[med-svn] [iva] 03/03: starting patches form scratch

[Jorge Soares]

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

commit f37aa4f55c0087936dde43c80582d27d5ce4edfc
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Mon Dec 8 11:19:59 2014 +0000

    starting patches form scratch
---
 debian/patches/add-pysam-dependency-from-pypi      | 11 ---
 debian/patches/adds-pysam-dependency-to-setup-py   | 12 ---
 .../patches/delay-import-and-remove-dependencies   | 90 ----------------------
 ...from-setuppy => remove-pypi-deps-from-setup-py} |  8 +-
 debian/patches/series                              |  3 +-
 5 files changed, 7 insertions(+), 117 deletions(-)

diff --git a/debian/patches/add-pysam-dependency-from-pypi b/debian/patches/add-pysam-dependency-from-pypi
deleted file mode 100644
index 25ae1b9..0000000
--- a/debian/patches/add-pysam-dependency-from-pypi
+++ /dev/null
@@ -1,11 +0,0 @@
-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
deleted file mode 100644
index 35f88d4..0000000
--- a/debian/patches/adds-pysam-dependency-to-setup-py
+++ /dev/null
@@ -1,12 +0,0 @@
-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/delay-import-and-remove-dependencies b/debian/patches/delay-import-and-remove-dependencies
deleted file mode 100644
index 213801d..0000000
--- a/debian/patches/delay-import-and-remove-dependencies
+++ /dev/null
@@ -1,90 +0,0 @@
-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/strip-dependencies-from-setuppy b/debian/patches/remove-pypi-deps-from-setup-py
similarity index 52%
rename from debian/patches/strip-dependencies-from-setuppy
rename to debian/patches/remove-pypi-deps-from-setup-py
index c1e81f4..93448ce 100644
--- a/debian/patches/strip-dependencies-from-setuppy
+++ b/debian/patches/remove-pypi-deps-from-setup-py
@@ -1,10 +1,14 @@
-Description: Removing pypi dependencies from setup.py
+Descripition: Deletes pypi deps
+Author: Jorge Soares <j.s.soares at gmail.com>
+Last-Update: 2014-12-08
+
 --- a/setup.py
 +++ b/setup.py
-@@ -17,6 +17,5 @@
+@@ -17,7 +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'],
+-    dependency_links=['http://github.com/sanger-pathogens/fastaq/tarball/master#egg=fastaq-1.7.0'],
      license='GPLv3',
  )
diff --git a/debian/patches/series b/debian/patches/series
index a584f4d..eb84497 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
-add-shebang-line-to-getMummerStats
-strip-dependencies-from-setuppy
+remove-pypi-deps-from-setup-py

-- 
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