Homework_2

[annamtown]

The goals of this assignment are to become more familiar with GitHub and to use and understand basic commands in linux. I should understand and remember how to find:

• [x] version/release numbers of linux systems
• [x] the type of shell utility used in zcluster
• [x] paths for shell utilities in zcluster
• [x] file permissions

[annamtown]

Please paste the commands you used to answer these questions and the output of these commands. a) What version and release number of linux is running on zcluster?

#uname -a
Linux zcluster.rcc.uga.edu 2.6.18-417.el5 #1 SMP Sat Nov 19 14:54:59 EST 2016 x86_64 x86_64 x86_64 GNU/Linux

#lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.11 (Tikanga)
Release:    5.11
Codename:   Tikanga

The version is 2.6.18 and the release number is 5.11.

b) What shell utility are you using when you log into zcluster? (hint: use the $SHELL environment variable)

#echo $SHELL
/bin/bash

I am using the bash shell utility on zcluster.

c) What is the absolute path for the shell utility you are using located on zcluster?

#echo $PATH /bin/bash
/usr/local/trans-abyss/1.4.4/bin:/usr/local/abyss/latest/bin/:/usr/local/trans-abyss/1.4.4:/usr/local/tax2tree/1.0/lib/:/usr/local/splicegrapher/latest/lib/python:/usr/local/sate/latest/lib/python:/usr/local/pynast/latest/lib/:/usr/local/dendropy/latest/lib/python:/usr/local/ceas/latest/lib/python:/usr/local/bx-python/latest/lib/python::/usr/local/dlcoal/1.0/lib/python2.7:/usr/local/htseq/0.6.1p1/lib/python:/usr/local/macs/1.4.2/lib/python2.7/site-packages:/usr/local/p4/latest/lib/python:/usr/local/lib/python2.4/site-packages:/usr/local/rvm/gems/ruby-2.1.2/bin:/usr/local/rvm/gems/ruby-2.1.2@global/bin:/usr/local/rvm/rubies/ruby-2.1.2/bin:/usr/local/rsa-tools/2012-11-03/bin:/usr/local/rsa-tools/2012-11-03/perl-scripts:/usr/local/rsa-tools/2012-11-03/python-scripts:/usr/local/qiime/latest/bin:/usr/local/mpich2/1.4.1p1/pgi123/bin:/usr/local/pgi/linux86-64/2012/mpi/mpich/bin:/usr/local/pgi/linux86-64/2012/bin:/usr/local/perl/5.14.1/bin:/opt/panasas/sbin:/opt/panasas/bin:/usr/local/ncbiblast/latest:/usr/local/ncbiblast/latest/bin:/usr/kerberos/bin:/usr/local/jmodeltest/latest/mpj/bin:/usr/local/java/jdk6u3/jdk7/bin:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/bin/intel64:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/mpirt/bin/intel64:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/debugger/gdb/intel64_mic/py24/bin:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/debugger/gdb/intel64/py24/bin:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/bin/intel64:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/bin/intel64_mic:/usr/local/intel/composer_xe/composer_xe_2013_sp1.0.080/debugger/gui/intel64:/usr/local/gridengine/bin:/usr/local/gridengine/utilbin/lx-amd64:/usr/local/gridengine/bin/lx-amd64:/usr/local/arb/latest/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/R/3.0.3/bin:/usr/local/allpathslg/latest/bin:/usr/local/ansys/v145/ansys/bin:/usr/local/ansys/shared_files/licensing/lic_admin:/usr/local/augustus/latest/bin:/usr/local/best/latest:/usr/local/ncbiblast+/latest/bin:/usr/local/blat/latest/bin:/usr/local/bowtie/latest/bin:/usr/local/bowtie2/latest/bin:/usr/local/cap3/latest:/usr/local/cegma/latest/bin/:/usr/local/clustalw/latest/bin:/opt/eclipse:/usr/local/exonerate/latest/bin:/usr/local/geneid/1.4.4/bin:/usr/local/genemark/latest:/usr/local/genemark/gmsuite:/usr/local//genemark/2.5p/gmsuite/:/usr/local/genemark/4.21/gmes_petap/:/usr/local/wise/latest/bin:/usr/local/genome/bin:/usr/local/git/latest/bin:/usr/local/godi/20121022/bin:/usr/local/godi/20121022/sbin:/usr/local/hmmer/latest/bin:/usr/local/lastz/latest/bin:/usr/local/mcl/latest/bin:/usr/local/memo/latest/bin:/usr/local/mp-est/latest/bin:/usr/local/mrbayes/latest:/usr/local/ocaml/latest/bin:/usr/local/p4/latest/bin:/usr/local/pftools/2.3.5/bin:/usr/local/repeatmasker/latest:/usr/local/repeatmodeler/latest:/usr/local/rnnotator/latest/scripts:/usr/local/rvm/bin:/usr/local/samtools/latest/bin:/usr/local/she-ra/latest:/usr/local/snap/latest:/usr/local/somaticcall/latest/bin:/usr/local/t_coffee/latest/bin:/usr/local/trf/latest:/usr/local/velvet/latest:/usr/local/velvetoptimiser/latest:/usr/local/wise/latest/bin:/usr/local/wublast/latest /bin/bash

d) Explain what the file permissions (read?, write?, execute?) are for non-root users for the shell utility you are using on zcluster? Who is the owner of this file? When was this file last modified? How big is this file?

#ls -lrth /bin/bash
-rwxr-xr-x 1 root root 784K Sep 25  2014 /bin/bash

For this shell utility, the owner (root user) can read, write, and execute. The group can read and execute, but cannot write. Other users can read and execute, but cannot write. The file was last edited on September 25th, 2014. The file is 784K.

[cbergman]

• you have the correct commands and output for all questions except for c). The absolute path for the bash utility is /bin/bash. Your command is asking to print the entire $PATH variable followed by the string /bin/bash. You can get the absolute path for an executable by typing e.g. which bash.
• For a) I was meaning for you to say that the version of the OS is Red Hat, but I admit my phrasing wasn't perfect. I'll change this version to "distribution" to be more clear in the future.
• Grade: 9/10