New topics, texts

Author: V-Z

presentation/linux_bash_metacentrum_course.tex

@@ -0,0 +1,12 @@
+The Way that can be told of is not the eternal Way;
+The name that can be named is not the eternal name.
+The Nameless is the origin of Heaven and Earth;
+The Named is the mother of all things.
+Therefore let there always be non-being,
+  so we may see their subtlety,
+And let there always be being,
+  so we may see their outcome.
+The two are the same,
+But after they are produced,
+  they have different names.
+

scripts/awk_test_file.tab

@@ -0,0 +1,14 @@
+The Nameless is the origin of Heaven and Earth;
+The named is the mother of all things.
+
+Therefore let there always be non-being,
+  so we may see their subtlety,
+And let there always be being,
+  so we may see their outcome.
+The two are the same,
+But after they are produced,
+  they have different names.
+They both may be called deep and profound.
+Deeper and more profound,
+The door of all subtleties!
+

scripts/cut_awk_test_file.tsv

@@ -1,11 +1,19 @@
 #!/bin/bash
+
 # Arguments are read from command line as parameters of the script
 # Order has to be kept (well, not in this case, but generally yes)
+
 echo "Sum of two numbers $1 and $2 is `expr $1 + $2` ."
+
 # "$#" is available every time and contains number of parameters
 # (variables) given to the script
+
 echo "Number of parameters is $# ."
+
 # "$*" is available every time and contains all supplied parameters
+
 echo "Those parameters were supplied: $*."
+
 echo
+
 exit

scripts/diff_test_file_1.txt

@@ -1,9 +1,17 @@
 #!/bin/bash
+
 # Arguments are read from user input (script asks for them)
+
 echo "Please, input first value to sum and press Enter"
+
 read V1
+
 echo "Please, input second value to sum and press Enter"
+
 read V2
+
 echo "Sum of two numbers $V1 and $V2 is `expr $V1 + $V2` ."
+
 echo
+
 exit

scripts/diff_test_file_2.txt

@@ -1,6 +1,8 @@
 #!/bin/bash
-# Script has only one parameter ($1) provided as its parameter
+
+# Script has only one parameter ($1) provided
 # "case" is evaluating provided parameter and behaving accordingly
+
 case "$1" in
   -d|--disk)
     echo "Your disk usage is:"
@@ -18,4 +20,5 @@ case "$1" in
       -u or --uptime for computer uptime"
       ;;
 esac
+
 exit

scripts/interactive1.sh

@@ -1,20 +1,30 @@
 #!/bin/bash
+
+# Regular expression explanation:
+# From the beginning of the line (^) there is number ([0-9])
+# at least one time (+) up to the end of the line ($)
 NUMBER='^[0-9]+$'
+
 if [ "$#" -ne "3" ]; then
     echo "Error! Requiring 3 parameters! Received $#.
-    Usage number1 -plus/-minus/-product/-quotient number2
+    Usage: number1 -plus/-minus/-product/-quotient number2
     Use -plus for sum, -minus for difference, -product
     for multiplication or -quotient for quotient."
     exit 1
   fi
+
+# "=~" means we are testing if $1 fits to regular expression in $NUMBER
+
 if [[ ! $1 =~ $NUMBER ]]; then
     echo "Parameter 1 is not an integer!"
     exit 1
   fi
+
 if [[ ! $3 =~ $NUMBER ]]; then
     echo "Parameter 3 is not an integer!"
     exit 1
   fi
+
 case $2 in
   -plus) expr $1 '+' $3;;
   -minus) expr $1 '-' $3;;
@@ -26,4 +36,5 @@ case $2 in
     -product for multiplication or -quotient
     for quotient.";;
 esac
+
 exit

scripts/interactive2.sh

@@ -1,26 +1,38 @@
 #!/bin/bash
+
 # Modify the script according to your needs!
+
 # Set data directories
 WORKDIR="bayes_batch"
 DATADIR="/storage/praha1/home/$LOGNAME"
+
 # So there is directory /storage/praha1/home/gunnera/bayes_batch containing all the data needed for calculations
+
 # Clean-up of SCRATCH (it is temporal directory created by server) - the commands will be launched on the end when the job is done
 trap 'clean_scratch' TERM EXIT
 trap 'cp -ar $SCRATCHDIR $DATADIR/ && clean_scratch' TERM
-# Prepare the task - copy all needed files from working directory
-# into particular computer which will finally do the calculations
+
+# Prepare the task - copy all needed files from working directory into particular computer which will finally do the calculations
 cp -ar $DATADIR/$WORKDIR/* $SCRATCHDIR/  || exit 1
+
 # Change working directory - script goes to the directory where calculations are done
 cd $SCRATCHDIR/ || exit 2 # If it fails, exit script
+
 # Prepare calculations - load required application modules
 # See https://wiki.metacentrum.cz/wiki/Kategorie:Applications
 # Every application module is loaded by "modile add XXX"
 . /packages/run/modules-2.0/init/sh
 module add parallel # In this case GNU Parallel and MrBayes
 module add mrbayes-3.2.2
+
 # Launch the analysis - calculate MrBayes for multiple files
 ls -1 *.nexus | parallel -j 8 'mb {} | tee -a {}.log'
+
 # Copy results back to home directory
 cp -ar $SCRATCHDIR $DATADIR/$WORKDIR || export CLEAN_SCRATCH=false
+
 # This is all needed, the script is ready to be launched...
+
 # Don't forget to make it executable and modify it according to your needs... If the script was written on Windows, convert EOL and possibly encoding as well...
+
+exit