Having trouble running "make" command
Closed this issue · 4 comments
Hi,
I'm having trouble running the "make" command for NxTrim. When I run this command, I get the following error message.
/usr/bin/ld: cannot find -lboost_program_options
collect2: error: ld returned 1 exit status
make: *** [mergeReads] Error 1
I don't know how to fix it as I'm very new to programming. Please advice. Thanks!
-Taruna
Hi Taruna,
You need to have the boost libraries installed on your system and set the BOOST_ROOT environment variable appropriately. See here.
I appreciate building boost can be a pain, perhaps a solution is for me to provide some pre-compiled nxtrim binaries on here. What operating system are you using?
best,
Jared
Hi Jared,
Thank you for your reply. I'm using MacOSX (10.10.2) and I did run the boost codes on your NxTrim site, but I got nowhere. I'm sorry if that's too vague. I'm just so new that I'm not helpful perhaps. I will read the info about boost libraries you sent me. Please let me know if you need additional information from me. Thanks!
-Taruna
Hi Jared,
I forgot to tell you that I'm trying to run NxTrim on a "super computer" through my school which I can access via terminal. I think that changes the whole reason why I can't install Boost libraries, doesn't it? Regardless, I installed NxTrim on my own computer and tried to run it, but I got a similar message.
g++ -Wall -g -I/usr//include -c fastqlib.cpp
In file included from fastqlib.cpp:1:
In file included from ./fastqlib.h:2:
./utilityfunc.h:10:10: fatal error: 'boost/iostreams/filtering_stream.hpp' file
not found
#include <boost/iostreams/filtering_stream.hpp>
^
1 error generated.
make: *** [fastqlib.o] Error 1
Tarunas-MacBook-Pro:NxTrim Taruna$ ./nxtrim
-bash: ./nxtrim: No such file or directory
Sorry for the trouble, but I appreciate your help!
-Taruna
Hi Jared,
It's working now. One of my advisors suggested that I run the following command and it worked!
export BOOST_ROOT=/usr
make
Thank you for your help though! I appreciate it!
Best,
Taruna