[med-svn] r18899 - trunk/packages/spades/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Tue Mar 3 20:03:50 UTC 2015
Author: tille
Date: 2015-03-03 20:03:50 +0000 (Tue, 03 Mar 2015)
New Revision: 18899
Added:
trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch
trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch
Removed:
trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch
Modified:
trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
trunk/packages/spades/trunk/debian/patches/series
Log:
Better organising of patches
Added: trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch 2015-03-03 20:03:50 UTC (rev 18899)
@@ -0,0 +1,84 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Tue, 03 Mar 2015 20:55:53 +0100
+Description: We are using Debian packaged python-yaml
+ Debian has its own way to distinguish Python versions and there is no point
+ in doing this inside the code.
+ .
+ The patch is non-intrusive since it conserves the original code and uses
+ Debian pyyaml only if the original method fails.
+
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -4,8 +4,6 @@ add_subdirectory(jemalloc)
+ add_subdirectory(nlopt)
+ add_subdirectory(python_libs/joblib2)
+ add_subdirectory(python_libs/joblib3)
+-add_subdirectory(python_libs/pyyaml2)
+-add_subdirectory(python_libs/pyyaml3)
+ add_subdirectory(yaml-cpp)
+ add_subdirectory(ConsensusCore)
+ add_subdirectory(bamtools)
+--- a/spades.py
++++ b/spades.py
+@@ -32,10 +32,13 @@ import hammer_logic
+ import spades_logic
+ import options_storage
+ addsitedir(ext_python_modules_home)
+-if sys.version.startswith('2.'):
++try:
++ if sys.version.startswith('2.'):
+ import pyyaml2 as pyyaml
+-elif sys.version.startswith('3.'):
++ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
++except:
++ import yaml as pyyaml
+
+ def print_used_values(cfg, log):
+ def print_value(cfg, section, param, pretty_param="", margin=" "):
+--- a/src/spades_pipeline/hammer_logic.py
++++ b/src/spades_pipeline/hammer_logic.py
+@@ -73,10 +73,13 @@ def prepare_config_bh(filename, cfg, log
+
+ def prepare_config_ih(filename, cfg, ext_python_modules_home):
+ addsitedir(ext_python_modules_home)
++ try:
+ if sys.version.startswith('2.'):
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
++ except:
++ import yaml as pyyaml
+
+ data = pyyaml.load(open(filename, 'r'))
+ data["dataset"] = cfg.dataset_yaml_filename
+@@ -90,10 +93,13 @@ def prepare_config_ih(filename, cfg, ext
+ def run_hammer(corrected_dataset_yaml_filename, configs_dir, execution_home, cfg,
+ not_used_dataset_data, ext_python_modules_home, log):
+ addsitedir(ext_python_modules_home)
++ try:
+ if sys.version.startswith('2.'):
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
++ except:
++ import yaml as pyyaml
+ dst_configs = os.path.join(cfg.output_dir, "configs")
+ if os.path.exists(dst_configs):
+ shutil.rmtree(dst_configs)
+--- a/src/spades_pipeline/spades_logic.py
++++ b/src/spades_pipeline/spades_logic.py
+@@ -68,10 +68,13 @@ def get_read_length(output_dir, K, ext_p
+ max_read_length = 0
+ if os.path.isfile(est_params_filename):
+ addsitedir(ext_python_modules_home)
++ try:
+ if sys.version.startswith('2.'):
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
++ except:
++ import yaml as pyyaml
+ est_params_data = pyyaml.load(open(est_params_filename, 'r'))
+ for reads_library in est_params_data:
+ if reads_library['type'] in READS_TYPES_USED_IN_CONSTRUCTION:
Added: trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch 2015-03-03 20:03:50 UTC (rev 18899)
@@ -0,0 +1,69 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Tue, 03 Mar 2015 20:55:53 +0100
+Description: We are using Debian packaged python-joblib
+ Debian has its own way to distinguish Python versions and there is no point
+ in doing this inside the code.
+ .
+ The patch is non-intrusive since it conserves the original code and uses
+ Debian pyyaml only if the original method fails.
+
+--- a/src/spades_pipeline/hammer_logic.py
++++ b/src/spades_pipeline/hammer_logic.py
+@@ -37,10 +37,13 @@ def compress_dataset_files(dataset_data,
+ support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
+ else:
+ addsitedir(ext_python_modules_home)
+- if sys.version.startswith('2.'):
+- from joblib2 import Parallel, delayed
+- elif sys.version.startswith('3.'):
+- from joblib3 import Parallel, delayed
++ try:
++ if sys.version.startswith('2.'):
++ from joblib2 import Parallel, delayed
++ elif sys.version.startswith('3.'):
++ from joblib3 import Parallel, delayed
++ except:
++ from joblib import Parallel, delayed
+ n_jobs = min(len(to_compress), max_threads)
+ outputs = Parallel(n_jobs=n_jobs)(delayed(support.sys_call)(['gzip', '-f', '-7', reads_file]) for reads_file in to_compress)
+ for output in outputs:
+@@ -148,4 +151,4 @@ def run_hammer(corrected_dataset_yaml_fi
+ log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
+
+ if os.path.isdir(cfg.tmp_dir):
+- shutil.rmtree(cfg.tmp_dir)
+\ No newline at end of file
++ shutil.rmtree(cfg.tmp_dir)
+--- a/src/spades_pipeline/lucigen_nxmate.py
++++ b/src/spades_pipeline/lucigen_nxmate.py
+@@ -36,12 +36,14 @@ except ImportError:
+ support.error("Can't process Lucigen NxMate reads! Python module regex is not installed!")
+
+ addsitedir(spades_init.ext_python_modules_home)
+-if sys.version.startswith('2.'):
+- from joblib2 import Parallel, delayed
+-elif sys.version.startswith('3.'):
+- from joblib3 import Parallel, delayed
++try:
++ if sys.version.startswith('2.'):
++ from joblib2 import Parallel, delayed
++ elif sys.version.startswith('3.'):
++ from joblib3 import Parallel, delayed
++except:
++ from joblib import Parallel, delayed
+
+-
+ # CONSTANTS
+ READS_PER_THREAD = 25000
+ READS_PER_BATCH = READS_PER_THREAD * options_storage.threads # e.g. 100000 for 4 threads
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -2,8 +2,6 @@
+
+ add_subdirectory(jemalloc)
+ add_subdirectory(nlopt)
+-add_subdirectory(python_libs/joblib2)
+-add_subdirectory(python_libs/joblib3)
+ add_subdirectory(yaml-cpp)
+ add_subdirectory(ConsensusCore)
+ add_subdirectory(bamtools)
Modified: trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch 2015-03-03 12:32:31 UTC (rev 18898)
+++ trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch 2015-03-03 20:03:50 UTC (rev 18899)
@@ -6,14 +6,8 @@
--- a/ext/src/CMakeLists.txt
+++ b/ext/src/CMakeLists.txt
-@@ -2,11 +2,6 @@
-
- add_subdirectory(jemalloc)
+@@ -4,5 +4,4 @@ add_subdirectory(jemalloc)
add_subdirectory(nlopt)
--add_subdirectory(python_libs/joblib2)
--add_subdirectory(python_libs/joblib3)
--add_subdirectory(python_libs/pyyaml2)
--add_subdirectory(python_libs/pyyaml3)
add_subdirectory(yaml-cpp)
add_subdirectory(ConsensusCore)
-add_subdirectory(bamtools)
Modified: trunk/packages/spades/trunk/debian/patches/series
===================================================================
--- trunk/packages/spades/trunk/debian/patches/series 2015-03-03 12:32:31 UTC (rev 18898)
+++ trunk/packages/spades/trunk/debian/patches/series 2015-03-03 20:03:50 UTC (rev 18899)
@@ -1,6 +1,7 @@
+0001_use_debian_packaged_python-yaml.patch
+0002_use_debian_packaged_python-joblib.patch
do_not_install_third_party_libs.patch
adapt_to_debian_pathes.patch
-use_debian_packaged_python-yaml.patch
use-debian-packaged-bwa.patch
# use-debian-packaged-samtools.patch
# bamtools-cmake.patch
Deleted: trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch 2015-03-03 12:32:31 UTC (rev 18898)
+++ trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch 2015-03-03 20:03:50 UTC (rev 18899)
@@ -1,79 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
-Description: We are using Debian packaged python-yaml and
- python-joblib. Debian has its own way to distinguish Python versions
- and there is no point in doing this inside the code
-
---- a/spades.py
-+++ b/spades.py
-@@ -32,10 +32,7 @@ import hammer_logic
- import spades_logic
- import options_storage
- addsitedir(ext_python_modules_home)
--if sys.version.startswith('2.'):
-- import pyyaml2 as pyyaml
--elif sys.version.startswith('3.'):
-- import pyyaml3 as pyyaml
-+import yaml as pyyaml
-
- def print_used_values(cfg, log):
- def print_value(cfg, section, param, pretty_param="", margin=" "):
---- a/src/spades_pipeline/hammer_logic.py
-+++ b/src/spades_pipeline/hammer_logic.py
-@@ -37,10 +37,7 @@ def compress_dataset_files(dataset_data,
- support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
- else:
- addsitedir(ext_python_modules_home)
-- if sys.version.startswith('2.'):
-- from joblib2 import Parallel, delayed
-- elif sys.version.startswith('3.'):
-- from joblib3 import Parallel, delayed
-+ from joblib import Parallel, delayed
- n_jobs = min(len(to_compress), max_threads)
- outputs = Parallel(n_jobs=n_jobs)(delayed(support.sys_call)(['gzip', '-f', '-7', reads_file]) for reads_file in to_compress)
- for output in outputs:
-@@ -73,10 +70,7 @@ def prepare_config_bh(filename, cfg, log
-
- def prepare_config_ih(filename, cfg, ext_python_modules_home):
- addsitedir(ext_python_modules_home)
-- if sys.version.startswith('2.'):
-- import pyyaml2 as pyyaml
-- elif sys.version.startswith('3.'):
-- import pyyaml3 as pyyaml
-+ import yaml as pyyaml
-
- data = pyyaml.load(open(filename, 'r'))
- data["dataset"] = cfg.dataset_yaml_filename
-@@ -90,10 +84,7 @@ def prepare_config_ih(filename, cfg, ext
- def run_hammer(corrected_dataset_yaml_filename, configs_dir, execution_home, cfg,
- not_used_dataset_data, ext_python_modules_home, log):
- addsitedir(ext_python_modules_home)
-- if sys.version.startswith('2.'):
-- import pyyaml2 as pyyaml
-- elif sys.version.startswith('3.'):
-- import pyyaml3 as pyyaml
-+ import yaml as pyyaml
- dst_configs = os.path.join(cfg.output_dir, "configs")
- if os.path.exists(dst_configs):
- shutil.rmtree(dst_configs)
-@@ -142,4 +133,4 @@ def run_hammer(corrected_dataset_yaml_fi
- log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
-
- if os.path.isdir(cfg.tmp_dir):
-- shutil.rmtree(cfg.tmp_dir)
-\ No newline at end of file
-+ shutil.rmtree(cfg.tmp_dir)
---- a/src/spades_pipeline/spades_logic.py
-+++ b/src/spades_pipeline/spades_logic.py
-@@ -68,10 +68,7 @@ def get_read_length(output_dir, K, ext_p
- max_read_length = 0
- if os.path.isfile(est_params_filename):
- addsitedir(ext_python_modules_home)
-- if sys.version.startswith('2.'):
-- import pyyaml2 as pyyaml
-- elif sys.version.startswith('3.'):
-- import pyyaml3 as pyyaml
-+ import yaml as pyyaml
- est_params_data = pyyaml.load(open(est_params_filename, 'r'))
- for reads_library in est_params_data:
- if reads_library['type'] in READS_TYPES_USED_IN_CONSTRUCTION:
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