what does edit makefile exactly mean

Question

[zizigolu]

sorry,

in mirdeep installation I read

cd randfold2.0

edit Makefile e.g. emacs Makefile

       change line with INCLUDE=-I. to

       INCLUDE=-I. -Iyour_path_to_squid-1.9g -Lyour_path_to_squid-1.9g

  e.g. INCLUDE=-I. -I/home/Pattern/squid-1.9g/ -L/home/Pattern/squid-1.9g/

does this mean I should go to makefile in ranfold folder and find word INCLUDE=-I and change that to INCLUDE=-I. -

I/home/Pattern/squid-1.9g/ -L/home/Pattern/squid-1.9g or I should type this command in terminal???

[GenoMax]

You actually need to edit the file called "Makefile". Use any editor you like. Even something as mundane as pico/nano would be fine on unix.

[John]

I love nano! How dare you call her mundane :P

[WouterDeCoster]

Your software has a gender?

[zizigolu]

sorry

what is gender? text editor?

[GenoMax]

This is not related to the thread. But since you asked, Gender as in male/female. Some languages assign a gender to objects. Perhaps German language does. I don't know.

[John]

Yes it's a habit I picked up in Germany. Everything has gender.

[GenoMax]

I do like Nano as well. Not many know about it or the pine email program which had a similar editor,

Answer 1

[WouterDeCoster]

It indeed means to edit the makefile with e.g. emacs. vim, nano, gedit, or any text editor you like (alternatively, you can also use sed but probably with caution)

Make sure to perform exactly the edit as described, unless you'll come across errors soon.

[zizigolu]

sorry I edited makefile with XEmacs text editor but when I tried make I got this error

[izadi@lbox200 randfold-2.0.1]$ make

gcc -c energy_par.c

gcc -c params.c

gcc -c fold.c

gcc -c fold_vars.c

gcc -c utils.c

gcc -O3 -I. -I/usr/data/nfs6/izadi/squid-1.9g/ -L/usr/data/nfs6/izadi/squid-1.9g/ -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid

randfold.c:25:18: fatal error: squid.h: No such file or directory

              ^

compilation terminated.

Makefile:7: recipe for target 'randfold' failed

make: * [randfold] Error 1

[WouterDeCoster]

Does this help: randfold-2.0.1 installation problem ?

And there is no need to start each post with "sorry", you don't have to be sorry for asking questions.

[zizigolu]

Thank you,

I tried this page already,

you know long time I am trying to run mirdeep or other tools written in perl but always error, once @genomax2 in a post mentioned that if I could get chance to contact with administrator he can install perl module. today I could email institute administrator but actually I don't know what I should ask him to install for me while installing Math::CDF , Font::TTF and everything giving error.

what in general I should ask him to be installed on my system might be I get rid of these errors???

[WouterDeCoster]

Do you have the latest perl? Which operating system do you use?

So installation of mirdeep fails? Or running?

[zizigolu]

I installed the lastest perl myself

im with fedora 22

you know it is too weird, I ran mirdeep2 on one sample successfully but for the second mapper worked but quantifier.pl did not work anymore then I re-installed mirdeep2 but this time nothing works and whenever I am trying install.pl telling

Installing PDF-API2 now

Warning: prerequisite Font::TTF 0 not found.

RNAfold was/is not installed properly

pdf was/is not installed properly

ttf was/is not installed properly

randfold was/is not installed properly

bowtie was/is not installed properly

Please run the install.pl script again to check if everything is properly installed.

[izadi@lbox200 mirdeep2_0_0_8]$ [izadi@lbox200 mirdeep2_0_0_8]$

even I tried mireap, mirnakey, randa, eRNA, IMIR, miarma but all error related to perl

I am totally getting mad and confused :( :( :(

I don't know ask him to install what for me

[WouterDeCoster]

Most straightforward would be to ask him to install mirdeep2 completely :-)

[zizigolu]

thank you both

I should go to ranfold folder and edit makefile as you described