install wgsim on ubuntu 16 (1 exit status)

Question

[marongiu.luigi]

Dear all,

I want to install wgsim on my Ubuntu 16.04 machine; I downloaded the zip file wgsim from the website, unpack it and moved it to /usr/local/lib/. I then ran the suggested commands (both with gcc and make) and I got:

:/usr/local/lib/wgsim$ sudo make wgsim
[sudo] password : 
cc     wgsim.c   -o wgsim
/tmp/ccUBK42c.o: In function `ks_getc':
wgsim.c:(.text+0xe1): undefined reference to `gzread'
/tmp/ccUBK42c.o: In function `ks_getuntil':
wgsim.c:(.text+0x1df): undefined reference to `gzread'
/tmp/ccUBK42c.o: In function `ran_normal':
wgsim.c:(.text+0xab2): undefined reference to `log'
wgsim.c:(.text+0xacc): undefined reference to `sqrt'
/tmp/ccUBK42c.o: In function `wgsim_core':
wgsim.c:(.text+0x17d5): undefined reference to `log'
wgsim.c:(.text+0x1825): undefined reference to `gzopen'
wgsim.c:(.text+0x18f9): undefined reference to `gzclose'
wgsim.c:(.text+0x190d): undefined reference to `gzopen'
wgsim.c:(.text+0x2499): undefined reference to `gzclose'
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'wgsim' failed
make: *** [wgsim] Error 1

:/usr/local/lib/wgsim$ sudo gcc -g -Wall -O2 wgsim.c -o wgsim
/tmp/ccexR4pu.o: In function `ks_getuntil':
/usr/local/lib/wgsim/wgsim.c:41: undefined reference to `gzread'
/tmp/ccexR4pu.o: In function `ran_normal':
/usr/local/lib/wgsim/wgsim.c:77: undefined reference to `log'
/usr/local/lib/wgsim/wgsim.c:77: undefined reference to `sqrt'
/tmp/ccexR4pu.o: In function `ks_getc':
/usr/local/lib/wgsim/wgsim.c:41: undefined reference to `gzread'
/usr/local/lib/wgsim/wgsim.c:41: undefined reference to `gzread'
/usr/local/lib/wgsim/wgsim.c:41: undefined reference to `gzread'
/usr/local/lib/wgsim/wgsim.c:41: undefined reference to `gzread'
/tmp/ccexR4pu.o: In function `wgsim_core':
/usr/local/lib/wgsim/wgsim.c:250: undefined reference to `gzopen'
/usr/local/lib/wgsim/wgsim.c:260: undefined reference to `gzclose'
/usr/local/lib/wgsim/wgsim.c:262: undefined reference to `gzopen'
/usr/local/lib/wgsim/wgsim.c:370: undefined reference to `gzclose'
/usr/local/lib/wgsim/wgsim.c:248: undefined reference to `log'
collect2: error: ld returned 1 exit status

What I am missing? are there some dependencies?

Thanks

G

Answer 1

[Pierre Lindenbaum]

gcc -o wgsim wgsim.c -lm -lz

[sacha]

Get from the github readme:

gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm

[marongiu.luigi]

I ran gcc -o wgsim wgsim.c -lm -lz and a wgsim command is created but when i run it on an example from the web i got:

:~/Documents/LAB/Lab book/Ery$ wgsim -N1000 -S1 ./genomes/NC_008253_1K.fna ./simulated_reads/sim_reads.fq /dev/null
No command 'wgsim' found, did you mean:
 Command 'dwgsim' from package 'dwgsim' (universe)
wgsim: command not found
:~/Documents/LAB/Lab book/Ery$ /usr/local/lib/wgsim/wgsim -N1000 -S1 ./genomes/NC_008253_1K.fna ./simulated_reads/sim_reads.fq /dev/null
[wgsim] file open error
$ sudo !!
sudo /usr/local/lib/wgsim/wgsim -N1000 -S1 ./genomes/NC_008253_1K.fna ./simulated_reads/sim_reads.fq /dev/null
[sudo] password for : 
[wgsim] file open error

[GenoMax]

Don't run user program using sudo. Not a good practice.

If you are trying to run wgsim from the directory where it is present then you need to either do it explicitly as ./wgsim or add the directory (in bash shell) where wgsim is located to $PATH simply by doing export PATH=$PATH:/path_to_wgsim You can add this line to ~/.profile file make the change permanent.

Answer 2

[Charles Plessy]

On Ubuntu 16, wgsim is also distributed in the samtools package.

[marongiu.luigi]

I installed samtools but there is no wgsim:

Version: 0.1.19-96b5f2294a

Usage:   samtools <command> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         cat         concatenate BAMs
         bedcov      read depth per BED region
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes
         bamshuf     shuffle and group alignments by name

[Charles Plessy]

It is in /usr/lib/samtools/wgsim, so not in your PATH.