Problem in installing software on ubuntu

[Diya v]

Hi Nils,

Thank you so much for the help. I could now install the software. But when I am trying to run the test data to see if everything worked well I have a list of errors.

Below is the list.
diya at ubuntu:~/test_data$ sudo tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Jan 14 12:23:13 2011] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Fri Jan 14 12:23:13 2011] Preparing output location ./tophat_out/
[Fri Jan 14 12:23:13 2011] Checking for Bowtie index files
[Fri Jan 14 12:23:13 2011] Checking for reference FASTA file
[Fri Jan 14 12:23:13 2011] Checking for Bowtie
    Bowtie version:             0.12.7.0
[Fri Jan 14 12:23:13 2011] Checking for Samtools
Traceback (most recent call last):
  File "/usr/local/bin/tophat", line 2174, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat", line 2088, in main
    check_samtools()
  File "/usr/local/bin/tophat", line 850, in check_samtools
    samtools_version = get_samtools_version()
  File "/usr/local/bin/tophat", line 837, 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'

Could you please tell me what this error mean?

Thanks in advance.

Diya


--- On Sat, 15/1/11, Nils Kassube <kassube at gmx.net> wrote:

From: Nils Kassube <kassube at gmx.net>
Subject: Re: Problem in installing software on ubuntu
To: ubuntu-users at lists.ubuntu.com
Date: Saturday, 15 January, 2011, 12:09 AM

Diya v wrote:
> I am trying to install a software on Ubuntu and it's giving me an
> error which I trying to do the make command.

> Below is the error message.

> /usr/bin/ld: cannot find -lbam

I think the message means that the loader can't find the bam library. 
You should install the package "libbam-dev", if your application has 
something to do with "manipulates nucleotide sequence alignments in BAM 
or SAM format" (that's what the package is used for).


Nils

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