, vcf-check
- This package provides several tools that (at least at the time of their creation)
- provide functionalities beyond the routine provided by samtools and other reverse
- dependencies of the htslib.
+ This package provides several tools that (at least at the time of their
+ creation) provide functionalities beyond the routine provided by samtools
+ and other reverse dependencies of the htslib.
  .
  These new tools are
-  • bam-filter    : filter BAM/CRAM/SAM files with a simple expression language
-  • count-reads   : count BAM/CRAM reads in regions given in a BED file
-  • vcf-check     : check regions of a VCF against a background for missing chunks
+  • bam-filter : filter BAM/CRAM/SAM files with a simple expression language
+  • count-reads: count BAM/CRAM reads in regions given in a BED file
+  • vcf-check  : check regions of a VCF against a background for missing chunks
  .
- and yes, as the name suggests, these tools are all implemented in nim, using the
- nim-hts (upstream: hts-nim) wrapper for the htslib.
+ and yes, as the name suggests, these tools are all implemented in nim,
+ using the nim-hts (upstream: hts-nim) wrapper for the htslib.


=====================================
debian/hts-nim-tools.install
=====================================
@@ -1 +1 @@
-src/hts_nim_tools usr/bin/
+bin/* usr/bin/


=====================================
debian/rules
=====================================
@@ -7,13 +7,17 @@ NIMCACHE=$(CURDIR)/nimcache
 	dh $@
 
 override_dh_auto_build:
-	nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim
-	nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr  -p:/usr/share/nimble/hts src/bam_filter.nim
-	nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim
-	nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim
-	nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper  -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim
+	#nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim
+	#nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr  -p:/usr/share/nimble/hts src/bam_filter.nim
+	#nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim
+	#nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim
+	nim c --debuginfo:on --nimcache:$(NIMCACHE) --out:bin/hts-nim-tools -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper  -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim
+
+override_dh_dwz:
+	echo "I: not executing dwz, which fails because of Unknown DWARF DW_OP_0"
 
 override_dh_auto_clean:
 	rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads src/copy_number_sampler
 	rm -rf $(NIMCACHE)
+	rm -rf bin
 



View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a

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View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a
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