Exemplo n.º 1
0
void link(void) {
    int i;
    FILE *fp;

    if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
        if ( get_dosex() != OPT_PMODE )
            fprintf( stderr, "LINK use only with PMODE!\n" );
        sprintf( args, "/NOIGNORECASE %s @" RESPONSE " ", 
            get_option(OPT_MAPFILE) ? "/MAP" : "" );	
        fp = response( RESPONSE );
        if (! get_option(OPT_NODEFLIB) ) {
            if ( get_option(OPT_DEBUG) )
                fprintf(fp,"%s\\C0DOSD.OBJ", get_syslib_path() );
            else
                fprintf(fp,"%s\\C0DOS.OBJ", get_syslib_path() );
        }
        for ( i = 0; i < obj_file_cnt(); i++ )
            fprintf( fp, " %s", obj_file(i) );
        fprintf( fp, "\n%s\n%s\n",  
            get_exe_name(),
            get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
        );
        if (! get_option(OPT_NODEFLIB) )
            fprintf(fp,"%s\\CLDOS.LIB", get_syslib_path() );
        for ( i = 0; i < lib_file_cnt(); i++ )
            fprintf( fp, " %s", lib_file(i) );
        fprintf( fp, "\n" );
        fclose(fp);
        exec("LINK", args );					
        if (! get_option(OPT_KEEPRSP) )
            unlink( RESPONSE );
    }
}
Exemplo n.º 2
0
void wlink(void) {
    int i;
    char *dosx;
    FILE *fp;

    if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
        switch ( get_dosex() ) {
            case OPT_PMODEW:dosx = "pmodew.exe"; break;
            case OPT_DOS4G:	dosx = "4gs.exe"; break;
            case OPT_WDOSX:	dosx = "wdosxle.exe"; break;
            case OPT_DOS32A:dosx = "dos32a.exe"; break;
            case OPT_ZRDX:	dosx = "zrdx.exe"; break;
            case OPT_CAUSEWAY:	dosx = "cwstub.exe"; break;
            case OPT_D3X: dosx = "d3xw.exe"; break;
            case OPT_PMODE:	
            
            default:
                fprintf( stderr, "WLINK NO use with PMODE!\n" );
                dosx = "4gs.exe";
                break;
        }
        fp = response( RESPONSE );
        fprintf( fp,
            "op osname=CC386[%s]\n"
            "format os2 le\n"
            "op nod\n"
            "op quiet\n"
            "op stub=%s\\%s\n"
            "name %s\n",
            dosx,
            get_syslib_path(),
            dosx,
            get_exe_name()
        );
        if ( get_option(OPT_MAPFILE) )
            fprintf( fp, "op map\n" );
        if ( get_option(OPT_DEBUG) )
            fprintf( fp, "debug all \nop symf\n" );
        if (! get_option(OPT_NODEFLIB) )
            fprintf( fp, "file %s\\C0DOSW.OBJ\n", get_syslib_path() );
        for( i = 0; i < obj_file_cnt(); i++)
            fprintf( fp, "file %s\n", obj_file(i) );
        if (! get_option(OPT_NODEFLIB) )
            fprintf( fp, "library %s\\CLDOS.LIB\n", get_syslib_path() );
        for( i = 0; i < lib_file_cnt(); i++)
            fprintf( fp, "library %s\n", lib_file(i) );
        fclose(fp);
        exec("WLINK", "@" RESPONSE );
        if (! get_option(OPT_KEEPRSP) )
            unlink( RESPONSE );
    }
}
Exemplo n.º 3
0
void tlink(void) {
    int i;
    FILE *fp;

    if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
        if ( get_dosex() != OPT_PMODE )
            fprintf( stderr, "TLINK use only with PMODE!\n" );
        fp = response( RESPONSE );
        fprintf( fp, "/3/c/d%s%s", 
            get_option(OPT_MAPFILE) ? "/m/l/s" : "/x",
            get_option(OPT_DEBUG) ? "/v" : ""
        );
        if ( lib_file_cnt() > 0 )
            fprintf(fp, "/L%s ", get_lib_path() );
        if (! get_option(OPT_NODEFLIB) ) {
            if ( get_option(OPT_DEBUG) )
                fprintf(fp,"%s\\C0DOSD.OBJ", get_syslib_path() );
            else
                fprintf(fp,"%s\\C0DOS.OBJ", get_syslib_path() );
        }
        for ( i = 0; i < obj_file_cnt(); i++ )
            fprintf( fp, " %s", obj_file(i) );
        fprintf( fp, ",%s,%s,",  
            get_exe_name(),
            get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
        );
        if (! get_option(OPT_NODEFLIB) )
            fprintf(fp,"%s\\CLDOS.LIB", get_syslib_path() );
        for ( i = 0; i < lib_file_cnt(); i++ )
            fprintf( fp, " %s", lib_file(i) );
        fprintf( fp, "\n" );
        fclose(fp);
        exec("TLINK", "@" RESPONSE );					
        if (! get_option(OPT_KEEPRSP) )
            unlink( RESPONSE );
    }
}
Exemplo n.º 4
0
/**
 * Non-Windows shared library constructor. This ensures that the environment
 * variable \c TWEEK_BASE_DIR is set as soon as this shared library is loaded.
 * If it is not set, then it sets it based on an assumption about the
 * structure of a Tweek installation. More specifically, an assumption is made
 * that this shared library lives in the \c lib subdirectory of the Tweek
 * installation. Therefore, the root of the Tweek installation is the parent
 * of the directory containing this shared library.
 */
extern "C" void __attribute ((constructor)) tweekLibraryInit()
{
   fs::path base_dir;
   const char* env_dir = std::getenv("TWEEK_BASE_DIR");

   // If TWEEK_BASE_DIR is not set, look up the path to this shared library
   // and use it to provide a default setting for that environment variable.
   if ( NULL == env_dir )
   {
      Dl_info info;
      info.dli_fname = 0;
      const int result =
#if defined(__GNUC__) && __GNUC_MAJOR__ < 4
         dladdr((void*) &tweekLibraryInit, &info);
#else
         dladdr(reinterpret_cast<void*>(&tweekLibraryInit), &info);
#endif

      // NOTE: dladdr(3) really does return a non-zero value on success.
      if ( 0 != result )
      {
         try
         {
            fs::path lib_file(info.dli_fname, fs::native);
            lib_file = fs::system_complete(lib_file);

#if defined(VPR_OS_IRIX) && defined(_ABIN32)
            const std::string bit_suffix("32");
#elif defined(VPR_OS_IRIX) && defined(_ABI64) || \
      defined(VPR_OS_Linux) && defined(__x86_64__)
            const std::string bit_suffix("64");
#else
            const std::string bit_suffix("");
#endif

            // Get the directory containing this shared library.
            const fs::path lib_path = lib_file.branch_path();

            // Start the search for the root of the Tweek installation in the
            // parent of the directory containing this shared library.
            base_dir = lib_path.branch_path();

            // Use the lib subdirectory to figure out when we have found the
            // root of the Tweek installation tree.
            const fs::path lib_subdir(std::string("lib") + bit_suffix);

            bool found(false);
            while ( ! found && ! base_dir.empty() )
            {
               try
               {
                  if ( ! fs::exists(base_dir / lib_subdir) )
                  {
                     base_dir = base_dir.branch_path();
                  }
                  else
                  {
                     found = true;
                  }
               }
               catch (fs::filesystem_error&)
               {
                  base_dir = base_dir.branch_path();
               }
            }

            if ( found )
            {
               setenv("TWEEK_BASE_DIR",
                      base_dir.native_directory_string().c_str(), 1);
            }
         }
         catch (fs::filesystem_error& ex)
         {
            std::cerr << "Automatic assignment of TWEEK_BASE_DIR failed:\n"
                      << ex.what() << std::endl;
         }
      }
   }
   else
   {
      try
      {
         base_dir = fs::path(env_dir, fs::native);
      }
      catch (fs::filesystem_error& ex)
      {
         std::cerr << "Invalid path set in TWEEK_BASE_DIR environment "
                   << "variable:\n" << ex.what() << std::endl;
      }
   }

   if ( ! base_dir.empty() )
   {
      // If base_dir were empty, this would result in data_dir being relative
      // to the current working directory.
      const fs::path data_dir = base_dir / TWEEK_SHARE_DIR;

      // We use the overwrite value of 0 as a way around testing whether the
      // environment variable is already set.
      setenv("TWEEK_DATA_DIR", data_dir.native_directory_string().c_str(), 0);
   }
}
Exemplo n.º 5
0
/**
 * Non-Windows shared library constructor. This ensures that the environment
 * variable \c GADGET_BASE_DIR is set as soon as this shared library is loaded.
 * If it is not set, then it sets it based on an assumption about the
 * structure of a Gadgeteer installation. More specifically, an assumption is
 * made that this shared library lives in the \c lib subdirectory of the
 * Gadgeteer installation. Therefore, the root of the Gadgeteer installation
 * is the parent of the directory containing this shared library.
 */
extern "C" void __attribute ((constructor)) gadgetLibraryInit()
{
   fs::path base_dir;
   const char* env_dir = std::getenv("GADGET_BASE_DIR");

   // If GADGET_BASE_DIR is not set, look up the path to this shared library
   // and use it to provide a default setting for that environment variable.
   if ( NULL == env_dir )
   {
      Dl_info info;
      info.dli_fname = 0;
      const int result =
#if defined(__GNUC__) && __GNUC_MAJOR__ < 4
         dladdr((void*) &gadgetLibraryInit, &info);
#else
         dladdr(reinterpret_cast<void*>(&gadgetLibraryInit), &info);
#endif

      // NOTE: dladdr(3) really does return a non-zero value on success.
      if ( 0 != result )
      {
         try
         {
            fs::path lib_file(
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
               info.dli_fname
#else
               info.dli_fname, fs::native
#endif
            );
            lib_file = fs::system_complete(lib_file);

#if defined(GADGET_LIBDIR_NAME)
            const std::string lib_dir_name(GADGET_LIBDIR_NAME);
#else
            const std::string lib_dir_name("lib");
#endif

            // Get the directory containing this shared library.
            const fs::path lib_path = lib_file.branch_path();

            // Start the search for the root of the Gadgeteer installation in
            // the parent of the directory containing this shared library.
            base_dir = lib_path.branch_path();

            // Use the lib subdirectory to figure out when we have found the
            // root of the Gadgeteer installation tree.
            const fs::path lib_subdir(lib_dir_name);

            bool found(false);
            while ( ! found && ! base_dir.empty() )
            {
               try
               {
                  if ( ! fs::exists(base_dir / lib_subdir) )
                  {
                     base_dir = base_dir.branch_path();
                  }
                  else
                  {
                     found = true;
                  }
               }
               catch (fs::filesystem_error&)
               {
                  base_dir = base_dir.branch_path();
               }
            }

            if ( found )
            {
               setenv("GADGET_BASE_DIR",
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
                      base_dir.native().c_str(),
#else
                      base_dir.native_directory_string().c_str(),
#endif
                      1);
            }
         }
         catch (fs::filesystem_error& ex)
         {
            std::cerr << "Automatic assignment of GADGET_BASE_DIR failed:\n"
                      << ex.what() << std::endl;
         }
      }
   }
   else
   {
      try
      {
         base_dir =
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
            fs::path(env_dir);
#else
            fs::path(env_dir, fs::native);
#endif
      }
      catch (fs::filesystem_error& ex)
      {
         std::cerr << "Invalid path set in GADGET_BASE_DIR environment "
                   << "variable:\n" << ex.what() << std::endl;
      }
   }

   if ( ! base_dir.empty() )
   {
      // If base_dir were empty, this would result in data_dir being relative
      // to the current working directory.
      const fs::path data_dir = base_dir / GADGET_SHARE_DIR;

      // We use the overwrite value of 0 as a way around testing whether the
      // environment variable is already set.
      setenv("GADGET_DATA_DIR",
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
             data_dir.native().c_str(),
#else
             data_dir.native_directory_string().c_str(),
#endif
             0);
   }
}
Exemplo n.º 6
0
bool SRAssembler::read_library_file() {
	ifstream lib_file(this->library_file.c_str());
	string line;
	Library* lib = NULL;
	while (getline(lib_file, line)){
		line = trim(line);
		if (line == "[LIBRARY]") {
			if (lib != NULL){
				if (lib->get_left_read() == ""){
					print_message("r1 file is expected in config file!");
					return false;
				}
				this->libraries.push_back(*lib);
			}
			lib = new Library(this->libraries.size(), this->data_dir, this->tmp_dir, this->logger);
		} else {
			vector<string> tokens;
			tokenize(line, tokens, "=");
			if (tokens.size() == 2){
				string param = trim(tokens[0]);
				string value = trim(tokens[1]);
				if (param == "r1" && lib != NULL) {
					lib->set_left_read(value);
					if (!file_exists(lib->get_left_read())) {
						print_message("r1 file in config file: " + lib->get_left_read() + " does not exist!");
						return false;
					}
				}
				if (param == "r2" && lib != NULL) {
					lib->set_right_read(value);
					if (!file_exists(lib->get_right_read())) {
						print_message("r2 file in config file: " + lib->get_right_read() + " does not exist!");
						return false;
					}
					lib->set_paired_end(true);
				}

				if (param == "insert_size" && lib != NULL) {
					lib->set_insert_size(str2int(value));
				}
				if (param == "direction" && lib != NULL) {
					lib->set_reversed(str2int(value));
				}
				if (param == "format" && lib != NULL) {
					if (value == "fastq") {
						lib->set_format(FORMAT_FASTQ);
					}
					else if (value == "fasta") {
						lib->set_format(FORMAT_FASTA);
					} else {
						print_message("format in config file should be 'fastq' or 'fasta'!");
						return false;
					}
				}
			}
		}
	}
	if (lib != NULL){
		if (lib->get_left_read() == ""){
			print_message("r1 file is expected in config file!");
			return false;
		}
		this->libraries.push_back(*lib);
	}
	if (this->libraries.size() == 0){
		print_message(" No [LIBRARY] section found in config file!");
		return false;
	}
	return true;

}
Exemplo n.º 7
0
void valx(void) {
    int i;
    FILE *fp;
    char *c0 = "C0DOS.OBJ";
    char *c0d= "C0DOSD.OBJ";
    char *cl = "CLDOS.LIB";
    char *ci = NULL;
    char *dosx = NULL;
   char *lnk_op = "/NCI /32";


    if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
        int sys = get_dosex();
        switch ( sys ) {
            case OPT_W32CON:
                c0d = c0 = "C0xwin.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB"; 
                lnk_op = "/NCI /PE";
                break;
            case OPT_W32GUI:
                c0d = c0 = "C0win.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB"; 
                lnk_op = "/NCI /PE /WIN";
                break;
            case OPT_W32DLL: 
                c0d = c0 = "C0dwin.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB";
                lnk_op = "/NCI /PE /BDL";
                break;
         case OPT_DOS32A:
            c0d = "c0doswd.obj" ;
            c0 = "c0dosw.obj" ;
            lnk_op = "/NCI /LE" ;
            dosx = "stub32a.exe" ;
            break ;
            case OPT_PMODEW:
                c0d = "c0doswd.obj" ;
                c0 = "c0dosw.obj" ;
                lnk_op = "/NCI /LE" ;
                dosx = "pmodew.exe"; 
                break;
            case OPT_DOS4G:	
                c0d = "c0doswd.obj" ;
                c0 = "c0dosw.obj" ;
                lnk_op = "/NCI /LE" ;
                dosx = "4gstub.exe"; 
                break;
            case OPT_WDOSX:	
                c0d = "c0doswd.obj" ;
                c0 = "c0dosw.obj" ;
                lnk_op = "/NCI /LE" ;
                dosx = "wdosxle.exe"; 
                break;
            case OPT_ZRDX:	
                c0d = "c0doswd.obj" ;
                c0 = "c0dosw.obj" ;
                lnk_op = "/NCI /LE" ;
                dosx = "zrdx.exe"; 
                break;
            case OPT_CAUSEWAY:	
                c0d = "c0doswd.obj" ;
                c0 = "c0dosw.obj" ;
                lnk_op = "/NCI /LE" ;
                dosx = "cwstub.exe"; 
                break;
            case OPT_HXDOS:
                c0d = c0 = "C0xwin.obj"; 
                cl = "CLWIN.LIB"; 
                ci = "CLIMP.LIB"; 
                lnk_op = "/NCI /PE";
                dosx = "dpmist32.bin";
                break;
            case OPT_WHXDOS:
                c0d = c0 = "C0doswhx.obj"; 
                lnk_op = "/NCI /PE";
                dosx = "hdld32.bin";
                break;
            case OPT_D3X:
                c0d = "c0doswd.obj";
                c0 = "c0dos.obj";
                lnk_op = "/NCI /LE" ;
                dosx = "d3xw.exe"; 
                break;
            default:
                fprintf( stderr, "VALX use only with PMODE!\n" );
            case OPT_PMODE:
                break;
        }
        fp = response( RESPONSE );
        fprintf( fp, "-NOCA -USE32 %s ",
            get_option(OPT_MAPFILE) ? "-MAP" : "-NOMAP" );	
        if ( lnk_op )
            fprintf( fp, "%s ", lnk_op);
        if (dosx)
            fprintf(fp, "-STB:(%s\\%s) ", get_syslib_path(), dosx);
        if (! get_option(OPT_NODEFLIB) ) {
            if ( get_option(OPT_DEBUG) )
            fprintf(fp,"\"%s\\%s\"", get_syslib_path(), c0d );
            else
            fprintf(fp,"\"%s\\%s\"", get_syslib_path(), c0 );
        }
        for ( i = 0; i < obj_file_cnt(); i++ )
            fprintf( fp, " %s", obj_file(i) );
        fprintf( fp, ",%s,%s,",  
            get_exe_name(),
            get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
        );
        if (! get_option(OPT_NODEFLIB) )
         fprintf(fp,"\"%s\\%s\"", get_syslib_path(), cl );
        if (ci)
         fprintf(fp," \"%s\\%s\"", get_syslib_path(), ci );
        for ( i = 0; i < lib_file_cnt(); i++ )
            fprintf( fp, " %s", lib_file(i) );
        fprintf( fp, "\n" );
        for ( i = 0; i < res_file_cnt(); i++ )
            fprintf( fp, " %s", res_file(i) );
        fprintf( fp, "\n\n" );
        fclose(fp);
        exec("VALX", "@" RESPONSE );
        if (! get_option(OPT_KEEPRSP) )
            unlink( RESPONSE );
          if ( !get_option(OPT_KEEPGEN) )
        {
            del_res_tmpfiles();
        }
        if (sys == OPT_WHXDOS)
        {
            exec("PATCHPE", get_exe_name());
        }
    }
}
Exemplo n.º 8
0
void olink(void) {
    int i;
    FILE *fp;
    char *c0 = "c0pm.o";
    char *c0d= "c0pmd.o";
    char *cl = "cldos.l";
    char *ci = NULL;
   char *lnk_op = "/T:PM";


    if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
        int sys = get_dosex();
        switch ( sys ) {
            case OPT_W32CON:
                c0d = c0 = "c0xpe.o"; cl = "clwin.l"; ci = "climp.l"; 
                lnk_op = "/T:CON32";
                break;
            case OPT_W32GUI:
                c0d = c0 = "c0pe.o"; cl = "clwin.l"; ci = "climp.l"; 
                lnk_op = "/T:GUI32";
                break;
            case OPT_W32DLL: 
                c0d = c0 = "c0dpe.o"; cl = "clwin.l"; ci = "climp.l";
                lnk_op = "/T:DLL32";
                break;
         case OPT_DOS32A:
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;sstub32a.exe" ;
            break ;
            case OPT_PMODEW:
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;spmodew.exe" ;
                break;
            case OPT_DOS4G:	
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;s4gstub.exe" ;
                break;
            case OPT_WDOSX:	
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;swdosxle.exe" ;
                break;
            case OPT_ZRDX:	
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;szrdx.exe" ;
                break;
            case OPT_CAUSEWAY:	
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;scwstub.exe" ;
                break;
            case OPT_HXDOS:
                c0d = c0 = "c0xpe.o"; 
                cl = "CLWIN.L"; 
                ci = "CLIMP.L"; 
                lnk_op = "/T:CON32;sdpmist32.bin";
                break;
            case OPT_WHXDOS:
                c0d = "c0hxd.o";
                c0 = "c0hx.o"; 
                lnk_op = "/T:CON32;shdld32.bin /DOBJECTALIGN=10000";
                break;
            case OPT_D3X:
            c0d = "c0watd.o" ;
            c0 = "c0wat.o" ;
            lnk_op = "/T:DOS32;sd3xw.exe" ;
                break;
            default:
                fprintf( stderr, "VALX use only with PMODE!\n" );
            case OPT_PMODE:
                break;
        }
        fp = response( RESPONSE );
        fprintf( fp, "-c%s",
            get_option(OPT_MAPFILE) ? " -m" : "" );	
        fprintf( fp, " -o%s%s", get_exe_name(),	get_option( OPT_MAPFILE) ? get_exe_name() : "");
        if ( lnk_op )
        {
            fprintf( fp, " %s", lnk_op);
        }
        if (! get_option(OPT_NODEFLIB) ) {
            if ( get_option(OPT_DEBUG) )
            fprintf(fp," \"%s\\%s\"", get_syslib_path(), c0d );
            else
            fprintf(fp," \"%s\\%s\"", get_syslib_path(), c0 );
        }
        for ( i = 0; i < obj_file_cnt(); i++ )
            fprintf( fp, " %s", obj_file(i) );
        for ( i = 0; i < lib_file_cnt(); i++ )
            fprintf( fp, " %s", lib_file(i) );
        if (! get_option(OPT_NODEFLIB) )
        {
            if (cl)
            {
                 fprintf(fp," \"%s\\%s\"", get_syslib_path(), cl );
            }
            if (ci)
            {
                 fprintf(fp," \"%s\\%s\"", get_syslib_path(), ci );
            }
        }
        for ( i = 0; i < res_file_cnt(); i++ )
            fprintf( fp, " %s", res_file(i) );
        fclose(fp);
        exec("olink", "@" RESPONSE );
        if (! get_option(OPT_KEEPRSP) )
            unlink( RESPONSE );
          if ( !get_option(OPT_KEEPGEN) )
        {
            del_res_tmpfiles();
        }
        if (sys == OPT_WHXDOS)
        {
            exec("PATCHPE", get_exe_name());
        }
    }
}