Im trying to run virusfinder, I got some problems before because I couldnt install trinity 2012 (must have that version to run virusfinder) in my ubuntu version 16.
Now I try with ubuntu version 15 64 bits.
And I get this error when "make" trinity, seems I have problem installing the plugin jellyfish, but I dont know if its a way to fix it...
In file included from ./jellyfish/square_binary_matrix.hpp:28:0, from jellyfish/square_binary_matrix.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr<T> ptr; ^ cc1plus: all warnings being treated as errors Makefile:1165: recipe for target 'jellyfish/libjellyfish_la-square_binary_matrix.lo' failed make: *** [jellyfish/libjellyfish_la-square_binary_matrix.lo] Error 1 make: Leaving directory '/home/cris/Desktop/tri/trinity-plugins/jellyfish-1.1.5' Makefile:650: recipe for target 'all' failed make: *** [all] Error 2 make: Leaving directory '/home/cris/Desktop/tri/trinity-plugins/jellyfish-1.1.5' Makefile:18: recipe for target 'all' failed make: *** [all] Error 2
Unfortunately, you didn't include the failing compiler command, always include the full command that is given by the make file, but I am guessing the problem is indicated by:
I was suposse to write this on my makefile?
KBUILD_CFLAGS += $(call cc-option,-Wno-error=unused-but-set-variable,)
I did but didnt worked for me....if I did right..I am not a programer, just have a tiny little idea
Anyhow I installed the trinity r2013 the next version..and worked!!!!!!!
Finally I can find my virus!!! ;;;___;;; Hapinesss
Thanks a lot!!!
Are you looking for a specific virus or "virii" in general? If former what is the use case for using trinity, why not a regular NGS aligner?
no, nothing in special, just curiosity to see what finds Virus finder (Im bit stubborn when wants to make something to work :P ),
I just use trinity because virusfinder uses it :) before I allready alligned my unmmaped secuencies to virus genomes.
Im wondering if all of these tools really works, if I would have an exom secuency with a know virus I asume would be more easy to find out, but in my case I dont have.