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This removes a workaround that is better fixed in Catchall than in
Mothur, so I did that (packaged in bio-linux-catchall just now as I
don't have the source compiling yet.)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -198,6 +198,7 @@ int CatchAllCommand::execute() {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ /* TB for Bio-Linux: Don't need this...
//get location of catchall
path = m->argv;
path = path.substr(0, (path.find_last_of("othur")-5));
@@ -246,6 +247,11 @@ int CatchAllCommand::execute() {
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
+ */
+
+ /* TB for Bio-Linux: We just need this, assuming catchall is properly wrapped to avoid
+ * the bug described above - see the bio-linux-catchall package */
+ string catchAllCommandExe = "catchall ";
if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
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