[med-svn] [iva] 03/05: remove obsolete patch files
Sascha Steinbiss
satta at debian.org
Mon Jan 29 13:56:09 UTC 2018
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository iva.
commit a4e9bffad79431b49ba2d1a04c2decdc93bb4276
Author: Sascha Steinbiss <satta at debian.org>
Date: Mon Jan 29 14:44:05 2018 +0100
remove obsolete patch files
---
debian/changelog | 9 +-
debian/patches/add-shebang-line-to-getMummerStats | 11 --
debian/patches/adjust_required_pysam_version.patch | 17 ---
debian/patches/remove-pypi-deps-from-setup-py | 17 ---
debian/patches/samtools_fix.patch | 120 ---------------------
debian/patches/spelling.patch | 13 ---
6 files changed, 7 insertions(+), 180 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 9c149c3..423d0b7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
-iva (1.0.8+ds-2) UNRELEASED; urgency=medium
+iva (1.0.9+ds-1) unstable; urgency=medium
+ [ Steffen Moeller ]
* debian/upstream/metadata: Added refs to registries
- -- Steffen Moeller <moeller at debian.org> Thu, 03 Aug 2017 14:33:14 +0200
+ [ Sascha Steinbiss ]
+ * New upstream release.
+ * Remove obsolete patch files.
+
+ -- Sascha Steinbiss <satta at debian.org> Fri, 26 Jan 2018 11:44:17 +0100
iva (1.0.8+ds-1) unstable; urgency=medium
diff --git a/debian/patches/add-shebang-line-to-getMummerStats b/debian/patches/add-shebang-line-to-getMummerStats
deleted file mode 100644
index d2f226c..0000000
--- a/debian/patches/add-shebang-line-to-getMummerStats
+++ /dev/null
@@ -1,11 +0,0 @@
-Description: Add shebang line to getMummerStats
-Author: Jorge Soares <j.s.soares at gmail.com>
-Last-Update: 2014-12-08
---- a/iva/gage/getMummerStats.sh
-+++ b/iva/gage/getMummerStats.sh
-@@ -1,3 +1,5 @@
-+#!/bin/sh
-+
- FILENAME=$1
- SCRIPT_PATH=$2
- JAVA_PATH=$2:.
diff --git a/debian/patches/adjust_required_pysam_version.patch b/debian/patches/adjust_required_pysam_version.patch
deleted file mode 100644
index d93fe85..0000000
--- a/debian/patches/adjust_required_pysam_version.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: relax pysam version
- Upstream has fixed pysm to version 0.8.3 because there are building issues
- with newer versions and pip. These are not present in Debian, so I'm relaxing the
- version requirements.
-Author: Sascha Steinbiss <sascha at steinbiss.name>
-Forwarded: not-needed, upstream insists on using 0.8.3
---- a/setup.py
-+++ b/setup.py
-@@ -60,7 +60,7 @@
- install_requires=[
- 'pyfastaq >= 3.10.0',
- 'networkx >= 1.7',
-- 'pysam >= 0.8.1, <= 0.8.3',
-+ 'pysam >= 0.8.1',
- ],
- license='GPLv3',
- classifiers=[
diff --git a/debian/patches/remove-pypi-deps-from-setup-py b/debian/patches/remove-pypi-deps-from-setup-py
deleted file mode 100644
index 946a8bf..0000000
--- a/debian/patches/remove-pypi-deps-from-setup-py
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Removes deps from setup.py
-Author: Jorge Soares <j.s.soares at gmail.com>
-Last-Update: 2014-12-08
---- a/setup.py
-+++ b/setup.py
-@@ -42,11 +42,6 @@
- scripts=glob.glob('scripts/*'),
- test_suite='nose.collector',
- tests_require=['nose >= 1.3'],
-- install_requires=[
-- 'pyfastaq >= 3.10.0',
-- 'networkx >= 1.7',
-- 'pysam >= 0.8.1, <= 0.8.3',
-- ],
- license='GPLv3',
- classifiers=[
- 'Development Status :: 4 - Beta',
diff --git a/debian/patches/samtools_fix.patch b/debian/patches/samtools_fix.patch
deleted file mode 100644
index 19233a9..0000000
--- a/debian/patches/samtools_fix.patch
+++ /dev/null
@@ -1,120 +0,0 @@
-From ed16c9b1a940fe11b14c8adfbe3853e889604ac4 Mon Sep 17 00:00:00 2001
-From: Sascha Steinbiss <sascha at steinbiss.name>
-Date: Tue, 3 May 2016 18:48:07 +0100
-Subject: [PATCH 1/3] make IVA compatible with new 'samtools sort' syntax
-
----
- iva/external_progs.py | 4 ++--
- iva/mapping.py | 6 +++++-
- 2 files changed, 7 insertions(+), 3 deletions(-)
-
-diff --git a/iva/external_progs.py b/iva/external_progs.py
-index 8b42054..c8056b1 100644
---- a/iva/external_progs.py
-+++ b/iva/external_progs.py
-@@ -23,10 +23,10 @@ def is_in_path(prog):
- 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
- 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
- 'smalt': ('smalt version', re.compile('^Version: (.*)$')),
-- 'samtools': ('samtools', re.compile('^Version: (.*)$')),
-+ 'samtools': ('samtools', re.compile('^Version: ([^ ]+)')),
- }
-
--
-+
- minimum_versions = {
- 'samtools': '0.1.19'
- }
-diff --git a/iva/mapping.py b/iva/mapping.py
-index 681b5be..63bfd90 100644
---- a/iva/mapping.py
-+++ b/iva/mapping.py
-@@ -5,6 +5,7 @@
- import pyfastaq
- import pysam
- from iva import common
-+from iva import external_progs
-
- class Error (Exception): pass
-
-@@ -78,7 +79,10 @@ def map_reads(reads_fwd, reads_rev, ref_fa, out_prefix, index_k=15, index_s=3, t
- if sort:
- threads = min(4, threads)
- thread_mem = int(500 / threads)
-- sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix
-+ if str(external_progs.get_version('samtools')) >= '1.2':
-+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M -o ' + final_bam + ' ' + intermediate_bam
-+ else:
-+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix
- index_cmd = 'samtools index ' + final_bam
- if verbose >= 2:
- print(' map reads. sort: ', sort_cmd)
-
-From 5fac89d891fb0932b60f06d8225f44a3642c2035 Mon Sep 17 00:00:00 2001
-From: Sascha Steinbiss <sascha at steinbiss.name>
-Date: Wed, 4 May 2016 08:52:50 +0000
-Subject: [PATCH 2/3] clean up test directories
-
----
- iva/qc_external.py | 7 ++++---
- 1 file changed, 4 insertions(+), 3 deletions(-)
-
-diff --git a/iva/qc_external.py b/iva/qc_external.py
-index b04bbb1..ae76718 100644
---- a/iva/qc_external.py
-+++ b/iva/qc_external.py
-@@ -142,9 +142,10 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c
- cwd = os.getcwd()
- try:
- os.mkdir(outdir)
-- os.chdir(outdir)
- except:
-- raise Error('Error mkdir ' + outdir)
-+ pass
-+ os.chdir(outdir)
-+ iva.common.syscall('rm -rf ./*')
-
- extractor = iva.egg_extract.Extractor(os.path.abspath(os.path.join(os.path.dirname(iva.__file__), os.pardir)))
- ratt_code_indir = os.path.join('iva', 'ratt')
-@@ -200,7 +201,7 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c
- except:
- pass
-
-- iva.common.syscall('rm query.* Reference.* nucmer.* out.*')
-+ iva.common.syscall('rm -f query.* Reference.* nucmer.* out.*')
-
- os.chdir(cwd)
- return stats
-
-From 3b25765ac1eeb4bab5246087ed3c2ef6c0648e36 Mon Sep 17 00:00:00 2001
-From: Sascha Steinbiss <sascha at steinbiss.name>
-Date: Wed, 4 May 2016 09:00:36 +0000
-Subject: [PATCH 3/3] make outdir recreation more robust
-
----
- iva/qc_external.py | 11 ++++++-----
- 1 file changed, 6 insertions(+), 5 deletions(-)
-
-diff --git a/iva/qc_external.py b/iva/qc_external.py
-index ae76718..bed1c58 100644
---- a/iva/qc_external.py
-+++ b/iva/qc_external.py
-@@ -140,12 +140,13 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c
- assembly = os.path.abspath(assembly)
-
- cwd = os.getcwd()
-- try:
-- os.mkdir(outdir)
-- except:
-- pass
-+ if os.path.exists(outdir):
-+ if os.path.isdir(outdir):
-+ shutil.rmtree(outdir)
-+ else:
-+ os.unlink(outdir)
-+ os.mkdir(outdir)
- os.chdir(outdir)
-- iva.common.syscall('rm -rf ./*')
-
- extractor = iva.egg_extract.Extractor(os.path.abspath(os.path.join(os.path.dirname(iva.__file__), os.pardir)))
- ratt_code_indir = os.path.join('iva', 'ratt')
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 128dec1..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: spelling fixes
-Author: Sascha Steinbiss <satta at debian.org>
---- a/scripts/iva_qc_make_db
-+++ b/scripts/iva_qc_make_db
-@@ -23,7 +23,7 @@
- )
-
- parser.add_argument('outdir', help='Name of output directory', metavar='Directory_name')
--parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segements, so put 8 GI numbers on one line for one flu reference)', metavar='Filename')
-+parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segments, so put 8 GI numbers on one line for one flu reference)', metavar='Filename')
- parser.add_argument('--skip_viruses', action='store_true', help='Do not run kraken-build --download-library viruses when building the database. If this option used, then --add_to_ref must also be used')
- parser.add_argument('--threads', type=int, help='Number of threads to use [%(default)s]', metavar='INT', default=1)
- parser.add_argument('--minimizer_len', type=int, help='Number to pass to kraken-build minimizer_len option [%(default)s]', default=13, metavar='INT')
--
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