Re: [Samtools-help] Installation problem for a new user

[Devon R. <dpr...@gm...>]

Hi David,

You didn't use samtools, you used the system sort command instead. You 
must fully type "samtools sort" at the beginning of the command to use 
samtools.

Devon


On 08/15/2016 09:58 PM, David Siegel wrote:
> Greetings
>
> I've installed Samtools successfully on my Mac (downloaded the file, 
> unpacked it, cd'd into the folder, typed "make" on the command line, 
> tested it on a SAM file, and it worked fine).  The command I'm using 
> is: sort -n --output testfile_sorted_aligned 
> ~/Documents/blahblahAligned.out.sam
>
> I also installed it onto my work cluster (a unix-based environment), 
> and it worked ok but had a weird bug: It sorted the header file 
> alphabetically in addition to the mapped SAM data.  So some of the 
> header data now comes at the end of the file, some of it comes at the 
> beginning.
>
> If this is really the only issue I can always just write code to get 
> around it.  But if it's a common symptom of some sort of error in 
> installation, could someone let me know how to fix it?
>
> I'm also not the most savvy individual when it comes to the unix/linux 
> environment, I've only been using it for a few months.
>
> Thanks,
>
> David
>
>
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-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpr...@gm...