Re: [Samtools-help] install samtools

[dong he <don...@gm...>]

Hi Erik
Thanks! it works!
I meet another problem which is related to samtools when I run tophat.

------------------------------

/bin/tophat-1.1.4.Linux_x86_64> ./tophat -r 20 test_data/test_ref reads_1.fq
test_data/reads_2.fq

[Wed Dec 29 13:42:59 2010] Beginning TopHat run (v1.1.4)
------------------------------------------------------------------------------------------------------------------------------------------------------------
[Wed Dec 29 13:42:59 2010] Preparing output location ./tophat_out/
[Wed Dec 29 13:42:59 2010] Checking for Bowtie index files
[Wed Dec 29 13:42:59 2010] Checking for reference FASTA file
[Wed Dec 29 13:42:59 2010] Checking for Bowtie
        Bowtie version:                  0.12.7.0
[Wed Dec 29 13:42:59 2010] Checking for Samtools
Traceback (most recent call last):
  File "./tophat", line 2223, in <module>
    sys.exit(main())
  File "./tophat", line 2136, in main
    check_samtools()
  File "./tophat", line 877, in check_samtools
    samtools_version = get_samtools_version()
  File "./tophat", line 864, in get_samtools_version
    samtools_version = [int(x.split('-')[0]) for x in
version_val.split('.')]
ValueError: invalid literal for int() with base 10: '12a'

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On Thu, Dec 30, 2010 at 12:28 PM, Erik Aronesty <er...@q3...> wrote:

> try ncurses:
>
> http://seqanswers.com/forums/showthread.php?t=6669
>
> > Hi,
> >
> > When I install samtools on my box ( 64bit suse), I got this error
> message.
> > Does anybody know what is wrong with it?
> >
> > Thanks!
> >
> > Dong
> >
> >
> > --------------------------
> >
> >  gcc -g -Wall -O2  -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o
> > sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o
> > bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o libbam.a -lm
> > -lcurses  -lz -Lbcftools -lbcf
> >
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
> > cannot find -lcurses
> > collect2: ld returned 1 exit status
> > make[1]: *** [samtools] Error 1
> > make[1]: Leaving directory `/home/hed/bin/samtools-0.1.12a'
> > make: *** [all-recur] Error 1
> >
> > -----------------------------
> >
> >
> ------------------------------------------------------------------------------
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> >
> >
>