From 5b89a84d52ef2a23456d90837c35c01b30a155b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Fri, 17 Feb 2017 10:00:46 +0100
Subject: [PATCH] general done

---
 .../graphical-user-interface/vnc.md           | 40 +++++++++----------
 .../x-window-system.md                        | 30 +++++++-------
 .../ssh-keys.md                               | 34 ++++++++--------
 .../certificates-faq.md                       | 15 ++++---
 .../obtaining-login-credentials.md            |  6 +--
 docs.it4i/index.md                            |  4 +-
 docs.it4i/software/bioinformatics.md          | 12 +++---
 docs.it4i/software/lmod.md                    | 32 +++++++--------
 docs.it4i/software/orca.md                    |  8 ++--
 9 files changed, 90 insertions(+), 91 deletions(-)

diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
index f064b2e6a..1778c429a 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -9,7 +9,7 @@ The recommended clients are [TightVNC](http://www.tightvnc.com) or [TigerVNC](ht
 !!! note
     Local VNC password should be set before the first login. Do use a strong password.
 
-```bash
+```console
 [username@login2 ~]$ vncpasswd
 Password:
 Verify:
@@ -24,16 +24,16 @@ Verify:
 
 You can find ports which are already occupied. Here you can see that ports " /usr/bin/Xvnc :79" and " /usr/bin/Xvnc :60" are occupied.
 
-```bash
+```console
 [username@login2 ~]$ ps aux | grep Xvnc
-username    5971 0.0 0.0 201072 92564 ?        SN   Sep22   4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
-username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
+username    5971 0.0 0.0 201072 92564 ?        SN   Sep22   4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/vop999/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
+username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/vop999/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/vop999/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
 .....
 ```
 
 Choose free port e.g. 61 and start your VNC server:
 
-```bash
+```console
 [username@login2 ~]$ vncserver :61 -geometry 1600x900 -depth 16
 
 New 'login2:1 (username)' desktop is login2:1
@@ -44,7 +44,7 @@ Log file is /home/username/.vnc/login2:1.log
 
 Check if VNC server is started on the port (in this example 61):
 
-```bash
+```console
 [username@login2 .vnc]$ vncserver -list
 
 TigerVNC server sessions:
@@ -55,10 +55,10 @@ X DISPLAY #     PROCESS ID
 
 Another command:
 
-```bash
+```console
 [username@login2 .vnc]$  ps aux | grep Xvnc
 
-username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
+username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/vop999/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
 ```
 
 To access the VNC server you have to create a tunnel between the login node using TCP **port 5961** and your machine using a free TCP port (for simplicity the very same, in this case).
@@ -70,13 +70,13 @@ To access the VNC server you have to create a tunnel between the login node usin
 
 At your machine, create the tunnel:
 
-```bash
+```console
 local $  ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
 ```
 
 Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):
 
-```bash
+```console
 local $ netstat -natp | grep 5961
 (Not all processes could be identified, non-owned process info
  will not be shown, you would have to be root to see it all.)
@@ -86,14 +86,14 @@ tcp6       0      0 ::1:5961                :::*                    LISTEN
 
 Or on Mac OS use this command:
 
-```bash
+```console
 local-mac $ lsof -n -i4TCP:5961 | grep LISTEN
 ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)
 ```
 
 Connect with the VNC client:
 
-```bash
+```console
 local $ vncviewer 127.0.0.1:5961
 ```
 
@@ -101,7 +101,7 @@ In this example, we connect to VNC server on port 5961, via the ssh tunnel. The
 
 You have to destroy the SSH tunnel which is still running at the background after you finish the work. Use the following command (PID 2022 in this case, see the netstat command above):
 
-```bash
+```console
 kill 2022
 ```
 
@@ -113,7 +113,7 @@ Start vncserver using command vncserver described above.
 
 Search for the localhost and port number (in this case 127.0.0.1:5961).
 
-```bahs
+```console
 [username@login2 .vnc]$ netstat -tanp | grep Xvnc
 (Not all processes could be identified, non-owned process info
  will not be shown, you would have to be root to see it all.)
@@ -160,7 +160,7 @@ Uncheck both options below the slider:
 
 If the screen gets locked you have to kill the screensaver. Do not to forget to disable the screensaver then.
 
-```bash
+```console
 [username@login2 .vnc]$ ps aux | grep screen
 username     1503 0.0 0.0 103244   892 pts/4    S+   14:37   0:00 grep screen
 username     24316 0.0 0.0 270564 3528 ?        Ss   14:12   0:00 gnome-screensaver
@@ -172,7 +172,7 @@ username     24316 0.0 0.0 270564 3528 ?        Ss   14:12   0:00 gnome-screensa
 
 You should kill your VNC server using command:
 
-```bash
+```console
 [username@login2 .vnc]$  vncserver  -kill :61
 Killing Xvnc process ID 7074
 Xvnc process ID 7074 already killed
@@ -180,7 +180,7 @@ Xvnc process ID 7074 already killed
 
 Or this way:
 
-```bash
+```console
 [username@login2 .vnc]$  pkill vnc
 ```
 
@@ -194,19 +194,19 @@ Open a Terminal (Applications -> System Tools -> Terminal). Run all the next com
 
 Allow incoming X11 graphics from the compute nodes at the login node:
 
-```bash
+```console
 $ xhost +
 ```
 
 Get an interactive session on a compute node (for more detailed info [look here](../../../anselm/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:
 
-```bash
+```console
 $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24
 ```
 
 Test that the DISPLAY redirection into your VNC session works, by running a X11 application (e. g. XTerm) on the assigned compute node:
 
-```bash
+```console
 $ xterm
 ```
 
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md
index b9c695129..961123f51 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -9,7 +9,7 @@ The X Window system is a principal way to get GUI access to the clusters. The **
 
 In order to display graphical user interface GUI of various software tools, you need to enable the X display forwarding. On Linux and Mac, log in using the -X option tho ssh client:
 
-```bash
+```console
  local $ ssh -X username@cluster-name.it4i.cz
 ```
 
@@ -19,13 +19,13 @@ On Windows use the PuTTY client to enable X11 forwarding. In PuTTY menu, go to C
 
 To verify the forwarding, type
 
-```bash
+```console
 $ echo $DISPLAY
 ```
 
 if you receive something like
 
-```bash
+```console
 localhost:10.0
 ```
 
@@ -44,8 +44,8 @@ Mac OS users need to install [XQuartz server](https://www.xquartz.org).
 There are variety of X servers available for Windows environment. The commercial Xwin32 is very stable and rich featured. The Cygwin environment provides fully featured open-source XWin X server. For simplicity, we recommend open-source X server by the [Xming project](http://sourceforge.net/projects/xming/). For stability and full features we recommend the
 [XWin](http://x.cygwin.com/) X server by Cygwin
 
-| How to use Xwin                                                                                                                                                                                                         | How to use Xming                                                                                     |
-| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
+| How to use Xwin | How to use Xming |
+|--- | --- |
 | [Install Cygwin](http://x.cygwin.com/) Find and execute XWin.exe to start the X server on Windows desktop computer.[If no able to forward X11 using PuTTY to CygwinX](#if-no-able-to-forward-x11-using-putty-to-cygwinx) | Use Xlaunch to configure the Xming. Run Xming to start the X server on Windows desktop computer. |
 
 Read more on [http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://www.math.umn.edu/systems_guide/putty_xwin32.shtml)
@@ -57,12 +57,12 @@ Read more on [http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://ww
 
 Then launch the application as usual. Use the & to run the application in background.
 
-```bash
-$ module load intel (idb and gvim not installed yet)
+```console
+$ ml intel (idb and gvim not installed yet)
 $ gvim &
 ```
 
-```bash
+```console
 $ xterm
 ```
 
@@ -72,7 +72,7 @@ In this example, we activate the intel programing environment tools, then start
 
 Allocate the compute nodes using -X option on the qsub command
 
-```bash
+```console
 $ qsub -q qexp -l select=2:ncpus=24 -X -I
 ```
 
@@ -80,7 +80,7 @@ In this example, we allocate 2 nodes via qexp queue, interactively. We request X
 
 **Better performance** is obtained by logging on the allocated compute node via ssh, using the -X option.
 
-```bash
+```console
 $ ssh -X r24u35n680
 ```
 
@@ -95,13 +95,13 @@ The Gnome 2.28 GUI environment is available on the clusters. We recommend to use
 To run the remote Gnome session in a window on Linux/OS X computer, you need to install Xephyr. Ubuntu package is
 xserver-xephyr, on OS X it is part of [XQuartz](http://xquartz.macosforge.org/landing/). First, launch Xephyr on local machine:
 
-```bash
+```console
 local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &
 ```
 
 This will open a new X window with size 1024 x 768 at DISPLAY :1. Next, ssh to the cluster with DISPLAY environment variable set and launch gnome-session
 
-```bash
+```console
 local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key
 ... cluster-name MOTD...
 yourname@login1.cluster-namen.it4i.cz $ gnome-session &
@@ -109,7 +109,7 @@ yourname@login1.cluster-namen.it4i.cz $ gnome-session &
 
 On older systems where Xephyr is not available, you may also try Xnest instead of Xephyr. Another option is to launch a new X server in a separate console, via:
 
-```bash
+```console
 xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- :1 vt12
 ```
 
@@ -122,7 +122,7 @@ Use Xlaunch to start the Xming server or run the XWin.exe. Select the "One windo
 
 Log in to the cluster, using PuTTY. On the cluster, run the gnome-session command.
 
-```bash
+```console
 $ gnome-session &
 ```
 
@@ -132,7 +132,7 @@ Use System-Log Out to close the gnome-session
 
 ### if No Able to Forward X11 Using PuTTY to CygwinX
 
-```bash
+```console
 [usename@login1.anselm ~]$ gnome-session &
 [1] 23691
 [usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
diff --git a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index a2a4d429f..00563525c 100644
--- a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -4,9 +4,9 @@
 
 After logging in, you can see .ssh/ directory with SSH keys and authorized_keys file:
 
-```bash
-    $ cd /home/username/
-    $ ls -la .ssh/
+```console
+$ cd /home/username/
+$ ls -la .ssh/
     total 24
     drwx------ 2 username username 4096 May 13 15:12 .
     drwxr-x---22 username username 4096 May 13 07:22 ..
@@ -25,14 +25,14 @@ After logging in, you can see .ssh/ directory with SSH keys and authorized_keys
 * Authorized_keys, known_hosts and public key (.pub file): 644 (-rw-r--r--)
 * Private key (id_rsa/id_rsa.ppk): 600 (-rw-------)
 
-```bash
-    cd /home/username/
-    chmod 700 .ssh/
-    chmod 644 .ssh/authorized_keys
-    chmod 644 .ssh/id_rsa.pub
-    chmod 644 .ssh/known_hosts
-    chmod 600 .ssh/id_rsa
-    chmod 600 .ssh/id_rsa.ppk
+```console
+$ cd /home/username/
+$ chmod 700 .ssh/
+$ chmod 644 .ssh/authorized_keys
+$ chmod 644 .ssh/id_rsa.pub
+$ chmod 644 .ssh/known_hosts
+$ chmod 600 .ssh/id_rsa
+$ chmod 600 .ssh/id_rsa.ppk
 ```
 
 ## Private Key
@@ -44,7 +44,7 @@ Private key file in "id_rsa" or `*.ppk` format is used to authenticate with the
 
 An example of private key format:
 
-```bash
+```console
     -----BEGIN RSA PRIVATE KEY-----
     MIIEpAIBAAKCAQEAqbo7jokygnBpG2wYa5NB45ns6+UKTNLMLHF0BO3zmRtKEElE
     aGqXfbYwvXlcuRb2d9/Y5dVpCZHV0kbY3NhtVOcEIe+1ROaiU9BEsUAhMNEvgiLV
@@ -80,7 +80,7 @@ Public key file in "\*.pub" format is used to verify a digital signature. Public
 
 An example of public key format:
 
-```bash
+```console
 ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCpujuOiTKCcGkbbBhrk0Hjmezr5QpM0swscXQE7fOZG0oQSURoapd9tjC9eVy5FvZ339jl1WkJkdXSRtjc2G1U5wQh77VE5qJT0ESxQCEw0S+CItWBKqXhC9E7gFY+UyP5YBZcOneh6gGHyCVfK6H215vzKr3x+/WvWl5gZGtbf+zhX6o4RJDRdjZPutYJhEsg/qtMxcCtMjfm/dZTnXeafuebV8nug3RCBUflvRb1XUrJuiX28gsd4xfG/P6L/mNMR8s4kmJEZhlhxpj8Th0iIc+XciVtXuGWQrbddcVRLxAmvkYAPGnVVOQeNj69pqAR/GXaFAhvjYkseEowQao1 username@organization.example.com
 ```
 
@@ -88,8 +88,8 @@ ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCpujuOiTKCcGkbbBhrk0Hjmezr5QpM0swscXQE7fOZ
 
 First, generate a new keypair of your public and private key:
 
-```bash
-    local $ ssh-keygen -C 'username@organization.example.com' -f additional_key
+```console
+local $ ssh-keygen -C 'username@organization.example.com' -f additional_key
 ```
 
 !!! note
@@ -99,8 +99,8 @@ You can insert additional public key into authorized_keys file for authenticatio
 
 Example:
 
-```bash
-    $ cat additional_key.pub > ~/.ssh/authorized_keys
+```console
+$ cat additional_key.pub > ~/.ssh/authorized_keys
 ```
 
 In this example, we add an additional public key, stored in file additional_key.pub into the authorized_keys. Next time we log in, we will be able to use the private addtional_key key to log in.
diff --git a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
index bf0b5c5ac..9ba3e09fb 100644
--- a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
@@ -57,7 +57,7 @@ It is worth noting that gsissh-term and DART automatically updates their CA cert
 
 Lastly, if you need the CA certificates for a personal Globus 5 installation, then you can install the CA certificates from a MyProxy server with the following command.
 
-```bash
+```console
     myproxy-get-trustroots -s myproxy-prace.lrz.de
 ```
 
@@ -77,14 +77,14 @@ The following examples are for Unix/Linux operating systems only.
 
 To convert from PEM to p12, enter the following command:
 
-```bash
+```console
     openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out
     username.p12
 ```
 
 To convert from p12 to PEM, type the following _four_ commands:
 
-```bash
+```console
     openssl pkcs12 -in username.p12 -out usercert.pem -clcerts -nokeys
     openssl pkcs12 -in username.p12 -out userkey.pem -nocerts
     chmod 444 usercert.pem
@@ -93,24 +93,23 @@ To convert from p12 to PEM, type the following _four_ commands:
 
 To check your Distinguished Name (DN), enter the following command:
 
-```bash
+```console
     openssl x509 -in usercert.pem -noout -subject -nameopt
     RFC2253
 ```
 
 To check your certificate (e.g., DN, validity, issuer, public key algorithm, etc.), enter the following command:
 
-```bash
+```console
     openssl x509 -in usercert.pem -text -noout
 ```
-
 To download openssl if not pre-installed, [please visit](https://www.openssl.org/source/). On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.
 
 ## Q: How Do I Create and Then Manage a Keystore?
 
 IT4innovations recommends the java based keytool utility to create and manage keystores, which themselves are stores of keys and certificates. For example if you want to convert your pkcs12 formatted key pair into a java keystore you can use the following command.
 
-```bash
+```console
     keytool -importkeystore -srckeystore $my_p12_cert -destkeystore
     $my_keystore -srcstoretype pkcs12 -deststoretype jks -alias
     $my_nickname -destalias $my_nickname
@@ -120,7 +119,7 @@ where $my_p12_cert is the name of your p12 (pkcs12) certificate, $my_keystore is
 
 You also can import CA certificates into your java keystore with the tool, e.g.:
 
-```bash
+```console
     keytool -import -trustcacerts -alias $mydomain -file $mydomain.crt -keystore $my_keystore
 ```
 
diff --git a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
index c97268c2b..a7cae2e6d 100644
--- a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
@@ -40,7 +40,7 @@ In order to authorize a Collaborator to utilize the allocated resources, the PI
 
 Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):
 
-```bash
+```console
     Subject: Authorization to IT4Innovations
 
     Dear support,
@@ -72,7 +72,7 @@ Once authorized by PI, every person (PI or Collaborator) wishing to access the c
 
 Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):
 
-```bash
+```console
     Subject: Access to IT4Innovations
 
     Dear support,
@@ -100,7 +100,7 @@ The clusters are accessed by the [private key](../accessing-the-clusters/shell-a
 
 On Linux, use
 
-```bash
+```console
 local $ ssh-keygen -f id_rsa -p
 ```
 
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 7e97161c1..b7a7bb2a7 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -47,13 +47,13 @@ In this documentation, you will find a number of pages containing examples. We u
 
 Cluster command prompt
 
-```bash
+```console
 $
 ```
 
 Your local linux host command prompt
 
-```bash
+```console
 local $
 ```
 
diff --git a/docs.it4i/software/bioinformatics.md b/docs.it4i/software/bioinformatics.md
index 76991fe78..91de9ca9c 100644
--- a/docs.it4i/software/bioinformatics.md
+++ b/docs.it4i/software/bioinformatics.md
@@ -6,7 +6,7 @@ In addition to the many applications available through modules (deployed through
 
 ## Starting the Environment
 
-```bash
+```console
 mmokrejs@login2~$ /apps/gentoo/startprefix
 ```
 
@@ -14,7 +14,7 @@ mmokrejs@login2~$ /apps/gentoo/startprefix
 
 Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment.
 
-```bash
+```console
 mmokrejs@login2~$ cat myjob.pbs
 #PBS -S /apps/gentoo/bin/sh
 #PBS -l nodes=1:ppn=16,walltime=12:00:00
@@ -37,14 +37,14 @@ $ qstat
 
 ## Reading Manual Pages for Installed Applications
 
-```bash
+```console
 mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man bwa
 mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man samtools
 ```
 
 ## Listing of Bioinformatics Applications
 
-```bash
+```console
 mmokrejs@login2~$ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
 sci-biology/ANGLE-bin-20080813-r1
 sci-biology/AlignGraph-9999
@@ -172,7 +172,7 @@ sci-biology/velvetk-20120606
 sci-biology/zmsort-110625
 ```
 
-```bash
+```console
 mmokrejs@login2~$ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt
 sci-libs/amd-2.3.1
 sci-libs/blas-reference-20151113-r1
@@ -228,7 +228,7 @@ sci-libs/umfpack-5.6.2
 
 Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools.
 
-```bash
+```console
 mmokrejs@login2~$ gcc-config -l
 mmokrejs@login2~$ java-config -L
 mmokrejs@login2~$ eselect
diff --git a/docs.it4i/software/lmod.md b/docs.it4i/software/lmod.md
index 3ddd5cc1d..8bb5e5498 100644
--- a/docs.it4i/software/lmod.md
+++ b/docs.it4i/software/lmod.md
@@ -18,7 +18,7 @@ Detailed documentation on Lmod is available at [here](http://lmod.readthedocs.io
 
 Create folder or file `.lmod` into your home folder. Logout and login. New Lmod enviroment will be active now.
 
-```bash
+```console
 $ mkdir ~/.lmod
 $ logout
 Connection to login4.salomon.it4i.cz closed.
@@ -65,7 +65,7 @@ Below you will find more details and examples.
 
 To get an overview of the currently loaded modules, use module list or ml (without specifying extra arguments).
 
-```bash
+```console
 $ ml
 Currently Loaded Modules:
    1) EasyBuild/3.0.0 (S)  2) lmod/7.2.2
@@ -80,7 +80,7 @@ Currently Loaded Modules:
 
 To get an overview of all available modules, you can use ml avail or simply ml av:
 
-```bash
+```console
 $ ml av
 ---------------------------------------- /apps/modules/compiler ----------------------------------------------
    GCC/5.2.0    GCCcore/6.2.0 (D)    icc/2013.5.192     ifort/2013.5.192    LLVM/3.9.0-intel-2017.00 (D)
@@ -104,7 +104,7 @@ In the current module naming scheme, each module name consists of two parts:
 
 If you just provide a software name, for example gcc, it prints on overview of all available modules for GCC.
 
-```bash
+```console
 $ ml spider gcc
 ---------------------------------------------------------------------------------
   GCC:
@@ -147,7 +147,7 @@ $ ml spider gcc
 
 If you use spider on a full module name like GCC/6.2.0-2.27 it will tell on which cluster(s) that module available:
 
-```bash
+```console
 $ module spider GCC/6.2.0-2.27
 --------------------------------------------------------------------------------------------------------------
   GCC: GCC/6.2.0-2.27
@@ -169,7 +169,7 @@ This tells you what the module contains and a URL to the homepage of the softwar
 To check which modules are available for a particular software package, you can provide the software name to ml av.
 For example, to check which versions of git are available:
 
-```bash
+```console
 $ ml av git
 
 -------------------------------------- /apps/modules/tools ----------------------------------------
@@ -187,7 +187,7 @@ Use "module keyword key1 key2 ..." to search for all possible modules matching a
 
 Lmod does a partial match on the module name, so sometimes you need to use / to indicate the end of the software name you are interested in:
 
-```bash
+```console
 $ ml av GCC/
 
 ------------------------------------------ /apps/modules/compiler -------------------------------------------
@@ -204,7 +204,7 @@ Use "module keyword key1 key2 ..." to search for all possible modules matching a
 
 To see how a module would change the environment, use ml show:
 
-```bash
+```console
 $ ml show Python/3.5.2
 
 help([[Python is a programming language that lets you work more quickly and integrate your systems more effectively. - Homepage: http://python.org/]])
@@ -240,7 +240,7 @@ If you're not sure what all of this means: don't worry, you don't have to know,
 The effectively apply the changes to the environment that are specified by a module, use ml and specify the name of the module.
 For example, to set up your environment to use intel:
 
-```bash
+```console
 $ ml intel/2017.00
 $ ml
 Currently Loaded Modules:
@@ -275,7 +275,7 @@ In addition, only **one single version** of each software package can be loaded
 To revert the changes to the environment that were made by a particular module, you can use ml -<modname>.
 For example:
 
-```bash
+```console
 $ ml
 Currently Loaded Modules:
   1) EasyBuild/3.0.0 (S)   2) lmod/7.2.2
@@ -299,7 +299,7 @@ $ which gcc
 
 To reset your environment back to a clean state, you can use ml purge or ml purge --force:
 
-```bash
+```console
 $ ml
 Currently Loaded Modules:
   1) EasyBuild/3.0.0 (S)   2) lmod/7.2.2   3) GCCcore/6.2.0   4) binutils/2.27-GCCcore-6.2.0 (H)
@@ -323,25 +323,25 @@ If you have a set of modules that you need to load often, you can save these in
 
 First, load all the modules you need, for example:
 
-```bash
-ml intel/2017.00 Python/3.5.2-intel-2017.00
+```console
+$ ml intel/2017.00 Python/3.5.2-intel-2017.00
 ```
 
 Now store them in a collection using ml save:
 
-```bash
+```console
 $ ml save my-collection
 ```
 
 Later, for example in a job script, you can reload all these modules with ml restore:
 
-```bash
+```console
 $ ml restore my-collection
 ```
 
 With ml savelist can you gets a list of all saved collections:
 
-```bash
+```console
 $ ml savelist
 Named collection list:
   1) my-collection
diff --git a/docs.it4i/software/orca.md b/docs.it4i/software/orca.md
index 8fcfd69bf..3f6241545 100644
--- a/docs.it4i/software/orca.md
+++ b/docs.it4i/software/orca.md
@@ -6,13 +6,13 @@ ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum c
 
 The following module command makes the latest version of orca available to your session
 
-```bash
+```console
 $ module load ORCA/3_0_3-linux_x86-64
 ```
 
 ### Dependency
 
-```bash
+```console
 $ module list
 Currently Loaded Modulefiles:
   1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
@@ -46,7 +46,7 @@ Create a file called orca_serial.inp that contains the following orca commands
 
 Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
 
-```bash
+```console
 !/bin/bash
 
 module load ORCA/3_0_3-linux_x86-64
@@ -55,7 +55,7 @@ orca orca_serial.inp
 
 Submit the job to the queue with the command
 
-```bash
+```console
 $ qsub -q qexp -I -l select=1
 qsub: waiting for job 196821.isrv5 to start
 qsub: job 196821.isrv5 ready
-- 
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