Fix finding foldseek binary as sibling of spacedust's binary

Author: milot-mirdita

src/commons/LocalParameters.cpp

@@ -1 +1,44 @@
 #include "LocalParameters.h"
+
+#ifdef __APPLE__
+#include <mach-o/dyld.h>
+#include <stdlib.h>
+#else
+#include <unistd.h>
+#endif
+
+std::string LocalParameters::getAbsExePath() {
+#ifdef __APPLE__
+    uint32_t bufSize = 0;
+    // determine required buffer size.
+    _NSGetExecutablePath(NULL, &bufSize);
+    char* pathBuffer = new char[bufSize];
+    if (_NSGetExecutablePath(pathBuffer, &bufSize) != 0) {
+        delete[] pathBuffer;
+        return std::string();
+    }
+    char* resolved = realpath(pathBuffer, NULL);
+    std::string result = resolved ? resolved : pathBuffer;
+    free(resolved);
+    delete[] pathBuffer;
+    return result;
+#else
+    const char* linkPath = "/proc/self/exe";
+    size_t bufSize = PATH_MAX;
+    while (true) {
+        std::vector<char> buf(bufSize);
+        ssize_t len = readlink(linkPath, buf.data(), bufSize);
+        if (len < 0) {
+            return std::string();
+        }
+        if (static_cast<size_t>(len) < bufSize) {
+            buf[len] = '\0';  // null-terminate
+            char* resolved = realpath(buf.data(), NULL);
+            std::string result = resolved ? resolved : std::string(buf.data());
+            free(resolved);
+            return result;
+        }
+        bufSize *= 2;
+    }
+#endif
+}

src/commons/LocalParameters.h

@@ -1,7 +1,8 @@
 #ifndef LOCALPARAMETERS_H
 #define LOCALPARAMETERS_H
 
-#include <Parameters.h>
+#include "Parameters.h"
+#include "FileUtil.h"
 
 const int CITATION_SPACEDUST = CITATION_END;
 
@@ -56,6 +57,7 @@ class LocalParameters : public Parameters {
     std::string fileExclude;
     std::string foldseekPath;
 
+    static std::string getAbsExePath();
 private:
     LocalParameters() : 
         Parameters(),
@@ -159,7 +161,8 @@ class LocalParameters : public Parameters {
         fileInclude = ".*";
         fileExclude = "^$";
         gffDir = "";
-        foldseekPath = "foldseek";
+        std::string binaryDir = FileUtil::dirName(getAbsExePath());
+        foldseekPath =  binaryDir.empty() ? "foldseek" : binaryDir + "/foldseek";
 
         //TODO: add citations (foldseek & mmseqs & clustersearch)
         citations.emplace(CITATION_SPACEDUST, "");

src/workflow/clusterdb.cpp

@@ -15,7 +15,6 @@ void setclusterDbDefaults(LocalParameters *p) {
 int clusterdb(int argc, const char **argv, const Command &command) {
     LocalParameters &par = LocalParameters::getLocalInstance();
     setclusterDbDefaults(&par);
-    par.foldseekPath = FileUtil::dirName(*(argv - 2)) + "/foldseek";
     par.parseParameters(argc, argv, command, true, 0, 0);
 
     if (FileUtil::directoryExists(par.db2.c_str()) == false) {

src/workflow/clustersearch.cpp

@@ -39,7 +39,6 @@ void setClusterSearchWorkflowDefaults(LocalParameters *p) {
 int clustersearch(int argc, const char **argv, const Command &command) {
     LocalParameters &par = LocalParameters::getLocalInstance();
     setClusterSearchWorkflowDefaults(&par);
-    par.foldseekPath = FileUtil::dirName(*(argv - 2)) + "/foldseek";
 
     par.PARAM_MAX_REJECTED.addCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_DB_OUTPUT.addCategory(MMseqsParameter::COMMAND_EXPERT);