Question: Program Installation - SINVICT
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gravatar for mrskkdennen
2.9 years ago by
mrskkdennen10
mrskkdennen10 wrote:

I am very new to bioinformatics and am trying to learn how to run a SNP and indel software package.

I have downloaded the files from this website: https://sfu-compbio.github.io/sinvict/

I am attempting to install it - and have this from the manual.

"To install SiNVICT, first you should fetch it from our git repository, or download one of the corresponding compressed zip/tar.gz packages. After downloading, change the current directory to the source directory sinvict, and run make in the terminal. The sinvict binary will be created, which is ready to use."

I do not understand the phrase "change the current directory to the source directory sinvict". Can someone explain this to me in very simple terms? Or help with a step by step instruction as to what I need to do to begin using this program?

Thanks so much in advance.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by mrskkdennen10

Do you have experience with command line? If not, that would be good to study before starting bioinformatics. Which operating system do you use?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by WouterDeCoster40k

I have a mac system, and have a little experience with running programs written in perl in the terminal - written within the program Komodo Edit.

Is there a good reference you suggest to study command line?

ADD REPLYlink written 2.9 years ago by mrskkdennen10

Googling mac command line tutorial brings up plenty of hits. I found this one useful: https://www.codecademy.com/learn/learn-the-command-line I'm most familiar with linux command line, not sure if there are important differences.

Just like in a graphical user interface (with which you are likely most familial) you operate in a directory. When you want to open a file, you go to the directory in which that file is. Same thing in command line interface. You just downloaded the package and should change your current directory to the folder you just downloaded (from git or directly the .tar.gz file). The command you need for this is cd

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k
0
gravatar for mrskkdennen
2.9 years ago by
mrskkdennen10
mrskkdennen10 wrote:

Prerequisites

g++ version: 4.8.3 Boost version: 1_53

I have since downloaded and installed Boost 1_62 and G++-6.1.0.

When I then go to the sinvict source directory and run the make command - this fatal error occurs:

$ make -j 4 g++ -c -g -std=c++0x main.cpp -o main.o g++ -c -g -std=c++0x Sample.cpp -o Sample.o g++ -c -g -std=c++0x ReadcountEntry.cpp -o ReadcountEntry.o g++ -c -g -std=c++0x Allele.cpp -o Allele.o main.cpp:1:10: fatal error: 'boost/program_options/options_description.hpp' file not found

include <boost program_options="" options_description.hpp="">

     ^

1 error generated. make: * [main.o] Error 1 make: * Waiting for unfinished jobs....

Any ideas why this might be occurring?

ADD COMMENTlink written 2.9 years ago by mrskkdennen10
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