[med-svn] [spades] 01/05: update patches
Sascha Steinbiss
sascha at steinbiss.name
Sat Feb 6 20:46:30 UTC 2016
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sascha-guest pushed a commit to branch master
in repository spades.
commit e7cb6bcc3876e317f6c8a731bad1a656a2b3d535
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Feb 6 19:45:00 2016 +0000
update patches
---
.../0001_use_debian_packaged_python-yaml.patch | 46 +++++++---------------
debian/patches/0003_accept-system-bwa.patch | 12 +++---
debian/patches/0103_use-debian-packaged-bwa.patch | 4 +-
3 files changed, 22 insertions(+), 40 deletions(-)
diff --git a/debian/patches/0001_use_debian_packaged_python-yaml.patch b/debian/patches/0001_use_debian_packaged_python-yaml.patch
index 5e5f2bd..0389734 100644
--- a/debian/patches/0001_use_debian_packaged_python-yaml.patch
+++ b/debian/patches/0001_use_debian_packaged_python-yaml.patch
@@ -7,9 +7,9 @@ Description: We are using Debian packaged python-yaml
The patch is non-intrusive since it conserves the original code and uses
Debian pyyaml only if the original method fails.
---- spades.orig/spades.py
-+++ spades/spades.py
-@@ -34,10 +34,13 @@
+--- a/spades.py
++++ b/spades.py
+@@ -34,10 +34,7 @@
import spades_logic
import options_storage
addsitedir(ext_python_modules_home)
@@ -17,19 +17,13 @@ Description: We are using Debian packaged python-yaml
- import pyyaml2 as pyyaml
-elif sys.version.startswith('3.'):
- import pyyaml3 as pyyaml
-+try:
-+ if sys.version.startswith('2.'):
-+ import pyyaml2 as pyyaml
-+ elif sys.version.startswith('3.'):
-+ import pyyaml3 as pyyaml
-+except:
-+ import yaml as pyyaml
++import yaml as pyyaml
import moleculo_postprocessing
import alignment
---- spades.orig/src/spades_pipeline/hammer_logic.py
-+++ spades/src/spades_pipeline/hammer_logic.py
-@@ -74,10 +74,13 @@
+--- a/src/spades_pipeline/hammer_logic.py
++++ b/src/spades_pipeline/hammer_logic.py
+@@ -74,10 +74,7 @@
def prepare_config_ih(filename, cfg, ext_python_modules_home):
addsitedir(ext_python_modules_home)
@@ -37,17 +31,11 @@ Description: We are using Debian packaged python-yaml
- import pyyaml2 as pyyaml
- elif sys.version.startswith('3.'):
- import pyyaml3 as pyyaml
-+ try:
-+ if sys.version.startswith('2.'):
-+ import pyyaml2 as pyyaml
-+ elif sys.version.startswith('3.'):
-+ import pyyaml3 as pyyaml
-+ except:
-+ import yaml as pyyaml
++ import yaml as pyyaml
data = pyyaml.load(open(filename, 'r'))
data["dataset"] = cfg.dataset_yaml_filename
-@@ -91,10 +94,13 @@
+@@ -91,10 +88,13 @@
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)
@@ -65,16 +53,16 @@ Description: We are using Debian packaged python-yaml
dst_configs = os.path.join(cfg.output_dir, "configs")
if os.path.exists(dst_configs):
shutil.rmtree(dst_configs)
-@@ -143,4 +149,4 @@
+@@ -143,4 +143,4 @@
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)
---- spades.orig/src/spades_pipeline/spades_logic.py
-+++ spades/src/spades_pipeline/spades_logic.py
-@@ -69,10 +69,13 @@
+--- a/src/spades_pipeline/spades_logic.py
++++ b/src/spades_pipeline/spades_logic.py
+@@ -69,10 +69,7 @@
max_read_length = 0
if os.path.isfile(est_params_filename):
addsitedir(ext_python_modules_home)
@@ -82,13 +70,7 @@ Description: We are using Debian packaged python-yaml
- import pyyaml2 as pyyaml
- elif sys.version.startswith('3.'):
- import pyyaml3 as pyyaml
-+ try:
-+ if sys.version.startswith('2.'):
-+ import pyyaml2 as pyyaml
-+ elif sys.version.startswith('3.'):
-+ import pyyaml3 as pyyaml
-+ except:
-+ import yaml 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:
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index 94e1653..087b47b 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -13,8 +13,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
---- spades.orig/src/spades_pipeline/support.py
-+++ spades/src/spades_pipeline/support.py
+--- a/src/spades_pipeline/support.py
++++ b/src/spades_pipeline/support.py
@@ -58,6 +58,22 @@
sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
sys.stdout.flush()
@@ -55,9 +55,9 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def check_file_existence(input_filename, message="", log=None, dipspades=False):
filename = abspath(expanduser(input_filename))
---- spades.orig/spades.py
-+++ spades/spades.py
-@@ -150,6 +150,22 @@
+--- a/spades.py
++++ b/spades.py
+@@ -144,6 +144,22 @@
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
@@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def fill_cfg(options_to_parse, log, secondary_filling=False):
skip_output_dir=secondary_filling
-@@ -421,7 +437,11 @@
+@@ -415,7 +431,11 @@
if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
cfg["mismatch_corrector"] = empty_config()
cfg["mismatch_corrector"].__dict__["skip-masked"] = None
diff --git a/debian/patches/0103_use-debian-packaged-bwa.patch b/debian/patches/0103_use-debian-packaged-bwa.patch
index 91a0168..9355359 100644
--- a/debian/patches/0103_use-debian-packaged-bwa.patch
+++ b/debian/patches/0103_use-debian-packaged-bwa.patch
@@ -13,8 +13,8 @@ Description: SPAdes originally contained a code copy of bwa since the version
ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
which enables successfull run of the test suite
---- spades.orig/ext/tools/CMakeLists.txt
-+++ spades/ext/tools/CMakeLists.txt
+--- a/ext/tools/CMakeLists.txt
++++ b/ext/tools/CMakeLists.txt
@@ -5,4 +5,3 @@
# See file LICENSE for details.
############################################################################
--
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