[med-svn] [ariba] 01/01: suggest sspace

[Sascha Steinbiss]

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satta pushed a commit to branch with_sspace
in repository ariba.

commit e874c7cf6c88203c72e718262a3212f95fbf4379
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jun 28 14:11:22 2016 +0000

    suggest sspace
---
 debian/changelog                   |  7 +++++++
 debian/control                     |  4 +++-
 debian/patches/rename-sspace.patch | 14 ++++++++++++++
 debian/patches/series              |  1 +
 4 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index d2a6ebc..5cf3942 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+ariba (1.0.0-2) unstable; urgency=medium
+
+  * Suggest SSPACE package.
+  * Adapt SSPACE executable call to Debian's naming scheme.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Thu, 09 Jun 2016 08:46:05 +0000
+
 ariba (1.0.0-1) unstable; urgency=low
 
   * Initial packaging (Closes: #825529)
diff --git a/debian/control b/debian/control
index 786513b..39266f2 100644
--- a/debian/control
+++ b/debian/control
@@ -21,7 +21,8 @@ Build-Depends: debhelper (>= 9),
                spades,
                fastaq (>= 3.10.0),
                help2man,
-               asciidoctor
+               asciidoctor,
+               sspace
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/ariba.git
@@ -43,6 +44,7 @@ Depends: ${misc:Depends},
          fastaq (>= 3.10.0),
          r-cran-ape,
          python3-lxml
+Suggests: sspace
 Description: Antibiotic Resistance Identification By Assembly
  ARIBA is a tool that identifies antibiotic resistance genes by running local
  assemblies.
diff --git a/debian/patches/rename-sspace.patch b/debian/patches/rename-sspace.patch
new file mode 100644
index 0000000..6db5c9b
--- /dev/null
+++ b/debian/patches/rename-sspace.patch
@@ -0,0 +1,14 @@
+Description: rename sspace
+ Debian's SSPACE executable is called 'sspace' instead of SSPACE_Basic_2.0.pl.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/ariba/external_progs.py
++++ b/ariba/external_progs.py
+@@ -17,7 +17,7 @@
+     'nucmer' : 'nucmer',
+     'samtools': 'samtools',
+     'spades': 'spades.py',
+-    'sspace': 'SSPACE_Basic_v2.0.pl',
++    'sspace': 'sspace',
+     'r': 'Rscript',
+ }
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 22823e7..13d5481 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 rename-cdhit.patch
+rename-sspace.patch
 fix-spades-call.patch
 relax-pysam-version.patch

-- 
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