fixed blast code path problem

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index ef8f737ee8bc5507b5c7a24dd71c3a1bd27d80ce..82b104e0380b2f8794ebf9e0ce2693d835dd8cc0 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -18,7 +18,9 @@ using namespace std;
 
 BlastDB::BlastDB(string fastaFileName, float gO, float gE, float m, float mM) : Database(fastaFileName), 
 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-
+       
+       globaldata = GlobalData::getInstance();
+       
        cout << "Generating the temporary BLAST database...\t"; cout.flush();
 
        int randNumber = rand();
@@ -36,7 +38,10 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        }
        unalignedFastaFile.close();
        
-       string formatdbCommand = "~/Pipeline/src/cpp/production/blast/bin/formatdb -p F -o T -i " + dbFileName; //      format the database, -o option gives us the ability
+       path = globaldata->argv;
+       path = path.substr(0, (path.find_last_of('m')));
+       
+       string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
        system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot
        cout << "DONE." << endl << endl;        cout.flush();
@@ -71,7 +76,7 @@ Sequence* BlastDB::findClosestSequence(Sequence* candidate){
 //     wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
 //     long.  With this setting, it seems comparable in speed to the suffix tree approach.
 
-       string blastCommand = "~/Pipeline/src/cpp/production/blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28";
+       string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28";
        blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
        system(blastCommand.c_str());