Merge branch 'master' into THchanges_post_LSI_Dec15

git_beginner/Makefile

@@ -94,7 +94,7 @@ epub:
 
 certificates:
 	mkdir -p $(BUILDDIR)/certificates
-	pdflatex -interaction=nonstopmode  -output-directory=$(BUILDDIR)/certificates "\def\coursetitle{Introductory Course:\\\\GIT for Beginners} \input{../general/CertificateOfParticipation.tex}"
+	pdflatex -interaction=nonstopmode  -output-directory=$(BUILDDIR)/certificates "\def\coursetitle{Introductory Course:\\\\GIT Fundamentals} \input{../general/CertificateOfParticipation.tex}"
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/certificates."
 

git_beginner/conf.py

@@ -41,7 +41,7 @@ source_encoding = 'utf-8'
 master_doc = 'index'
 
 # General information about the project.
-project = u'git basics'
+project = u'git fundamentals'
 copyright = u'2013-2015, Holger Dinkel & Grischa Toedt'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -110,7 +110,7 @@ html_theme = 'nature'
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = "git basics"
+html_title = "git fundamentals"
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
@@ -194,7 +194,7 @@ latex_elements = {
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'gitintro.tex', u'GIT Basics',
+  ('index', 'gitintro.tex', u'GIT Fundamentals',
    u'Holger Dinkel \& Grischa Toedt', 'manual'),
 ]
 
@@ -224,7 +224,7 @@ latex_show_urls = False
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'gitintro', u'GIT Basics',
+    ('index', 'gitintro', u'GIT Fundamentals',
      [u'Holger Dinkel & Grischa Toedt'], 1)
 ]
 
@@ -238,8 +238,8 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'gitintro', u'GIT Basics',
-   u'Holger Dinkel & Grischa Toedt', 'gitintro', 'GIT Basics',
+  ('index', 'gitintro', u'GIT Fundamentals',
+   u'Holger Dinkel & Grischa Toedt', 'gitintro', 'GIT Fundamentals',
    'Miscellaneous'),
 ]
 

linux_intermediate/basic_scripting.rst

@@ -202,11 +202,12 @@ You can mix multiple ``&&`` and ``||`` controls into a single line.
     /home/fthommen/a
     $
 
-  Example: Count the heterogens described in a gzipped PDB file or, if it doesn't exist, 
-  download the file::
-    
-    $ gzip -c 4ZZN.pdb.gz && sed -n '/^HET /p' || wget "http://www.rcsb.org/pdb/files/4ZZN.pdb.gz"
-    $
+.. not working:
+.. Example: Count the heterogens described in a gzipped PDB file or, if it doesn't exist,
+..   download the file::
+..     
+..     $ { gunzip -c 4ZZN.pdb.gz | sed -n '/^HET /p' } || wget "http://www.rcsb.org/pdb/files/4ZZN.pdb.gz"
+..     $
 
 *( cmds )* --
   Group commands to create one single output stream: The commands are run in a subshell (i.e. a new shell is opened to run them):
@@ -367,7 +368,7 @@ B) Evaluating of conditions or comparisons:
 
 
 
-  Examples: Test for the existence of /etc/passwd::
+  Examples: Test for the existence of the directory `sequence_files`::
 
     if [ -e ./sequence_files ]
     then
@@ -640,7 +641,7 @@ $@:
 .. image:: _static/arguments.png
 
 
-If you run the script ::
+If you run the following script ::
 
     #!/bin/sh
     echo The script is $0
@@ -809,9 +810,9 @@ becomes: ::
            -q clngnew                 \
            -M 150000                  \
            -R "select[(mem > 15000)]" \
-        /g/software/bin/pymol-1.4 -r -p < pymol.pml
+        /g/software/bin/pymol -c -r pymol.pml
 
-Which is way better to read and to maintain
+Which is way better to read and to maintain...
 
 Script Debugging
 ----------------