[med-svn] [iva] 01/01: managed to inject local package, but build fails due to incompatibility python-pysam and iva is python3

[Jorge Soares]

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jssoares-guest pushed a commit to branch master
in repository iva.

commit 60e611cc5c08fd988f47cf3bc4b7d0599c60fb14
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Fri Nov 21 17:14:40 2014 +0000

    managed to inject local package, but build fails due to incompatibility python-pysam and iva is python3
---
 debian/control                                  |  2 +-
 debian/patches/remove-all-deps-from-setup-py    | 10 ++++++++++
 debian/patches/remove-fastaq-setuppy-dependency | 16 ----------------
 debian/patches/series                           |  2 +-
 4 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/debian/control b/debian/control
index e606a04..7d05709 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,7 @@ Build-Depends: debhelper (>= 9),
 	       samtools,
 	       mummer,
 	       smalt,
-	       fastaq,
+	       fastaq (>= 1.6),
 	       trimmomatic,
 	       bioperl,
 	       help2man
diff --git a/debian/patches/remove-all-deps-from-setup-py b/debian/patches/remove-all-deps-from-setup-py
new file mode 100644
index 0000000..4494fd9
--- /dev/null
+++ b/debian/patches/remove-all-deps-from-setup-py
@@ -0,0 +1,10 @@
+Description: Relying on debian dependencies instead
+--- a/setup.py
++++ b/setup.py
+@@ -17,6 +17,5 @@
+     url='https://github.com/sanger-pathogens/iva',
+     scripts=glob.glob('scripts/*'),
+     test_suite='nose.collector',
+-    install_requires=['nose >= 1.3', 'fastaq >= 1.6.0', 'networkx'],
+     license='GPLv3',
+ )
diff --git a/debian/patches/remove-fastaq-setuppy-dependency b/debian/patches/remove-fastaq-setuppy-dependency
deleted file mode 100644
index fe34282..0000000
--- a/debian/patches/remove-fastaq-setuppy-dependency
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Removes the fastaq 1.6 depedency form setup.py.
-It keeps on looking for fasataq 1.6 in: https://pypi.python.org/simple/fastaq/
-Since it's not there and debian already has fastaq 1.6 I'm removing it to see
-if package builds
-Index: iva/setup.py
-===================================================================
---- iva.orig/setup.py
-+++ iva/setup.py
-@@ -17,6 +17,6 @@ setup(
-     url='https://github.com/sanger-pathogens/iva',
-     scripts=glob.glob('scripts/*'),
-     test_suite='nose.collector',
--    install_requires=['nose >= 1.3', 'fastaq >= 1.6.0', 'networkx'],
-+    install_requires=['nose >= 1.3', 'networkx'],
-     license='GPLv3',
- )
diff --git a/debian/patches/series b/debian/patches/series
index fe7fa0f..fb9dc55 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-remove-fastaq-setuppy-dependency
+remove-all-deps-from-setup-py

-- 
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