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 r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
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