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Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Update: Thu, 24 Apr 2014 18:41:42 +0100
Description: Mothur ships with some .pat files which are needed by a couple of commands.
Default behaviour is to fall back to looking in the exec dir, which makes
no sense in a package, so redirect it.
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -314,10 +314,10 @@
for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
exepath = exepath.substr(0, (tempPath.find_last_of('m')));
- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
+ string tryPath = "/usr/share/mothur/";
+ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
in2.close();
lookupFileName = tryPath;
}
@@ -334,10 +334,10 @@
for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
exepath = exepath.substr(0, (tempPath.find_last_of('m')));
- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
+ string tryPath = "/usr/share/mothur/";
+ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
ifstream in2;
- int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
in2.close();
lookupFileName = tryPath;
--- a/sffmultiplecommand.cpp
+++ b/sffmultiplecommand.cpp
@@ -315,10 +315,10 @@
for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
exepath = exepath.substr(0, (tempPath.find_last_of('m')));
- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
+ string tryPath = "/usr/share/mothur/";
+ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
ifstream in2;
- int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
in2.close();
lookupFileName = tryPath;
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