# Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

diff --git a/debian/rules b/debian/rules
index f5aaa941ac480eca83e1755e4d647648bbbbbedd..40822dde3cc5cb3b3b51edba4b3b353a87a2d820 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -9,7 +9,11 @@ DEB_MAKE_BUILD_TARGET = all all-recur razip lib
 DEB_MAKE_CHECK_TARGET = -C examples all
 
 clean::
-       $(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg
+       $(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+
+binary-install/samtools::
+       install -m 644 bcftools/README $(CURDIR)/debian/samtools/usr/share/doc/samtools/README.bcftools
+       ln -s samtools.1.gz $(CURDIR)/debian/samtools/usr/share/man/man1/bcftools.1.gz
 
 binary-fixup/samtools::
        sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py

diff --git a/debian/samtools.examples b/debian/samtools.examples
index 92114a2c6993e8fa129121206b96651be966dde5..5a2547271587a2d3e3f877dae865aa8913a6863c 100644 (file)
--- a/debian/samtools.examples
+++ b/debian/samtools.examples
@@ -2,3 +2,5 @@ examples/ex1.bam
 examples/ex1.fa
 examples/ex1.sam.gz
 examples/00README.txt
+examples/toy.fa
+examples/toy.sam

diff --git a/debian/samtools.install b/debian/samtools.install
index a4bdb28a3e89f4cba02be01f0381969e35430a79..acf372a7997d2cbd90e9cceecdedd16853982630 100644 (file)
--- a/debian/samtools.install
+++ b/debian/samtools.install
@@ -1,6 +1,9 @@
 #bgzip usr/bin
+bcftools/bcftools      usr/bin
 razip  usr/bin
 samtools       usr/bin
+bcftools/bcf-fix.pl    usr/share/samtools
+bcftools/vcfutils.pl   usr/share/samtools
 misc/*.pl      usr/share/samtools
 misc/*.py      usr/share/samtools
 misc/wgsim     usr/lib/samtools