[med-svn] [iva] 01/01: patch to remove fastaq dependency from setup.py. Leaving this dependency to be fullfilled by Debian

[Jorge Soares]

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

commit 81bfc20442000f25a3542538286f4b5fada50e55
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Fri Nov 21 14:13:06 2014 +0000

    patch to remove fastaq dependency from setup.py. Leaving this dependency to be fullfilled by Debian
---
 ...ules-in-scripts-to-generate-manpages-from-usage | 91 ----------------------
 patches/remove-fastaq-setuppy-dependency           | 15 ++++
 patches/series                                     |  2 +-
 3 files changed, 16 insertions(+), 92 deletions(-)

diff --git a/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage b/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage
deleted file mode 100644
index aea9e58..0000000
--- a/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage
+++ /dev/null
@@ -1,91 +0,0 @@
-Description: Delays import of several modules.
-This allows manpage creation directly form the scripts usage
-statementsIndex: iva/scripts/iva
-===================================================================
---- iva.orig/scripts/iva
-+++ iva/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('--strand_bias'
- 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)
- 
-Index: iva/scripts/iva_qc
-===================================================================
---- iva.orig/scripts/iva_qc
-+++ iva/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>',
-@@ -17,7 +14,6 @@ ref_group = parser.add_argument_group('R
- ref_group.add_argument('--embl_dir', help='Directory of reference EMBL files. If not used, must use --ref_db', metavar='Directory')
- ref_group.add_argument('--ref_db', help='Directory of database made by iva_qc_make_db. If not used, must use --embl_dir', metavar='Directory')
- 
--
- reads_group = parser.add_argument_group('Reads options (REQUIRED: either --fr, or (-f and -r))')
- reads_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forwards reads fasta or fastq file. Must be used with --reads_rev', metavar='filename[.gz]')
- reads_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta or fastq file. Must be used with --reads_rev', metavar='filename[.gz]')
-@@ -54,6 +50,10 @@ other_group.add_argument('--version', ac
- 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)
-Index: iva/scripts/iva_qc_make_db
-===================================================================
---- iva.orig/scripts/iva_qc_make_db
-+++ iva/scripts/iva_qc_make_db
-@@ -1,8 +1,6 @@
- #!/usr/bin/env python3
- 
--import sys
- import argparse
--import iva
- 
- parser = argparse.ArgumentParser(
-     usage = '%(prog)s [options] <output directory>',
-@@ -18,6 +16,10 @@ parser.add_argument('--verbose', action=
- 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(
diff --git a/patches/remove-fastaq-setuppy-dependency b/patches/remove-fastaq-setuppy-dependency
new file mode 100644
index 0000000..af1fca7
--- /dev/null
+++ b/patches/remove-fastaq-setuppy-dependency
@@ -0,0 +1,15 @@
+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 buildsIndex: 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/patches/series b/patches/series
index ee5e4bc..fe7fa0f 100644
--- a/patches/series
+++ b/patches/series
@@ -1 +1 @@
-delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage
+remove-fastaq-setuppy-dependency

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