Pikachu_2014 wrote:Au passage, la racine "/var/www/html/" pour ton installation est-elle vraiment justifiée ? Cela ne me semble guère standard...

make clean

[Elegans@localhost cisortho-1.1]$ ./configure --prefix=/var/www/html/

cisortho.cpp: In function 'int Cutoff(int, char**)':
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp: In function 'int main(int, char**)':
cisortho.cpp:223: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:223: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:224: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:224: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:225: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:225: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:226: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:226: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:227: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:227: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:228: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:228: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:229: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:229: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:230: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:230: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:231: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:231: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:232: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:232: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:233: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:233: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:234: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:234: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:235: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:235: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:236: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:236: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:237: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:237: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:238: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:238: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:239: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:239: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:246: warning: deprecated conversion from string constant to 'char*'

[...]

make[1]: *** [load.o] Error 1
make[1]: Leaving directory `/var/www/html/cisortho-1.1/src'
make: *** [all-recursive] Error 1

make: *** [all-recursive] Error 1

#include <iostream>
#include <sstream>

#include "opt.h"
#include "index_trie.h"
#include "dnacol.h"
#include "dna_scanning.h"
#include "dnastats.h"
#include "dna.h"
#include "litestream.h"

#include <unistd.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>


using std::cerr;
using std::cout;
using std::endl;
using std::string;

int MinTreeDepth = 6;
int MaxTreeDepth = 50;
int MaxSuffixLoad = 2;
int PrefixLength = 2;
int ChunkSize = 100000;
char *OutfilePrefix = NULL;
char *SinglePrefix = NULL;
char *FolderPrefix = NULL;

char * DataDirectory = const_cast<char *>(".");

int n_DNA, n_Species;
char **DNA, **Species;

int GenomeIndex(int argc, char const** argv){

  if (OutfilePrefix == NULL){
    cerr<<"Please provide an output file prefix (option -o)"<<endl;
    exit(53);
  }

    
  std::ostringstream TreeTempDir; 
  std::ostringstream PosTempDir; 

  if (FolderPrefix == NULL){
    PosTempDir<<getpid()<<"_gpos";
    TreeTempDir<<getpid()<<"_itrie";
  }
  else {
    PosTempDir<<FolderPrefix<<"_gpos";
    TreeTempDir<<FolderPrefix<<"_itrie";
  }
    
  //parse dna from SequenceFile, build a dna_collection from it
  if (n_Species != n_DNA) {
    cerr<<"You must have the same number of species names as genomic sequence files."<<endl;
    exit(53);
  }

  std::vector<string> sSpecies(n_Species);
  std::string sDataDirectory(DataDirectory);

  for (int g=0; g < n_Species; g++) sSpecies[g] = Species[g];

  cis::dna_collection dnac;
  for (int g=0; g < n_DNA; g++){
    try {
      std::cout<<"Parsing "<<DNA[g]<<" genomic sequence file..."<<std::endl;
      dnac.add(sSpecies[g], sDataDirectory, DNA[g]);
    }
    catch (string &msg){ cerr<<msg<<endl; return 2; }
}

  dnac.calc_offsets();
  dnac.open_dnas();

  mkdir(TreeTempDir.str().c_str(), 0755);
  mkdir(PosTempDir.str().c_str(), 0755);
  DIR * treedir = opendir(TreeTempDir.str().c_str());
  DIR * posdir = opendir(PosTempDir.str().c_str());

  std::ofstream treefile, posfile;
  std::ifstream tree_bufbase;
  litestream tree_bufstream(tree_bufbase, ChunkSize);

//   bfs::path treedir(TreeTempDir.str());
//   bfs::path posdir(PosTempDir.str());
//   bfs::create_directory(treedir);
//   bfs::create_directory(posdir);

  index_trie::set_max_suffix_load(MaxSuffixLoad);
  index_trie * root = new index_trie();
  
  cout<<"Scanning all dna for prefixes...";
  cout.flush();

  std::set<cis::dnastring> Prefixes, ptmp;
  std::set<cis::dnastring>::iterator prefix_iter;

  if (FolderPrefix != NULL){

    dirent * current_file;
    while ((current_file = readdir(treedir)) != NULL){

//     bfs::directory_iterator end_itr; // default construction yields past-the-end
//     for (bfs::directory_iterator itr(treedir); itr != end_itr; ++itr){

      string prefix = current_file->d_name;
      //string prefix = itr->leaf();
      cis::dnastring dprefix = cis::ToDNAString(prefix);
      Prefixes.insert(dprefix);
    }


    cis::dnastring pfx;
    for (prefix_iter = Prefixes.begin();
         prefix_iter != Prefixes.end(); ++prefix_iter){

      pfx = *prefix_iter;

      string spfx = cis::FromDNAString(pfx);

      string treepath = TreeTempDir.str() + spfx;
      string pospath = PosTempDir.str() + spfx;

      tree_bufstream.open(treepath.c_str());

      if (! tree_bufstream.good()){
        cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
        exit(50);
      }

      node_info subroot = readNode(tree_bufstream);

      root->insertfile(pfx.c_str(), pfx.size(),
                       treepath, subroot.subtree_size,
                       pospath, subroot.suffix_count);

      tree_bufstream.close();
    }
  }

  else {

    for (cis::DNAS::iterator dna_it = dnac.begin(); 
         dna_it != dnac.end(); ++dna_it){
      
      ptmp = dnastats::Spectrum(*(*dna_it), PrefixLength, ChunkSize);
      Prefixes.insert(ptmp.begin(), ptmp.end());
    }
    
    cout<<"found "<<Prefixes.size()<<" prefixes."<<endl;
    
    cis::dnastring pfx;
    for (prefix_iter = Prefixes.begin();
         prefix_iter != Prefixes.end(); ++prefix_iter){
      
      pfx = *prefix_iter;
      
      index_trie * subroot = new index_trie();
      subroot->build_subtree(pfx, dnac, MinTreeDepth, MaxTreeDepth, ChunkSize);
      subroot->push();
      
      cis::NUC lastNuc = *pfx.rbegin();
      
      if (! subroot->empty()){
        
        subroot->count();
        
        string spfx = cis::FromDNAString(pfx);
        string treepath = TreeTempDir.str() + string("/") + spfx;
        string pospath = PosTempDir.str() + string("/") + spfx;
        
        treefile.open(treepath.c_str(), std::ios::out | std::ios::binary);
        //treefile.open(treedir / spfx, std::ios::out | std::ios::binary);
        if (! treefile){
          cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
          exit(50);
        }
        
        posfile.open(pospath.c_str(), std::ios::out | std::ios::binary);
        //posfile.open(posdir / spfx, std::ios::out | std::ios::binary);
        if (! posfile){
          cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
          exit(50);
        }

        cout<<"Writing subtree with prefix "<<spfx<<", "
            <<subroot->nbytes<<" bytes, "
            <<subroot->nsuffixes<<" patterns...";
        cout.flush();
        
        subroot->write(lastNuc, treefile, posfile);
        treefile.close();
        posfile.close();

        root->insertfile(pfx.c_str(), pfx.size(), 
                         treepath, subroot->nbytes,
                         pospath, subroot->nsuffixes);
//         root->insertfile(pfx.c_str(), pfx.size(), 
//                          treedir / spfx, subroot->nbytes,
//                          posdir / spfx, subroot->nsuffixes);

        cout<<"done."<<endl;

        //return 0;

      } 
        
      delete subroot; //memory
    }

  }



  string tree(OutfilePrefix); tree += ".itrie";
  treefile.open(tree.c_str(), std::ios::out | std::ios::binary);

  string pos(OutfilePrefix); pos += ".gpos";
  posfile.open(pos.c_str(), std::ios::out | std::ios::binary);

  //return 0;

  root->push();
  root->count();
  root->write(cis::X, treefile, posfile);

  cout<<"Wrote "<<root->nbytes<<" bytes and "
      <<root->nsuffixes<<" patterns."<<endl;

  delete root;

  treefile.close();
  posfile.close();

  string dnasrc(OutfilePrefix); dnasrc += ".dnas";
  std::ofstream dnafile;
  dnafile.open(dnasrc.c_str());

  for (cis::DNAS::iterator dna_it = dnac.begin(); 
       dna_it != dnac.end(); ++dna_it) 
    dnafile<<*(*dna_it)<<endl;

  dnafile.close();


  //delete all files in treedir, posdir
  cout<<"Removing all files in "
      <<TreeTempDir.str().c_str()
      <<" and "<<PosTempDir.str().c_str()<<"."<<endl;

  dirent * current_file;
  while ((current_file = readdir(treedir)) != NULL) {
    cout<<"Would be unlinking "<<current_file->d_name<<endl;
    //unlink(current_file->d_name);
  }
  rmdir(TreeTempDir.str().c_str());

  while ((current_file = readdir(posdir)) != NULL) {
    cout<<"Would be unlinking "<<current_file->d_name<<endl;
    //unlink(current_file->d_name);
  }
  rmdir(PosTempDir.str().c_str());
  
//   bfs::remove_all(treedir);
//   bfs::remove_all(posdir);

  return 0;
}


int main(int argc, char const**argv){

  OptRegister(&MinTreeDepth,OPT_INT,               'x', "min-tree-depth","minimum pattern length to search.");
  OptRegister(&MaxTreeDepth,OPT_INT,               'y', "max-tree-depth","maximum depth of the index tree.");
  OptRegister(&PrefixLength,OPT_INT,               'p', "prefix-length","length of prefix (3 is good) for splitting the subtree building.");
  OptRegister(&MaxSuffixLoad,OPT_INT,               'l', "max-suffix-load","maximum number of suffixes at a leaf before pushing further");
  OptRegister(&ChunkSize,OPT_INT,                  'c', "chunk-size","size of reading a chunk of DNA sequence for scanning");
  optrega_array(&n_Species, &Species, OPT_STRING,'n', "species-names","species names (comma-separated)");
  optrega_array(&n_DNA, &DNA, OPT_STRING,        's', "sequence-files","sequence files (comma-separated)");
  OptRegister(&DataDirectory, OPT_STRING,        't', "dna-directory", "directory containing 'sequence-files'");
  OptRegister(&OutfilePrefix,OPT_STRING,         'o', "outfile-prefix","prefix on output files with extensions 'gpos', 'itree', and 'dnas'");
  OptRegister(&SinglePrefix,OPT_STRING,          'f', "single-prefix","for testing");
  OptRegister(&FolderPrefix,OPT_STRING,          'd', "folder-prefix","for partial runs");

  optMain(GenomeIndex);

  if (argc==1){
    char const** myargv;
    char const* mybuf[2];
    mybuf[0]=argv[0];
    mybuf[1]="$";
    myargv=mybuf;
    int myargc=2;
    cout<<endl<<endl
        <<"Build a tree and genome position index file from a sequence file"<<endl
        <<"for fast, ungapped pattern searching."<<endl;

    opt(&myargc,&myargv);
  }
    
  else opt(&argc,&argv);
  return GenomeIndex(argc,argv);
}

[Elegans@localhost opt-3.19]$ make
Making all in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/www/html/opt-3.19/src'
Making all in test
make[1]: Entering directory `/var/www/html/opt-3.19/test'
g++ -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testcc.cc
testcc.cc: In function 'int go(int, char**)':
testcc.cc:17: error: 'cout' was not declared in this scope
testcc.cc:19: error: 'endl' was not declared in this scope
testcc.cc:23: error: 'cout' was not declared in this scope
testcc.cc:23: error: 'endl' was not declared in this scope
testcc.cc: In function 'int main(int, char**)':
testcc.cc:70: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:76: warning: deprecated conversion from string constant to 'char*'
testcc.cc:77: warning: deprecated conversion from string constant to 'char*'
testcc.cc:80: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:86: warning: deprecated conversion from string constant to 'char*'
testcc.cc:87: warning: deprecated conversion from string constant to 'char*'
make[1]: *** [testcc.o] Error 1
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
make: *** [all-recursive] Error 1

Pikachu_2014 wrote:1) Ne compile pas en root. Jamais.

Pikachu_2014 wrote:2) Peux-tu poster le contenu du fichier test/testcc.cc ?

/* testcc.cc */

#include <iostream.h>
#include <stdio.h>
#include <opt.h>

int month=4;
int day=24;
int year=1993;
int julian=0;
char *who=NULL;
int version=99;

int go(int argc, char **argv)
{
    if (argc>1) {
    cout << 
    "In program: " << argv[0] <<
    "Extra option: " << argv[1] << endl;
    }

    if (optinvoked(&month)) {
    cout << "User set month..." << endl;
    }

    if (month == 9 && day == 11 && year == 1989) {
        printf("Happy birthday, Max\n");
    } else {
        printf("Hello, %s: %4d/%02d/%02d %s\n",(who==NULL ? "world" : who),
               year,month,day,(julian ? "(Julian)" : ""));
    }
    return OPT_OK;
}

int checkyear(void *v)
{
    if (year == 2000) {
        printf("Watch out for that year=2000 bug!\n");
        return OPT_ERROR;
    }
    return OPT_OK;
}
int quit()
{
    printf("Bye...\n");
    return OPT_OK;
}
int write_version(void *v)
{
    /* it's a little hokey that this requires an argument... */
    v = &version; 
    printf("Version %d\n",version);
    optExitNumber(12);
    return OPT_EXIT;
}
int fix_mon(void *v)
{
    int m;
    /* fix whatever int variable v is pointing to */
    m = *((int *)v);
    if (m < 1 || m > 12) 
        m=1;
    *((int *)v) = m;
    return OPT_OK;
} 

int
main(int argc, char **argv)
{
    OptRegister(&month,'m',"month");
    opthook(&month,fix_mon);

    OptRegister(&day,'d',"day","Day");
    opthelp(&day,"Use day of month, should be less than 32");
    
    OptRegister(&year,"year");
    optdescript(&year,"What Year");
    opthook(&year,checkyear);

    OptRegister(&julian,OPT_BOOL,"julian");

    optregp(&who,OPT_STRING,"who","Who to say hello to");

    optexec("version",write_version,"Write version number and exit");

    optEnvVarName( "OPT" );
    optDefaultFile( "testoptrc" ); /* in practice, you do ~/.testoptrc */
    
    optMain(go);
    optQuit(quit);

    opt(&argc,&argv);
    return go(argc,argv);
}

[root@localhost ~]# yum install gcc-c++ gcc
Loaded plugins: refresh-packagekit
fedora                                                                                                                                 | 2.8 kB     00:00     
updates                                                                                                                                | 3.4 kB     00:00     
Setting up Install Process
Package gcc-4.3.2-7.i386 already installed and latest version
Resolving Dependencies
--> Running transaction check
---> Package gcc-c++.i386 0:4.3.2-7 set to be updated
--> Processing Dependency: libstdc++-devel = 4.3.2-7 for package: gcc-c++-4.3.2-7.i386
--> Running transaction check
---> Package libstdc++-devel.i386 0:4.3.2-7 set to be updated
--> Finished Dependency Resolution

Dependencies Resolved

==============================================================================================================================================================
 Package                                     Arch                             Version                                Repository                          Size
==============================================================================================================================================================
Installing:
 gcc-c++                                     i386                             4.3.2-7                                fedora                             3.9 M
Installing for dependencies:
 libstdc++-devel                             i386                             4.3.2-7                                fedora                             3.8 M

Transaction Summary
==============================================================================================================================================================
Install      2 Package(s)         
Update       0 Package(s)         
Remove       0 Package(s)         

Total download size: 7.7 M
Is this ok [y/N]: y
Downloading Packages:
(1/2): gcc-c++-4.3.2-7.i386.rpm                                                                                                        | 3.9 MB     00:10     
(2/2): libstdc++-devel-4.3.2-7.i386.rpm                                                                                                | 3.8 MB     00:09     
--------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                         369 kB/s | 7.7 MB     00:21     
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing     : libstdc++-devel-4.3.2-7.i386                                                                                                           1/2 
  Installing     : gcc-c++-4.3.2-7.i386                                                                                                                   2/2 

Installed:
  gcc-c++.i386 0:4.3.2-7                                                                                                                                      

Dependency Installed:
  libstdc++-devel.i386 0:4.3.2-7                                                                                                                              

Complete!

[root@localhost html]# tar xvf opt-3.19.tar.gz 
opt-3.19/
opt-3.19/Makefile.in
opt-3.19/README
opt-3.19/AUTHORS
opt-3.19/COPYING
opt-3.19/ChangeLog
opt-3.19/INSTALL
opt-3.19/Makefile.am
opt-3.19/NEWS
opt-3.19/aclocal.m4
opt-3.19/configure
opt-3.19/configure.in
opt-3.19/install-sh
opt-3.19/mdate-sh
opt-3.19/missing
opt-3.19/mkinstalldirs
opt-3.19/opt.spec.in
opt-3.19/stamp-vti
opt-3.19/texinfo.tex
opt-3.19/version.texi
opt-3.19/opt.texi
opt-3.19/opt.spec
opt-3.19/COPYING.gpl
opt-3.19/src/
opt-3.19/src/Makefile.in
opt-3.19/src/Makefile.am
opt-3.19/src/opt_util.c
opt-3.19/src/opt_reg.c
opt-3.19/src/opt_regt.c
opt-3.19/src/opt_menu.c
opt-3.19/src/opt_proc.c
opt-3.19/src/ag.c
opt-3.19/src/opt_regcc.cc
opt-3.19/src/opt_num.c
opt-3.19/src/opt.h
opt-3.19/src/opt_sf.h
opt-3.19/src/ag.h
opt-3.19/src/opt_p.h
opt-3.19/src/makeopth.pl
opt-3.19/test/
opt-3.19/test/Makefile.am
opt-3.19/test/Makefile.in
opt-3.19/test/t_num.c
opt-3.19/test/testopt.c
opt-3.19/test/birthday.c
opt-3.19/test/hooktest.c
opt-3.19/test/iloop.c
opt-3.19/test/testmain.c
opt-3.19/test/testtypes.c
opt-3.19/test/tstring.c
opt-3.19/test/tnull.c
opt-3.19/test/manyopts.c
opt-3.19/test/tarray.c
opt-3.19/test/testcc.cc
opt-3.19/test/testlong.c
opt-3.19/test/checkopt
opt-3.19/test/checkoptcc
opt-3.19/ext/
opt-3.19/ext/Makefile.in
opt-3.19/ext/Makefile.am
opt-3.19/ext/Opt.pm
opt-3.19/ext/tkopt
opt-3.19/opt.info
opt-3.19/opt.info-1
opt-3.19/opt.info-2
[root@localhost html]# ls
cisortho-0.9.0  ICeE  ICeE_save  ICeE.tar  ICeE_version_1.5  maqgene  opt-3.19  opt-3.19.tar.gz
[root@localhost html]# cd opt-3.19
[root@localhost opt-3.19]# ls
aclocal.m4  configure     COPYING.gpl  install-sh   mdate-sh       NEWS        opt.info-2   opt.texi  stamp-vti    version.texi
AUTHORS     configure.in  ext          Makefile.am  missing        opt.info    opt.spec     README    test
ChangeLog   COPYING       INSTALL      Makefile.in  mkinstalldirs  opt.info-1  opt.spec.in  src       texinfo.tex
[root@localhost opt-3.19]# ./configure 
creating cache ./config.cache
checking for a BSD compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets ${MAKE}... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for working makeinfo... missing
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking for c++... c++
checking whether the C++ compiler (c++  ) works... yes
checking whether the C++ compiler (c++  ) is a cross-compiler... no
checking whether we are using GNU C++... yes
checking whether c++ accepts -g... yes
checking for a BSD compatible install... /usr/bin/install -c
checking whether make sets ${MAKE}... (cached) yes
checking for ranlib... ranlib
checking for strdup... yes
checking for snprintf... yes
checking for longjmp... yes
checking how to run the C preprocessor... gcc -E
checking for signal.h... yes
checking return type of signal handlers... void
updating cache ./config.cache
creating ./config.status
creating test/Makefile
creating src/Makefile
creating ext/Makefile
creating Makefile
creating opt.spec

[root@localhost opt-3.19]# make
Making all in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_util.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_reg.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_regt.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_menu.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_proc.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c ag.c
g++ -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_regcc.cc
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_num.c
rm -f libopt.a
ar cru libopt.a opt_util.o opt_reg.o opt_regt.o opt_menu.o opt_proc.o ag.o opt_regcc.o opt_num.o 
ranlib libopt.a
make[1]: Leaving directory `/var/www/html/opt-3.19/src'
Making all in test
make[1]: Entering directory `/var/www/html/opt-3.19/test'
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c t_num.c
gcc  -g -O2  -o t_num  t_num.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testopt.c
gcc  -g -O2  -o testopt  testopt.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c birthday.c
gcc  -g -O2  -o birthday  birthday.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c hooktest.c
gcc  -g -O2  -o hooktest  hooktest.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c iloop.c
gcc  -g -O2  -o iloop  iloop.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testmain.c
gcc  -g -O2  -o testmain  testmain.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testtypes.c
gcc  -g -O2  -o testtypes  testtypes.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tstring.c
gcc  -g -O2  -o tstring  tstring.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tnull.c
gcc  -g -O2  -o tnull  tnull.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c manyopts.c
gcc  -g -O2  -o manyopts  manyopts.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tarray.c
gcc  -g -O2  -o tarray  tarray.o ../src/libopt.a 
g++ -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testcc.cc
testcc.cc:3:22: error: iostream.h: No such file or directory
testcc.cc: In function 'int go(int, char**)':
testcc.cc:17: error: 'cout' was not declared in this scope
testcc.cc:19: error: 'endl' was not declared in this scope
testcc.cc:23: error: 'cout' was not declared in this scope
testcc.cc:23: error: 'endl' was not declared in this scope
testcc.cc: In function 'int main(int, char**)':
testcc.cc:70: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:76: warning: deprecated conversion from string constant to 'char*'
testcc.cc:77: warning: deprecated conversion from string constant to 'char*'
testcc.cc:80: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:86: warning: deprecated conversion from string constant to 'char*'
testcc.cc:87: warning: deprecated conversion from string constant to 'char*'
make[1]: *** [testcc.o] Error 1
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
make: *** [all-recursive] Error 1

OVERVIEW of CisOrtho:

The CisOrtho website runs on two machines, which I'll call WEB and
BACKEND.  WEB runs a perl-CGI script that accepts the user query and
writes the input in a scan directory monitored by a crontab-driven
shell script running on BACKEND, called 'launch.bash'.  When
launch.bash finds a file there, it calls cisortho through a perl
wrapper called 'results'.  Finally, cisortho runs and produces html
results files to the directory out/, that the user can browse for a
limited time.

This process accumulates files in scan/ and out/ that are monitored by
another crontab-driven shell script, 'cleanup.bash' that deletes them
when they are more than a few weeks old.

Soon, this crude file-based, crontab-dependent communication between
two machines will be replaced by SOAP communication.  Thus, the
'listening ears' will be a CGI server running on BACKEND rather than a
crontab job.  Also, there will be no need for temporary files that
must be mounted on both machines.  Instead, the user input data will
be sent directly from WEB to BACKEND as a SOAP message.

Please let me know if there is a better way to achieve this.  


The entire set of software consists of the following:

in WEBROOT:

index.html
methods.html
download.html

per/              #directory of permanent cisortho input files
per/CElegans      #elegans non-exonic genomic sequences in RDB format
per/CBriggsae     #briggsae non-exonic genomic sequences in RDB format
per/eb_geneinfo   #contains gene name, chromosome, start, end, strand
per/eb.null       #HMMER 'null' stats file, containing nucleotide freq. in
                  #elegans and briggsae genomes combined
per/eb.pri        #HMMER priors stats file
per/options       #file containing input options for the cisortho binary
scan/               #directory that the CGI script '$CGIROOT/query' deposits user submitted
                    #input data.  This directory is scanned by a bash script called 'launch.bash'
                    #that is controlled by 'cisortho.cron', a crontab job
out/                #directory where cisortho writes output html search results files.
download/
graphics/           #contain extra html files for the cisortho website
log/                #log files for cisortho

launch.bash         #bash script, scans 'scan/' for the presence of new input files and if found,
                    #calls '$CGIROOT/results', a perl script that launches cisortho
cleanup.bash        #scans 'scan/' and 'out/', deleting old files and directories periodically
cisortho.cron       #launches 'launch.bash', and 'cleanup.bash'
cisortho            #the actual c++ binary.                


in CGIROOT:

CGIsubs.pm        #perl module with helper CGI subroutines
query             #perl CGI script for accepting user input submission, writes the input to 'scan/'
results           #perl script for parsing the user input and calling cisortho


Other notes:

* launch.bash implements a primitive lock-file based mechanism for
  limiting to 2 concurrently running instances of CisOrtho.

* launch.bash is run once per minute by cisortho.cron.  During that minute,
  launch.bash itself checks the presence of new files once per second.  This way,
  there is no delay for the user to see that the input is being processed.  This
  is essentially a poor-man's implementation of SOAP or other
  message-based response system.

* upon clicking 'submit', the input is evaluated by the query script,
  and there is no deposit to 'scan/' if the input contains errors.