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Author: Andreas Tille <tille@debian.org>
Last-Changed: Tue, 03 Mar 2015 20:55:53 +0100
Description: Enable using Debian packaged bwa instead of bwa-spades
Users might have installed a local version of bwa which is used independently
from SPAdes. This is specifically true on Debian systems where the
dependency system ensures the installation of bwa. This patch uses the
local installed bwa as fallback if bwa-spades is not found.
.
The patch is non-intrusive since it conserves the original code and uses
Debian bwa only if bwa-spades is not available.
.
Note: The duplicated which() in two files is for sure not the best solution.
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
--- a/assembler/src/spades_pipeline/support.py
+++ b/assembler/src/spades_pipeline/support.py
@@ -61,6 +61,22 @@ def warning(warn_str, log=None, prefix="
sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
sys.stdout.flush()
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
def check_python_version():
def __next_version(version):
@@ -99,8 +115,14 @@ def check_binaries(binary_dir, log):
for binary in ["spades-hammer", "spades-ionhammer", "spades-core", "spades-bwa"]:
binary_path = os.path.join(binary_dir, binary)
if not os.path.isfile(binary_path):
- error("SPAdes binaries not found: " + binary_path + "\n" + get_spades_binaries_info_message(), log)
-
+ if binary == "bwa-spades":
+ localbwa = which('bwa')
+ if localbwa:
+ warning("Spades is using local bwa at %s." % localbwa, log)
+ else:
+ error("SPAdes binaries not found: " + binary_path + "\nThere is also no local bwa installation available\n" + get_spades_binaries_info_message(), log)
+ else:
+ error("SPAdes binaries not found: " + binary_path + "\n" + get_spades_binaries_info_message(), log)
def check_file_existence(input_filename, message="", log=None):
filename = abspath(expanduser(input_filename))
--- a/assembler/spades.py
+++ b/assembler/spades.py
@@ -156,6 +156,22 @@ def print_used_values(cfg, log):
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
def fill_cfg(options_to_parse, log, secondary_filling=False):
skip_output_dir = secondary_filling
@@ -509,7 +525,11 @@ def fill_cfg(options_to_parse, log, seco
if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
cfg["mismatch_corrector"] = empty_config()
cfg["mismatch_corrector"].__dict__["skip-masked"] = None
- cfg["mismatch_corrector"].__dict__["bwa"] = os.path.join(bin_home, "spades-bwa")
+ if which("bwa-spades"):
+ cfg["mismatch_corrector"].__dict__["bwa"] = os.path.join(bin_home, "bwa-spades")
+ else:
+ # as far as I can see it is checked later if this exists
+ cfg["mismatch_corrector"].__dict__["bwa"] = which("bwa")
cfg["mismatch_corrector"].__dict__["threads"] = options_storage.threads
cfg["mismatch_corrector"].__dict__["output-dir"] = options_storage.output_dir
cfg["run_truseq_postprocessing"] = options_storage.run_truseq_postprocessing
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