bcftools inastallation problem

[zillur]

Hi there,
I wanted to try to install bcftools in my linux workstation. But it gave me the following error report. What should I do now?

Best Regards
Zillur

[zillur@workstation01 ~]$ cd Desktop/zillur/Tools/bcftools-1.2/
[zillur@workstation01 bcftools-1.2]$ ls
AUTHORS Makefile consensus.c filter.c kmin.c ploidy.h prob1.h tsv2vcf.c vcfconcat.c vcfisec.c vcfroh.c vcmp.c
HMM.c README convert.c filter.h kmin.h plot-vcfstats rbuf.h tsv2vcf.h vcfconvert.c vcfmerge.c vcfsom.c vcmp.h
HMM.h bcftools.h convert.h gvcf.c main.c plugins reheader.c vcfannotate.c vcffilter.c vcfnorm.c vcfstats.c version.c
INSTALL call.h doc htslib-1.2.1 mcall.c polysomy.c tabix.c vcfcall.c vcfgtcheck.c vcfplugin.c vcfutils.pl
LICENSE ccall.c em.c khash_str2str.h ploidy.c prob1.c test vcfcnv.c vcfindex.c vcfquery.c vcfview.c
[zillur@workstation01 bcftools-1.2]$ nano README
[zillur@workstation01 bcftools-1.2]$ nano INSTALL
[zillur@workstation01 bcftools-1.2]$ sudo make
[sudo] password for zillur:
cd htslib-1.2.1 && make lib-static
make[1]: Entering directory `/home/zillur/Desktop/zillur/Tools/bcftools-1.2/htslib-1.2.1'
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
In file included from bgzf.c:37:0:
htslib/bgzf.h:34:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make[1]: *** [bgzf.o] Error 1
make[1]: Leaving directory `/home/zillur/Desktop/zillur/Tools/bcftools-1.2/htslib-1.2.1'
make: *** [htslib-1.2.1/libhts.a] Error 2
[zillur@workstation01 bcftools-1.2]$

[GenoMax]

$ sudo apt-get install zlib zlib-devel

[zillur]

Another problem

Thank you very much for your kind help. This command worked perfectly but another problem, after installation.

Best Regards
Zillur

[zillur@workstation01 samtools-1.2]$ bcftools
bash: bcftools: command not found...

[GenoMax]

You only compiled the program. You would need to amend your $PATH to include the location of the program e.g. "/path_to/samtools-1.2/src/bcftools-1.2/" or copy the bcftools executable to a directory already in your $PATH (e.r. /usr/local/bin).

[zillur]

Thank you very much for your quick answer. How can I amend my $PATH or get info about my current $PATH.
Best Regards
Zillur

[zillur@workstation01 bcftools-1.2]$ pwd
/home/zillur/Desktop/zillur/Tools/bcftools-1.2

[GenoMax]

Thank you very much for your quick answer. How can I amend my $PATH or get info about my current $PATH.
Best Regards
Zillur

[zillur@workstation01 bcftools-1.2]$ pwd
/home/zillur/Desktop/zillur/Tools/bcftools-1.2

https://kb.iu.edu/d/acar

We have gone over this last year: http://seqanswers.com/forums/showpos...9&postcount=77

[zillur]

Thank you very much for your kind response. bacfools is working now perfectly. But when I was trying to install samtools it gave me the following error report:

[zillur@workstation01 samtools-1.2]$ sudo make install
[sudo] password for zillur:
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c:30:20: fatal error: curses.h: No such file or directory
#include <curses.h>
^
compilation terminated.
make: *** [bam_tview_curses.o] Error 1

The installation instructions are :


Compilation
===========

'cd' to the samtools-1.x directory containing the package's source and type
'make' to compile samtools.

This samtools release contains a copy of HTSlib which will be used to build
samtools. If you already have a system-installed HTSlib or another HTSlib
that you would prefer to build against, you can arrange this by overriding
$(HTSDIR) by typing 'make HTSDIR=/path/to/htslib-source' -- see the makefile
for details.


Installation
============

Type 'make install' to install the samtools executable and various scripts
and executables from misc/ and a manual page to /usr/local.

Type 'make prefix=/path/to/dir install' to install everything under your
choice of installation directory. The install target also understands
DESTDIR and the other usual installation directory variables.

The bgzip and tabix utilities are provided by HTSlib. If you have not also
installed HTSlib separately, you may wish to install these utilities by hand
by copying samtools-1.x/htslib-1.x/{bgzip,tabix} to the same bin directory
to which you have installed samtools et al.

[GenoMax]

$ sudo apt-get install libncurses5-dev

[zillur]

Thank you very much for your kind help. I was trying like this, but:

[zillur@workstation01 samtools-1.2]$ sudo yum install libncurses5-dev
[sudo] password for zillur:
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: mirrors.uprm.edu
* extras: mirrors.uprm.edu
* updates: mirrors.uprm.edu
No package libncurses5-dev available.
Error: Nothing to do
[zillur@workstation01 samtools-1.2]$ sudo apt-get install libncurses5-dev
sudo: apt-get: command not found

[GenoMax]

Try

$ sudo apt-get install ncurses-dev

See this link for general help with package installations: http://askubuntu.com/questions/37855...ackages-by-apt

[zillur]

Thank you very much for your kind reply. I have tried like this:

[zillur@workstation01 Tools]$ sudo apt-get install ncurses-dev
[sudo] password for zillur:
sudo: apt-get: command not found
[zillur@workstation01 Tools]$ sudo yum install ncurses-dev
Failed to set locale, defaulting to C
Loaded plugins: fastestmirror, langpacks
base | 3.6 kB 00:00:00
Not using downloaded repomd.xml because it is older than what we have:
Current : Tue Mar 31 20:19:44 2015
Downloaded: Tue Mar 31 18:50:46 2015
extras | 3.4 kB 00:00:00
updates | 3.4 kB 00:00:00
updates/7/x86_64/primary_db | 3.3 MB 00:00:00
Determining fastest mirrors
* base: mirrors.uprm.edu
* extras: mirrors.uprm.edu
* updates: mirrors.uprm.edu
No package ncurses-dev available.
Error: Nothing to do

BUT THEN I HAVE TRIED THIS:

[zillur@workstation01 samtools-1.2]$ sudo yum install ncurses
[sudo] password for zillur:
Failed to set locale, defaulting to C
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: mirrors.uprm.edu
* extras: mirrors.uprm.edu
* updates: mirrors.uprm.edu
Package ncurses-5.9-13.20130511.el7.x86_64 already installed and latest version
Nothing to do
[zillur@workstation01 samtools-1.2]$ make
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c:30:20: fatal error: curses.h: No such file or directory
#include <curses.h>
^
compilation terminated.
make: *** [bam_tview_curses.o] Error 1

[jmarshall]

On RPM-based distributions, this package is often called ncurses-devel.

[zillur]

Thank you very much for your kind suggestions. It is working now perfectly. Another question, whenever I logout or shut down my computer and login again why I need to specify the paths (export PATH="/dir/:PATH"). Is there any way to avoid it?

[GenoMax]

Thank you very much for your kind suggestions. It is working now perfectly. Another question, whenever I logout or shut down my computer and login again why I need to specify the paths (export PATH="/dir/:PATH"). Is there any way to avoid it?

There are many ways of doing this. You can edit .profile (or .bashrc) file in your home directory (~) and put that export statement in there. If you already have an export statement for PATH in the file(s) then amend it as needed.

[zillur]

Thank you very much for your kind reply. Here is my bash_profile file:# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/.local/bin:$HOME/bin

export PATH


I am not sure which part I need to edit. I have different tools in different directory, like:

/home/zillur/Desktop/zillur/Tools/bcftools-1.2

/home/zillur/Desktop/zillur/Tools/samtools-1.2

/home/zillur/Desktop/zillur/Tools/bowtie2-2.2.5