[med-svn] [iva] 01/01: applied quilt patches successfuly. Sitll issues with pysam

[Jorge Soares]

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

commit cea28fcbe4a9e0fa8e3eca0fcf20d90b739ada8e
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Mon Nov 24 11:22:48 2014 +0000

    applied quilt patches successfuly. Sitll issues with pysam
---
 .../patches/delay-import-and-remove-dependencies   | 90 ++++++++++++++++++++++
 debian/patches/remove-all-deps-from-setup-py       | 10 ---
 debian/patches/series                              |  2 +-
 3 files changed, 91 insertions(+), 11 deletions(-)

diff --git a/debian/patches/delay-import-and-remove-dependencies b/debian/patches/delay-import-and-remove-dependencies
new file mode 100644
index 0000000..213801d
--- /dev/null
+++ b/debian/patches/delay-import-and-remove-dependencies
@@ -0,0 +1,90 @@
+Description: Delaying module import and removing pypi dependencies
+Module import delay is done so we can extract usage for building
+man pages.
+Pypi dependencies are not needed, since iva's dependencies are
+stated in the Debian control file
+--- a/scripts/iva
++++ b/scripts/iva
+@@ -1,12 +1,6 @@
+ #!/usr/bin/env python3
+ 
+ import argparse
+-import os
+-import sys
+-import multiprocessing
+-import fastaq
+-import iva
+-
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] {-f reads_fwd -r reads_rev | --fr reads} <output directory>')
+@@ -69,6 +63,14 @@
+ other_group.add_argument('--version', action='version', version=iva.common.version)
+ 
+ options = parser.parse_args()
++
++
++import os
++import sys
++import multiprocessing
++import fastaq
++import iva
++
+ if options.seed_stop_length == 0:
+     options.seed_stop_length = int(0.9 * options.max_insert)
+ 
+--- a/scripts/iva_qc
++++ b/scripts/iva_qc
+@@ -1,9 +1,6 @@
+ #!/usr/bin/env python3
+ 
+ import argparse
+-import os
+-import sys
+-import iva
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] {(-f <reads_1.fq> -r <reads_2.fq>) | --fr reads.fq} {(--embl_dir | --ref_db) <directory>} <assembly.fasta> <prefix of output files>',
+@@ -54,6 +51,10 @@
+ options = parser.parse_args()
+ 
+ 
++import os
++import sys
++import iva
++
+ if options.embl_dir == options.ref_db == None:
+     print('You must use one of --embl_dir or --ref_db. Cannot continue.', file=sys.stderr)
+     sys.exit(1)
+--- a/scripts/iva_qc_make_db
++++ b/scripts/iva_qc_make_db
+@@ -1,8 +1,7 @@
+ #!/usr/bin/env python3
+ 
+-import sys
++
+ import argparse
+-import iva
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] <output directory>',
+@@ -18,6 +17,10 @@
+ parser.add_argument('--version', action='version', version=iva.common.version)
+ options = parser.parse_args()
+ 
++
++import sys
++import iva
++
+ iva.external_progs.write_prog_info('iva_qc_make_db', '-')
+ 
+ db = iva.kraken.Database(
+--- 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-all-deps-from-setup-py b/debian/patches/remove-all-deps-from-setup-py
deleted file mode 100644
index 4494fd9..0000000
--- a/debian/patches/remove-all-deps-from-setup-py
+++ /dev/null
@@ -1,10 +0,0 @@
-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/series b/debian/patches/series
index fb9dc55..2c9007b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-remove-all-deps-from-setup-py
+delay-import-and-remove-dependencies

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