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  • zillur
    replied
    Thank you very much for your kind suggestions. After editing the bash_profile my system is working perfectly and I can run all the tools. Now I want to allow other users to use this tools. How can I manage it.

    Best Regards
    Zillur

    Leave a comment:


  • GenoMax
    replied
    Originally posted by zillur View Post
    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
    If the executables that you want to run are directly under those top level directories then you would need to edit the PATH line like so:
    Code:
    PATH=$PATH:$HOME/.local/bin:$HOME/bin:/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
    BTW: what do you see when you do

    Code:
    $ echo $HOME

    Leave a comment:


  • zillur
    replied
    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

    Leave a comment:


  • GenoMax
    replied
    Originally posted by zillur View Post
    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.

    Leave a comment:


  • zillur
    replied
    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?

    Leave a comment:


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

    Leave a comment:


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

    [[email protected] Tools]$ sudo apt-get install ncurses-dev
    [sudo] password for zillur:
    sudo: apt-get: command not found
    [[email protected] 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:

    [[email protected] 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
    [[email protected] 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

    Leave a comment:


  • GenoMax
    replied
    Try

    Code:
    $ sudo apt-get install ncurses-dev
    See this link for general help with package installations: http://askubuntu.com/questions/37855...ackages-by-apt

    Leave a comment:


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

    [[email protected] 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
    [[email protected] samtools-1.2]$ sudo apt-get install libncurses5-dev
    sudo: apt-get: command not found

    Leave a comment:


  • GenoMax
    replied
    Code:
    $ sudo apt-get install libncurses5-dev

    Leave a comment:


  • zillur
    replied
    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:

    [[email protected] 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.

    Leave a comment:


  • GenoMax
    replied
    Originally posted by zillur View Post
    Thank you very much for your quick answer. How can I amend my $PATH or get info about my current $PATH.
    Best Regards
    Zillur

    [[email protected] 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

    Leave a comment:


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

    [[email protected] bcftools-1.2]$ pwd
    /home/zillur/Desktop/zillur/Tools/bcftools-1.2

    Leave a comment:


  • GenoMax
    replied
    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).

    Leave a comment:


  • zillur
    replied
    Another problem

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

    Best Regards
    Zillur

    [[email protected] samtools-1.2]$ bcftools
    bash: bcftools: command not found...

    Leave a comment:

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