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Problems installing ecoPCR and ecoPRIMERS
#1
Hi,

I'm having a problem installing ecoPCR and ecoPrimers. I can use OBITools fine, but when trying to run the ecoPCR make file It returns the following :

global.mk:18: ecopcr.P: No such file or directory
global.mk:18: ecofind.P: No such file or directory
global.mk:18: ecoisundertaxon.P: No such file or directory
gcc -DMAC_OS_X -M  -o ecoisundertaxon.d ecoisundertaxon.c
gcc -DMAC_OS_X -M  -o ecofind.d ecofind.c
gcc -DMAC_OS_X -M  -o ecopcr.d ecopcr.c
gcc -DMAC_OS_X -W -Wall -O2 -g -c -o ecopcr.o ecopcr.c
ecopcr.c: In function ‘printRepeat’:
ecopcr.c:146:11: warning: variable ‘tm’ set but not used [-Wunused-but-set-variable]
  double   tm=0;
           ^
ecopcr.c: In function ‘main’:
ecopcr.c:513:9: warning: variable ‘tm’ set but not used [-Wunused-but-set-variable]
  double tm,tm1,tm2;
         ^
ecopcr.c:337:16: warning: variable ‘amplifiatCount’ set but not used [-Wunused-but-set-variable]
  int32_t       amplifiatCount  = 0;
                ^
ecopcr.c:336:16: warning: variable ‘positiveSequence’ set but not used [-Wunused-but-set-variable]
  int32_t       positiveSequence= 0;
                ^
ecopcr.c:312:17: warning: variable ‘scname’ set but not used [-Wunused-but-set-variable]
  char          *scname;
                 ^
make -C libapat
make[1]: Entering directory `/home/jori/Documents/ecoPCR/src/libapat'
../global.mk:18: apat_parse.P: No such file or directory
../global.mk:18: apat_search.P: No such file or directory
../global.mk:18: libstki.P: No such file or directory
 

and so on as it goes through all of the subfolders.

I'm on Ubuntu14.04. I don't have a ton of experience with line commands programs or linux; I would really appreciate some help pointing me in the right direction!
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#2
I just see warning not error...
At the end have you the ecoPCR file in the directory ?
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#3
Hi Eric,

The ecoPrimers does actually make the file, but when I try to use the command ecoPCR -d ./wolf/embl_last -e 3 -l 50 -L 150 \
TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG > v05.ecopcr (from the wolf tutorial), it says 'ecoPCR command not found'. I had assumed this was a result of not compiling properly; but maybe there is a different problem?

The ecoPrimers DOES kick back a fatal error:

make -C libecoPCR
make[1]: Entering directory `/home/jori/Documents/ecoPrimers/src/libecoPCR'
gcc -DMAC_OS_X -W -Wall -m64 -g -c -o ecoseq.o ecoseq.c
In file included from ecoseq.c:4:0:
/usr/include/zlib.h:34:19: fatal error: zconf.h: No such file or directory
#include "zconf.h"
^
compilation terminated.
make[1]: *** [ecoseq.o] Error 1
make[1]: Leaving directory `/home/jori/Documents/ecoPrimers/src/libecoPCR'
make: *** [libecoPCR/libecoPCR.a] Error 2

and there is no ecoPrimers file created. Not sure if I have a wrong version of gcc (I have the latest version), or if I need to be running 64bit (I'm on a 32bit version), or something else that I'm not thinking of?

Thanks so much for your help.
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#4
Forgot to update this in case anyone else had this problem, but I reinstalled everything in a 64 bit environment and it seemed to solve the problem. Not sure if it was a dependency issue or if it was just resolved by reinstalling the OS period, but so far so good.
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