Problem in installing software on ubuntu

[Nils Kassube]

Diya v wrote:
> Thank you so much for the help. I could now install the software. 

Great!

> 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.
[...]
> [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'

I'm not so sure what it means - after all I don't know anything about 
that tophat software. But I would guess that either your software 
expects a different version of samtools or you don't have those samtools 
installed. Searching for samtools in synaptic reveals two possible 
packages: "samtools" and "libbio-samtools-perl". Maybe you need them 
both installed. If that doesn't help, have a look at the source 
directory of your application and check if there is a file "README" or 
"INSTALL" which might give a hint which version is needed and check if 
you have that version is installed.


Nils