edit bioinformatics

docs.it4i/software/bioinformatics.md

@@ -6,12 +6,11 @@ Introduction
 
 In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from [Gentoo Linux](https://www.gentoo.org/). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ([links](https://wiki.gentoo.org/wiki/Prefix/libc)).
 
-
 Starting the environment
 ------------------------
 
 ```bash
-$ /apps/gentoo/startprefix
+mmokrejs@login2~$ /apps/gentoo/startprefix
 ```
 
 Starting PBS jobs using the applications
@@ -20,7 +19,7 @@ Starting PBS jobs using the applications
 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
-$ cat myjob.pbs
+mmokrejs@login2~$ cat myjob.pbs
 #PBS -S /apps/gentoo/bin/sh
 #PBS -l nodes=1:ppn=16,walltime=12:00:00
 #PBS -q qfree
@@ -44,15 +43,15 @@ Reading manual pages for installed applications
 -----------------------------------------------
 
 ```bash
-$ man -M /apps/gentoo/usr/share/man bwa
-$ man -M /apps/gentoo/usr/share/man samtools
+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
-mmokrejs@login2 ~ $ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
+mmokrejs@login2~$ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
 sci-biology/ANGLE-bin-20080813-r1
 sci-biology/AlignGraph-9999
 sci-biology/Atlas-Link-0.01-r1
@@ -180,7 +179,7 @@ sci-biology/zmsort-110625
 ```
 
 ```bash
-mmokrejs@login2 ~ $ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt 
+mmokrejs@login2~$ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt
 sci-libs/amd-2.3.1
 sci-libs/blas-reference-20151113-r1
 sci-libs/camd-2.3.1
@@ -213,7 +212,7 @@ sci-libs/umfpack-5.6.2
 Classification of applications
 ------------------------------
 
-|Applications for bioinformatics at IT4I	|
+|Applications for bioinformatics at IT4I|
 |---|---|
 |error-correctors|6|
 |aligners|20|
@@ -232,14 +231,13 @@ Classification of applications
 
 ![graphs](../img/bio-graphs.png)
 
-
 Other applications available through Gentoo Linux
 -------------------------------------------------
 
 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
-$ gcc-config -l
-$ java-config -L
-$ eselect
+mmokrejs@login2~$ gcc-config -l
+mmokrejs@login2~$ java-config -L
+mmokrejs@login2~$ eselect
 ```