This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository parsnp.
commit 4dde0e6ba3f105dd45c94eb9f5d89364f073058b Author: Andreas Tille <[email protected]> Date: Thu Jul 21 09:02:20 2016 +0200 Some plain debugging was helpful to understand how parsnp works - leave this as a deactivated patch --- debian/patches/debug.patch | 75 ++++++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 76 insertions(+) diff --git a/debian/patches/debug.patch b/debian/patches/debug.patch new file mode 100644 index 0000000..87785a7 --- /dev/null +++ b/debian/patches/debug.patch @@ -0,0 +1,75 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Wed, 20 Apr 2016 10:31:32 +0200 +Description: Some plain debugging was helpful to understand how parsnp works + leave this as a deactivated patch + +--- a/Parsnp.py ++++ b/Parsnp.py +@@ -936,6 +936,7 @@ if __name__ == "__main__": + #3)run parsnp (cores, grid?) + print "-->Running Parsnp multi-MUM search and libMUSCLE aligner.." + if not os.path.exists(outputDir+os.sep+"blocks"): ++ print "DEBUG: mkdir", outputDir+os.sep+"blocks" + os.mkdir(outputDir+os.sep+"blocks") + command = "" + run_parsnp = 1 +@@ -951,14 +952,16 @@ if __name__ == "__main__": + command = "/usr/lib/parsnp/parsnp %sparsnpAligner.ini"%(outputDir+os.sep) + else: + command = "/usr/lib/parsnp/parsnp %spsnn.ini"%(outputDir+os.sep) ++ print "DEBUG not inifile_exists -> command:", command + else: + if not os.path.exists(inifile): + sys.stderr.write("Error: ini file %s does not exist!\n"%(inifile)) + sys.exit(1) + command = "/usr/lib/parsnp/parsnp %s"%(inifile) ++ print "DEBUG inifile_exists -> command:", command + run_command(command) + +- ++ print "DEBUG command successful:", command + if not os.path.exists(outputDir+os.sep+"parsnpAligner.xmfa"): + + successful_run = False +@@ -971,6 +974,7 @@ if __name__ == "__main__": + runcnt +=1 + break + os.system("mv "+outputDir+os.sep+"parsnpAligner.xmfa "+outputDir+os.sep+"parsnp.xmfa") ++ print "DEBUG 'if run_parsnp' is done" + xmfafile = open(outputDir+os.sep+"parsnp.xmfa",'r') + + file2hdr_dict = {} +@@ -995,6 +999,7 @@ if __name__ == "__main__": + sys.exit(1) + + #update thresholds ++ print "DEBUG update thresholds" + if coverage <= 0.01: + sys.stderr.write( " |->["+ERROR_RED+"ERROR"+ENDC+"]"+": aligned regions cover less than 1% of reference genome, something is not right.. please adjust params and rerun. If problem persists please contact developers ([email protected])"+ENDC) + sys.exit(1) +--- a/src/parsnp.cpp ++++ b/src/parsnp.cpp +@@ -517,6 +517,7 @@ void Aligner::writeOutput(string psnp,ve + test.append("/parsnpAligner.log"); + lcbdir.append("/blocks/"); + lcbprefix.append("/blocks/b"); ++cerr << "DEBUG: Try to create testfile " << test.c_str() << endl; + try + { + ofstream testfile ( test.c_str() ); +@@ -525,12 +526,13 @@ void Aligner::writeOutput(string psnp,ve + } + catch ( char const * str ) + { +- string command = "mkdir "; ++cerr << "DEBUG: Opening testfile " << test.c_str() << " failed - try to create directory " << this->outdir << endl; ++ string command = "mkdir -p "; + command.append(this->outdir); + int result = system(command.c_str()); + if ( result ) + { +- cerr << "ParSNP:: error creating output directory, exiting.." << endl; ++ cerr << "ParSNP:: error creating output directory" << this->outdir << ", exiting.." << endl; + exit(1); + } + } diff --git a/debian/patches/series b/debian/patches/series index 6ac76e5..9e77cc9 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,3 +4,4 @@ fix_install_path.patch avoid_rpath.patch add_missing_interpreter_line.patch proper_calls_to_tools.patch +# debug.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/parsnp.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
