Problems using wgsim in Linux/Ubuntu

[Kimist99]

Hello All!

I'm a relative newbie to Bioinformatics and I'm having problems with the code I'm using to generate reads from a reference sequence.

I'm using Linux/Ubuntu, and here is the code I'm using along with the error message:

Kimist@Kimist99:~/seqaln$ ./wgsim.c -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt
./wgsim.c: line 1: /bin: Is a directory
./wgsim.c: line 3: syntax error near unexpected token `c'
./wgsim.c: line 3: ` Copyright (c) 2008 Genome Research Ltd (GRL).'


Any help you can provide is greatly appreciated, I feel like this is something easy and that I just don't have the expertise to figure it out. My classmates all use Macs.

[lindenb]

wgsim is a C program. If it hasn't been done, you need to compile it with MAKE it before using it.
the command will be:


/path/to/wgsim -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt

[Kimist99]

wgsim is a C program. If it hasn't been done, you need to compile it with MAKE it before using it.
the command will be:


/path/to/wgsim -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt

Thanks for the quick repsonse!

I thought I did compile it with MAKE, but apparently I didn't.

How can I confirm the compiling was done?

Thanks again!

[dnafp]

At the command prompt type:
file /path/to/wgsim
this should return you something like "elf executable" ...

If you can open that file in an editor, it's usually not compiled yet. You'll likely need to find the execuable wgsim without the ending ".c".

[lindenb]

go in the wgsim.c folder (samtools/misc) and type "make" or "make wgsim"

[Kimist99]

go in the wgsim.c folder (samtools/misc) and type "make" or "make wgsim"

Now I'm getting the following error:

:~/seqaln$ make wgsim
gcc -g -Wall -O2 wgsim.c -o wgsim
wgsim.c:39:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [wgsim] Error 1

Thanks again for the advice!

[lindenb]

install zlib and zlib-devel packages :

sudo apt-get install zlib-devel

[Kimist99]

install zlib and zlib-devel packages :

sudo apt-get install zlib-devel

After a couple hours of trying to trouble shoot this myself, I get nothing but the following message:

~/seqaln$ sudo apt-get install zlib-devel
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package zlib-devel

I assumed the package was part of Samtools-0.1.19.

[GenoMax]

Package you need to install is called "zlib1g-dev". Package page: http://packages.ubuntu.com/lucid/libdevel/zlib1g-dev

If you are new to ubuntu doing the installs through the "package/software manager" is probably a better idea.

[Kimist99]

Package you need to install is called "zlib1g-dev". Package page: http://packages.ubuntu.com/lucid/libdevel/zlib1g-dev

If you are new to ubuntu doing the installs through the "package/software manager" is probably a better idea.

Worked like a charm, thanks again!

[Kimist99]

Bottom line for folks using samtools in Ubuntu, you need to make sure you download all the necessary packages before trying to run it.

[eco32i]

The easiest way to use samtools on ubuntu is just to install the package via apt-get:

$ sudo apt-get install samtools

[Kimist99]

The easiest way to use samtools on ubuntu is just to install the package via apt-get:

$ sudo apt-get install samtools

Unforntuantely, doing that didn't work until after I donwloaded the packages mentioned above.