You can debug kallisto with gdb and valgrind even if you can't compile it on your machine.
In order to do this you need to download the Debuggable binary, which is found on this gist.
You also need to place the source code in the same directory as where you will be debugging
wget https://github.com/pachterlab/kallisto/archive/v0.42.4.tar.gz
tar xzvf v0.42.4.tar.gz
this will enable gdb to see the source code.
First check that you can really run and debug the code
#check for running code
./kallisto_bin_Debug_0.42.4
kallisto 0.42.4
Usage: kallisto <CMD> [arguments] ..
Where <CMD> can be one of:
index Builds a kallisto index
quant Runs the quantification algorithm
h5dump Converts HDF5-formatted results to plaintext
version Prints version information
Running kallisto <CMD> without arguments prints usage information for <CMD>
and now for debugging
gdb ./kallisto_bin_Debug_0.42.4
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-75.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/pmelsted/kallisto/debug/kallisto_bin_Debug_0.42.4...done.
(gdb) list main
719
720 // chomp off the newline
721 return ret.substr(0, ret.size() - 1);
722 }
723
724 int main(int argc, char *argv[]) {
725 std::cout.sync_with_stdio(false);
726 setvbuf(stdout, NULL, _IOFBF, 1048576);
727
728
(gdb)
If you don't see the source code, like line 724 for main, then gdb is not finding the source directories.
Now for some basic debugging, first we set a breakpoint in main and run the program.
(gdb) b main
Breakpoint 1 at 0x475035: file /kallisto-0.42.4/src/main.cpp, line 725.
(gdb) r
Starting program: /home/pmelsted/kallisto/debug/kallisto_bin_Debug_0.42.4
[Thread debugging using libthread_db enabled]
Breakpoint 1, main (argc=1, argv=0x7fffffffdf48) at /kallisto-0.42.4/src/main.cpp:725
725 std::cout.sync_with_stdio(false);
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el6.x86_64 libgcc-4.4.7-11.el6.x86_64
It complains about not having debugging info for some libraries, but that's normal. Now let's see the source code with l
and step through the lines with n.
(gdb) l
720 // chomp off the newline
721 return ret.substr(0, ret.size() - 1);
722 }
723
724 int main(int argc, char *argv[]) {
725 std::cout.sync_with_stdio(false);
726 setvbuf(stdout, NULL, _IOFBF, 1048576);
727
728
729 if (argc < 2) {
(gdb) n
726 setvbuf(stdout, NULL, _IOFBF, 1048576);
(gdb) n
729 if (argc < 2) {
(gdb)
Finally when we're ready to continue we hit c
(gdb) c
Continuing.
kallisto 0.42.4
Usage: kallisto <CMD> [arguments] ..
Where <CMD> can be one of:
index Builds a kallisto index
quant Runs the quantification algorithm
h5dump Converts HDF5-formatted results to plaintext
version Prints version information
Running kallisto <CMD> without arguments prints usage information for <CMD>
Program exited with code 01.
(gdb)
which shows that nothing went wrong.
There are many excellent tutorials on debugging, but the most useful information is usually from the backtrace bt and if an assert is hit you can navigate to the kallisto function that was potentially misbehaving by goint up or down the call stack.