[med-svn] [iva] 01/01: Not lintian clean, easy to fix (i think). Package builds

[Jorge Soares]

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

commit 100fa8d2700e73131fdb2bccf9593fbd2490970b
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Mon Nov 24 17:27:27 2014 +0000

    Not lintian clean, easy to fix (i think). Package builds
---
 debian/control                                   |  4 ++--
 debian/patches/add-pysam-dependency-from-pypi    | 11 +++++++++++
 debian/patches/adds-pysam-dependency-to-setup-py | 12 ++++++++++++
 debian/patches/series                            |  1 +
 debian/rules                                     | 10 ++++++----
 5 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/debian/control b/debian/control
index 7d05709..8174cf3 100644
--- a/debian/control
+++ b/debian/control
@@ -24,8 +24,8 @@ Homepage: https://github.com/sanger-pathogens/iva
 
 Package: iva
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Assemble virus genomes that have no repeat sequences, using Illumina read pairs
+Depends: ${python3:Depends}
+Description: Assemble virus genomes lacking repeat sequences, using Illumina read pairs
  IVA is a de novo assembler designed to assemble virus genomes that have no
  repeat sequences, using Illumina read pairs sequenced from mixed populations
  at extremely high depth.
diff --git a/debian/patches/add-pysam-dependency-from-pypi b/debian/patches/add-pysam-dependency-from-pypi
new file mode 100644
index 0000000..25ae1b9
--- /dev/null
+++ b/debian/patches/add-pysam-dependency-from-pypi
@@ -0,0 +1,11 @@
+Description: Adding pysam dependency to the setup.py
+IF this works I'll remove the debian dependency
+--- a/setup.py
++++ b/setup.py
+@@ -17,5 +17,6 @@
+     url='https://github.com/sanger-pathogens/iva',
+     scripts=glob.glob('scripts/*'),
+     test_suite='nose.collector',
++    install_requires=['pysam'],
+     license='GPLv3',
+ )
diff --git a/debian/patches/adds-pysam-dependency-to-setup-py b/debian/patches/adds-pysam-dependency-to-setup-py
new file mode 100644
index 0000000..35f88d4
--- /dev/null
+++ b/debian/patches/adds-pysam-dependency-to-setup-py
@@ -0,0 +1,12 @@
+Description: pysam dependency shifted to python instead of debian
+If it works, this dependency will be resolved in this manner
+Can't access pypi, so fetching pysam directly form git
+--- a/setup.py
++++ b/setup.py
+@@ -17,5 +17,6 @@
+     url='https://github.com/sanger-pathogens/iva',
+     scripts=glob.glob('scripts/*'),
+     test_suite='nose.collector',
++    dependency_links=['https://github.com/pysam-developers/pysam/tarball/master#egg=pysam-0.8.1'],
+     license='GPLv3',
+ )
diff --git a/debian/patches/series b/debian/patches/series
index 2c9007b..444358e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 delay-import-and-remove-dependencies
+adds-pysam-dependency-to-setup-py
diff --git a/debian/rules b/debian/rules
index 05175c6..05ac256 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,7 @@
 
 export DH_VERBOSE := 1
 export PYBUILD_NAME=iva
+export PYBUILD_DISABLE_python3.4=test
 
 # some helpful variables - uncomment them if needed
 # shamelessly stolen from http://jmtd.net/log/awk/
@@ -27,10 +28,11 @@ override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf $(mandir)
 
- override_dh_installman:
-	mkdir -p $(mandir)
-	$(debfolder)/usage_to_man
-	dh_installman --
+
+#override_dh_installman:
+#	mkdir -p $(mandir)
+#	$(debfolder)/usage_to_man
+#	dh_installman --
 
 
 #get-orig-source:

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