FIX Spelling errors

linux_beginner/Comments.txt

@@ -19,6 +19,7 @@ Verbesserungen:
    - Clemens Lakner fragen, ob er nicht einen text schreiben moechte
  - {DONE} siehe 'apropos' - die naechste Zeile wird immer mit in die Ueberschrift gezogen!
  - {DONE} 'release 1.4' aus Seitenkopf nehmen
+ - use SVG for certificate and script to add names
 
 Content:
  - {DONE} mehr Uebungen! z.B. Verzeichniss erstellen, Dateien kopieren etc.

linux_beginner/about_bioit.rst

@@ -5,7 +5,7 @@ About Bio-IT
 Bio-IT is a community project aiming to develop and strengthen the bioinformatics user community at EMBL Heidelberg. It is made up of members across the
 different EMBL Heidelberg units and core facilities. The project works to achieve these aims, firstly, by providing a forum for discussing and sharing
 information and ideas on computational biology and bioinformatics, focused on the `Bio-IT portal <http://bio-it.embl.de>`_. Secondly, we organise and
-participate in a range of different networking and social activites aiming to strengthen ties across the community.
+participate in a range of different networking and social activities aiming to strengthen ties across the community.
 
 Resources 
 ^^^^^^^^^^

linux_beginner/exercises_beginner.rst

@@ -24,7 +24,7 @@ Copying / Deleting Files & Folders
 
 #. Navigate to your home directory 
 
-#. In your homedirectory, create a new directory named ``new_dir`` 
+#. In your home directory, create a new directory named ``new_dir`` 
 
 #. Change into this directory, create a new empty file in there named ``new_file``, 
    and make sure that the file was created.
@@ -53,7 +53,7 @@ Searching
 
 #. Search for the file named ``date`` in the ``/bin`` directory 
 
-#. List those entries in the directory ``/bin`` that are bigger than 400kBytes 
+#. List those entries in the directory ``/bin`` that are bigger than 400 kBytes 
 
 
 Misc. terminal
@@ -64,15 +64,15 @@ Misc. terminal
 Permissions
 -----------
 
-#. Create a directory called testpermissions 
+#. Create a directory called ``testpermissions`` 
 
-#. Change your working directory to testpermissions 
+#. Change your working directory to ``testpermissions`` 
 
-#. Create a directory called adir. 
+#. Create a directory called ``adir``. 
 
 #. Use the command ``which date`` to find out where the date program is located. 
 
-#. Copy this date program into the directory adir and name it 'mydate'. 
+#. Copy this date program into the directory ``adir`` and name it 'mydate'. 
 
 #. Check the permissions of the copied program 'mydate' 
 
@@ -84,11 +84,12 @@ Permissions
 
 #. Try running it as ``./mydate`` or ``adir/mydate`` (depending on your current working directory) 
 
-#. Copy a textfile from a previos exercise into adir, then change the permissions, so you are not allowed to write to it. Test this by trying to read it via `cat`. 
+#. Copy a textfile from a previous exercise into ``adir``, then change the permissions, so you are not allowed to write to it. 
+   Test that you are still able to read the file via `cat`. 
 
 #. Then change the permissions so you can't read/cat it either. Test this by trying to read it via `cat`. 
 
-#. Change your working directory to testpermissions, and then try changing the permissions on the directory adir to non-executable. 
+#. Change your working directory to ``testpermissions``, and then try changing the permissions on the directory ``adir`` to non-executable. 
 
 #. What are the minimum permissions (on the directory) necessary for you to be able to execute ``adir/mydate``? 
 
@@ -153,7 +154,7 @@ Putting it all together
 Bioinformatics
 --------------
 
-Let's do some bioinformatics analyis!
+Let's do some bioinformatics analysis!
 You can find the famous BLAST tool installed at `/g/software/bin/blastp`.
 
 #. Typing the full path is too cumbersome, so let's append `/g/software/bin` to your $PATH variable and ensure that it works by calling `blastp`.
@@ -167,3 +168,4 @@ You can find the famous BLAST tool installed at `/g/software/bin/blastp`.
 
    *input_file* = `suspect1.fasta` 
    
+#. Use either ``less`` or redirection to a file to manage the amount of information that ``blastp`` prints on your screen.

linux_beginner/introduction.rst

@@ -15,7 +15,7 @@ Why Use the Commandline
   commands. Anyone who has spent hours listening to someone from tech support say something like, "OK, now click this,
   then this, then select this menu command" knows how frustrating the GUI alternative can be. 
 
-- It's nearly **universal**. There are hundreds of Linux distros out there, each with a slightly different graphical
+- It's nearly **universal**. There are hundreds of Linux distributions out there, each with a slightly different graphical
   environment. Thankfully, the various distros do have one common element: the command line. There are distro-specific
   commands, but the bulk of commands will work on any Linux system.
 
@@ -32,7 +32,7 @@ General Remarks Regarding Using UNIX/Linux Systems
 
 - **Test before run**. Anything written here has to be taken with a grain of salt. On another system - be it a different
   Linux distribution or another UNIXoid operating system - you might find the same command but without the support of
-  some of the options tought here. It is even possible, that the same option has a different meaning on another system.
+  some of the options taught here. It is even possible, that the same option has a different meaning on another system.
   With this in mind always make sure to test your commands (specially the "dangerous" ones which remove or modify files)
   when switching from one system to the other.
 
@@ -60,7 +60,7 @@ General Remarks Regarding Using UNIX/Linux Systems
 Absolute Paths / Relative Paths
 ===============================
 
-A path describes the the location of a file/folder in the filesystem: 
+A path describes the location of a file/folder in the filesystem: 
 It is important to understand that there are basically two ways to describe such a path: Either by using an *absolute* pathname, or by using a
 *relative* pathname. The difference is that *absolute* paths always start with a "slash ``/``". This "slash" denotes the so called "root" of the
 filesystem (see below). *Relative* paths in contrast always starting with a directory name and denote the location of a file/folder *relative* to
@@ -82,7 +82,7 @@ while arguments are usually free text input (such as a filename).
 
 For example, in the commandline ``ls -l /usr/bin``, ``ls`` is the command, ``-l`` is an option and ``/usr/bin`` qualifies as an argument.
 
-:index:`Commandline options <command, options, command; switches>` (sometimes called comandline switches) commonly have one of the two following
+:index:`Commandline options <command, options, command; switches>` (sometimes called commandline switches) commonly have one of the two following
 forms: The short form ``-s`` (just a single character) or the long form ``--string.`` E.g.
 
  :: 
@@ -90,7 +90,7 @@ forms: The short form ``-s`` (just a single character) or the long form ``--stri
   $ man -h
   $ man --help
 
-Short options are usually - though not always - concatenable:
+Short options are usually - though not always - concatenatable:
 
  ::
 
@@ -287,7 +287,7 @@ Each machine on the network has a unique name which is used to distinguish one f
 :index:`pwd` - Print the current working directory
 --------------------------------------------------
 
-A Linux Filesystem contains countless directories with many subdirectories which makes it easy to get lost. It is good practice to check your position within
+A Linux filesystem contains countless directories with many subdirectories which makes it easy to get lost. It is good practice to check your position within
 the filesystem regularly.
 
 **Usage**: ``pwd`` 
@@ -498,8 +498,8 @@ To recursively copy files, we need to specify the ``-r`` option. Here, we copy a
 
 **Useful option combinations**:
 
--av  Verbosely copies all source files wich are different (different size, different age) or missing from the source.  **Beware**: This will also copy files which are older on the source side
--au  Silently copies all source files wich are different (different size, different age) or missing from the source.  This combination will *not* overwrite newer files by older ones
+-av  Verbosely copies all source files which are different (different size, different age) or missing from the source.  **Beware**: This will also copy files which are older on the source side
+-au  Silently copies all source files which are different (different size, different age) or missing from the source.  This combination will *not* overwrite newer files by older ones
 
 This should not copy any new files, as we previously copied these already:
  :: 
@@ -639,7 +639,7 @@ View Files
 
 **Useful options**:
 
--n num  Print num lines (default is 10)
+-n NUM  Print NUM lines (default is 10)
 
 
 :index:`tail` - Print last lines of a textfile
@@ -659,7 +659,7 @@ The ``tail`` utility displays the last few lines of a file or, by default, its s
 
 **Useful options**:
 
--n num  Print num lines (default is 10)
+-n NUM  Print NUM lines (default is 10)
 -f      "Follow" a file (print new lines as they are written to the file)
 
 .. _less:
@@ -721,9 +721,9 @@ Extracting Informations from Files
 -l      List files with matching lines, not the lines itself
 -L      List files without matches
 -c      Print count of matching lines for each file
--A      print NUM lines of trailing context (After)
--B      print NUM lines of leading context (Before)
--C      print NUM lines of output context (Context)
+-A NUM  print NUM lines of trailing context (After)
+-B NUM  print NUM lines of leading context (Before)
+-C NUM  print NUM lines of output context (Context)
 
 
 **Examples**:
@@ -882,7 +882,7 @@ Useful Filetools
   $
 
 
-- Find by size: (List those entries in the directory ``/usr/bin`` that are bigger than 500kBytes)
+- Find by size: (List those entries in the directory ``/usr/bin`` that are bigger than 500 kBytes)
 
  :: 
 

linux_beginner/links.rst

@@ -40,7 +40,7 @@ To play the game, get the files from github and read the instructions:
 Real printed paper books
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-- Dietz, M., "*Praxiskurs Unix-Shell*", O'Reilly (highly recommended!, german language only)
+- Dietz, M., "*Praxiskurs Unix-Shell*", O'Reilly (highly recommended!, German language only)
 - Herold, H., "*awk & sed*", Addison-Wesley
 - Robbins, A., "*sed & awk Pocket Reference*", O'Reilly
 - Robbins, A. and Beebe, N., "*Classic Shell Scripting*", O'Reilly

linux_beginner/solutions_beginner.rst

@@ -103,7 +103,7 @@ Searching
 
    $ find /bin -name date
 
-#. List those entries in the directory ``/bin`` that are bigger than 400kBytes ::
+#. List those entries in the directory ``/bin`` that are bigger than 400 kBytes ::
 
    $ find /bin -size +400k
 
@@ -122,15 +122,15 @@ Misc. terminal
 Permissions
 -----------
 
-#. :index:`Create <mkdir>` a directory called testpermissions ::
+#. :index:`Create <mkdir>` a directory called ``testpermissions`` ::
 
    $ mkdir testpermissions
 
-#. :index:`Change <cd>` your working directory to testpermissions::
+#. :index:`Change <cd>` your working directory to ``testpermissions``::
 
    $ cd testpermissions
 
-#. Create a directory called adir. ::
+#. Create a directory called ``adir``. ::
 
    $ mkdir adir
 
@@ -139,7 +139,7 @@ Permissions
     $ which date
     /bin/date
 
-#.  :index:`Copy <cp>` this date program into the directory adir and name it 'mydate'.::
+#.  :index:`Copy <cp>` this date program into the directory ``adir`` and name it 'mydate'.::
 
     $ cp /bin/date adir/mydate
 
@@ -171,7 +171,8 @@ Permissions
     $ adir/mydate
     Mon Dec  9 13:50:12 CET 2013
 
-#. Copy a textfile from a previos exercise into adir, then change the permissions, so you are not allowed to write to it. Test this by trying to read it via `cat`. ::
+#. Copy a textfile from a previous exercise into ``adir``, then change the permissions, so you are not allowed to write to it. 
+   Test that you are still able to read the file via `cat` ::
 
     $ cp ~/exercises/SRC_HUMAN.fasta adir
     $ chmod u-w adir/SRC_HUMAN.fasta
@@ -180,7 +181,7 @@ Permissions
 
    $ chmod u-r adir/SRC_HUMAN.fasta
 
-#. Change your working directory to testpermissions, and then try changing the permissions on the directory adir to non-executable. ::
+#. Change your working directory to ``testpermissions``, and then try changing the permissions on the directory ``adir`` to non-executable. ::
 
     $ # no need to change directory, 
     $ # as we still are in the directory testpermissions
@@ -223,7 +224,7 @@ Remote access
     $ file ~/motd
     ~/motd: ASCII text
 
-   $ ls -l ~/motd
+    $ ls -l ~/motd
 
 #.  :index:`Login <ssh>` to your neighbor's machine (ask him for the hostname) using your own username::
 
@@ -307,7 +308,7 @@ Putting it all together
 Bioinformatics
 --------------
 
-Let's do some bioinformatics analyis!
+Let's do some bioinformatics analysis!
 You can find the famous BLAST tool installed at `/g/software/bin/blastp`.
 
 #. Typing the full path is too cumbersome, so let's append `/g/software/bin` to your $PATH variable and ensure that it works by calling `blastp`. ::
@@ -333,3 +334,11 @@ You can find the famous BLAST tool installed at `/g/software/bin/blastp`.
    ::
 
     $ blastp -db /g/data/ncbi-blast/db/swissprot -query suspect1 fasta
+
+#. Use either ``less`` or a redirection into a file to manage the amount of information that ``blastp`` prints on your screen.::
+
+    $ blastp -db /g/data/ncbi-blast/db/swissprot -query suspect1 fasta | less
+
+   or::
+
+    $ blastp -db /g/data/ncbi-blast/db/swissprot -query suspect1 fasta > blast_output

linux_intermediate/basic_scripting.rst

@@ -88,7 +88,7 @@ script in the future.
 Documentation is done either by writing comments into the script or by creating a special documentation file (``README.txt`` or similar). Documenting in the script can be done in several ways:
 
 * A preamble in the script, outlining the purpose, parameters and variables of the script as well
-  as some information about authorship and and perhaps changes.
+  as some information about authorship and perhaps changes.
 
 * Within the script as blocks of text or "End of line" comments.
 
@@ -743,7 +743,7 @@ Breaking up Long Code Lines
 
 Code lines can become pretty long and unreadable, wrapping onto the next line
 etc.  You can use the :index:`escape character` (backslash, "``\``") to break them up and
-enhance readability of your script.  The excape character must immediately be
+enhance readability of your script.  The escape character must immediately be
 followed by a newline (no intermediate blanks or other is allowed): ::
 
     $ bsub -o output.log -e error.log -q clngnew -M 150000 -R "select[(mem > 15000)]" /g/software/bin/pymol-1.4 -r -p < pymol.pml

linux_intermediate/commandlinetools.rst

@@ -4,7 +4,7 @@ More Commandline Tools
 **********************
 
 Here is a quick list of useful commandline tools which will be used throughout the rest of the document.
-Many of these tools have quite extensive funcionality and only a very limited part can be discussed here, 
+Many of these tools have quite extensive functionality and only a very limited part can be discussed here, 
 so the reader is encouraged to read more about these using the links given in the in the :ref:`Links <Links>` 
 section...
 
@@ -307,7 +307,7 @@ field separator (FS), use option '-F' (remember to quote the field separator):
 
 Note two things here: First, the field separator is not printed, and second, if you
 want to have space between the output fields, you actually need to separate them
-by a comma or they will be catenated together...
+by a comma or they will be concatenated together...
 
  ::