<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"> <blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <div id="yiv1554157209"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top">Hi 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@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' The sam version that I installed is samtools-0.1.12a Could you please tell me what this error mean? Thanks in advance. Diya --- On Sat, 15/1/11, Nils Kassube <kassube@gmx.net> wrote: <blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> From: Nils Kassube <kassube@gmx.net> Subject: Re: Problem in installing software on ubuntu To: ubuntu-users@lists.ubuntu.com Date: Saturday, 15 January, 2011, 12:09 AM <div class="yiv1554157209plainMail">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 -- ubuntu-users mailing list <a rel="nofollow">ubuntu-users@lists.ubuntu.com</a> Modify settings or unsubscribe at: <a rel="nofollow" target="_blank" href="https://lists.ubuntu.com/mailman/listinfo/ubuntu-users">https://lists.ubuntu.com/mailman/listinfo/ubuntu-users</a> </div></blockquote></td></tr></tbody></table> </div></blockquote></td></tr></table>