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