[med-svn] [pbgenomicconsensus] 01/02: Remove convenience script for poa

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository pbgenomicconsensus.

commit d380f83f2bd8c17a7e13f42c448cba0f8cb351f1
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Jul 16 11:49:44 2016 -0700

    Remove convenience script for poa
    
    This script conflicts with the poa package. It is not really
    necessary for us because users can use
    
      variantCaller --algorithm=poa [...]
    
    Closes: #831220
---
 debian/man/poa.1                               | 22 ----------------------
 debian/patches/no-poa-convenience-script.patch | 18 ++++++++++++++++++
 debian/patches/series                          |  1 +
 debian/rules                                   |  3 +++
 4 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/debian/man/poa.1 b/debian/man/poa.1
deleted file mode 100644
index 3116a2a..0000000
--- a/debian/man/poa.1
+++ /dev/null
@@ -1,22 +0,0 @@
-.TH POA 1
-
-.SH NAME
-
-poa \- consensus caller for Pacific Biosciences data
-
-.SH DESCRIPTION
-
-See
-.BR genomicconsensus (7)
-for a more detailed description of \f[B]poa\f[P].
-
-.SH OPTIONS
-
-.TP
-.B \-h, \-\-help
-Show summary of options.
-
-.SH SEE ALSO
-.BR genomicconsensus (7)
-.BR variantCaller (1)
-.BR blasr (1)
diff --git a/debian/patches/no-poa-convenience-script.patch b/debian/patches/no-poa-convenience-script.patch
new file mode 100644
index 0000000..1775d85
--- /dev/null
+++ b/debian/patches/no-poa-convenience-script.patch
@@ -0,0 +1,18 @@
+Description: Don't use poa convenience script in test suite
+ We can't install that convenience script because it conflicts with another
+ package, so change the test suite to use `variantCaller --algorithm=poa`
+ instead.
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-07-16
+--- pbgenomicconsensus.orig/tests/cram/poa-all4mer.t
++++ pbgenomicconsensus/tests/cram/poa-all4mer.t
+@@ -6,7 +6,7 @@
+ 
+ Run quiver.
+ 
+-  $ poa $INPUT -r $REFERENCE -o v.gff -o css.fa -o css.fq
++  $ variantCaller --algorithm=poa $INPUT -r $REFERENCE -o v.gff -o css.fa -o css.fq
+ 
+ No variants!
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 264dbf0..95723a6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 spelling.patch
 verbose-testing.patch
 disable-arrow-tests.patch
+no-poa-convenience-script.patch
diff --git a/debian/rules b/debian/rules
index 8cc36f9..a449350 100755
--- a/debian/rules
+++ b/debian/rules
@@ -42,6 +42,9 @@ override_dh_install:
 # Place executable programs in the main package
 	mkdir -p $(BINDIR)
 	mv debian/python-$(DEB_SOURCE)/usr/bin/* $(BINDIR)
+# Remove convenience script for poa; it conflicts with the poa package
+# See #831220
+	$(RM) $(BINDIR)/poa
 
 override_dh_auto_clean: clean-docs
 	dh_auto_clean

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git