Re: [Samtools-help] help installing samtools

[Robert D. <rm...@sa...>]

On Tue, 14 Nov 2017, Ricardo Fong Zazueta wrote:

> Hello, i am a new samtools user and i am having trouble installing the 
>package on my ubuntu 16.4 virtual machine (installed in a windows 7 host 
>machine).
>
>
> I have read the INSTALL script written in the samtools main folder after 
>downloading samtools from http://www.htslib.org/download/ .
>
> as required, i have installed the required packages: zlib, bzip2, 
>liblzma, and ncurses, after browsing for the correct versions required 
>for the ubuntu 16.4 environment. The instalation of such packages was 
>made through the following scripts:
>
> sudo apt-get update
>
> sudo apt-get install libncurses5-dev
>
> sudo apt-get install zlib1g-dev
>
> sudo apt-get install libbz2-dev
>
> sudo apt-get install liblzma-dev
>
> i ran as well ./configure as suggested, in order to verify all the 
>parameters were correct
>
> after that i ran the command "make" as the basic installation demands, 
>and it all went well, but the trouble came when i gave the last "make 
>install" command, it gave me an error, which i write on the following 
>lines:
>
>
> mkdir -p -m755 /usr/local/bin /usr/local/bin /usr/local/share/man/man1
>
> mkdir: cannot create directory ´/usr/local/share/man/man´: Permission denied
>
> Makefile:292: recipe for target 'install' failed

You don't have permission, as a normal user, to write to these 
directories.  If you try:

   sudo make install

then it should work.

Alternatively, you can use the configure --prefix option to say where you 
want it to be installed.  This can be useful if you want to keep more 
than one version, for example (most output removed for brevity):

   ./configure --prefix=$HOME/opt/samtools-1.6/
   make
   make install
   cd
   ls -R opt/samtools-1.6/
opt/samtools-1.6/:
bin  share

opt/samtools-1.6/bin:
ace2sam		    maq2sam-short  sam2vcf.pl		  wgsim
blast2sam.pl	    md5fa	   samtools		  wgsim_eval.pl
bowtie2sam.pl	    md5sum-lite    samtools.pl		  zoom2sam.pl
export2sam.pl	    novo2sam.pl    seq_cache_populate.pl
interpolate_sam.pl  plot-bamstats  soap2sam.pl
maq2sam-long	    psl2sam.pl	   varfilter.py

opt/samtools-1.6/share:
man

opt/samtools-1.6/share/man:
man1

opt/samtools-1.6/share/man/man1:
samtools.1  wgsim.1


Note that the program gets installed to "$HOME/opt/samtools-1.6/bin" in 
this case.  You would need to add this to your PATH environment variable 
if you want to run it by just typing "samtools":

   PATH="$HOME/opt/samtools-1.6/bin:$PATH"
   samtools

Program: samtools (Tools for alignments in the SAM format)
.. etc ...

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919


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