Merge branch 'add_changes]' into 'master'

This closes #14

Closes #14

See merge request !47

docs.it4i/salomon/software/chemistry/nwchem.md

@@ -44,4 +44,4 @@ Options
 Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
 
 -   MEMORY : controls the amount of memory NWChem will use
--   SCRATCH_DIR : set this to a directory in [SCRATCH     filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
+-   SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"

docs.it4i/salomon/software/numerical-languages/r.md

@@ -20,7 +20,7 @@ Modules
 |Application|Version|module|
 |---|---|
 |**R**|R 3.1.1|R/3.1.1-intel-2015b|
-|**Rstudio**|Rstudio 0.97|Rstudio|
+|**Rstudio**|Rstudio 0.98.1103|Rstudio|
 
 ```bash
     $ module load R
@@ -97,7 +97,7 @@ Download the package [parallell](package-parallel-vignette.pdf) vignette.
 
 The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.
 
-!!! Note "Note"
+!!! warning
 	Forking via package parallel provides functionality similar to OpenMP construct omp parallel for
 
 	Only cores of single node can be utilized this way!

docs.it4i/anselm-cluster-documentation/software/bio-gentoo.md → docs.it4i/software/bio-gentoo.md

@@ -51,13 +51,201 @@ $ man -M /apps/gentoo/usr/share/man samtools
 Listing of bioinformatics applications
 --------------------------------------
 
-[gentoo_apps_on_anselm.doc](src/gentoo_apps_on_anselm.doc)
+```bash
+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
+sci-biology/BRANCH-9999
+sci-biology/EBARDenovo-1.2.2
+sci-biology/FLASH-1.2.9
+sci-biology/GAL-0.2.2
+sci-biology/Gambit-0.4.145
+sci-biology/HTSeq-0.6.1
+sci-biology/InterMine-0.98
+sci-biology/MochiView-1.45
+sci-biology/MuSeqBox-5.4
+sci-biology/ONTO-PERL-1.41
+sci-biology/ORFcor-20130507
+sci-biology/Rcorrector-9999
+sci-biology/SSAKE-3.8.2
+sci-biology/STAR-9999
+sci-biology/YASRA-2.33
+sci-biology/abacas-1.3.1
+sci-biology/align_to_scf-1.06
+sci-biology/assembly-stats-9999
+sci-biology/bambus-2.33
+sci-biology/bamtools-9999
+sci-biology/bcftools-1.2
+sci-biology/bedtools-2.22.1
+sci-biology/bfast-0.7.0a
+sci-biology/biobambam2-9999
+sci-biology/bismark-0.13.0
+sci-biology/blat-34-r1
+sci-biology/blue-1.1.3
+sci-biology/bowtie-2.2.9
+sci-biology/brat-1.2.4
+sci-biology/bwa-0.7.13
+sci-biology/bx-python-9999
+sci-biology/cast-bin-20080813
+sci-biology/cd-hit-4.6.5
+sci-biology/cdbfasta-0.1
+sci-biology/clover-2011.10.24
+sci-biology/clustalw-2.1
+sci-biology/cnrun-2.0.3
+sci-biology/codonw-1.4.4-r2
+sci-biology/conform-gt-1174
+sci-biology/conifer-0.2.2
+sci-biology/coral-1.4
+sci-biology/cross_genome-20140822
+sci-biology/cutadapt-9999
+sci-biology/dawg-1.1.2
+sci-biology/dna2pep-1.1
+sci-biology/edena-3.131028
+sci-biology/epga-9999
+sci-biology/erpin-5.5b
+sci-biology/estscan-3.0.3
+sci-biology/eugene-4.1d
+sci-biology/exonerate-gff3-9999
+sci-biology/fastx_toolkit-0.0.14
+sci-biology/gemini-9999
+sci-biology/geneid-1.4.4
+sci-biology/genepop-4.2.1
+sci-biology/glimmerhmm-3.0.1-r1
+sci-biology/gmap-2015.12.31.5
+sci-biology/hexamer-19990330
+sci-biology/hts-python-9999
+sci-biology/jellyfish-2.1.4
+sci-biology/jigsaw-3.2.10
+sci-biology/kallisto-9999
+sci-biology/karect-1.0.0
+sci-biology/lastz-1.03.66
+sci-biology/libgtextutils-0.6.1
+sci-biology/lucy-1.20
+sci-biology/megahit-9999
+sci-biology/merlin-1.1.2
+sci-biology/miranda-3.3a
+sci-biology/mreps-2.5
+sci-biology/mrfast-2.6.0.1
+sci-biology/mummer-3.22-r1
+sci-biology/muscle-3.8.31
+sci-biology/nrcl-110625
+sci-biology/nwalign-0.3.1
+sci-biology/oases-9999
+sci-biology/parafly-20130121
+sci-biology/phrap-1.080812-r1
+sci-biology/phred-071220
+sci-biology/phylip-3.696-r1
+sci-biology/plinkseq-0.10
+sci-biology/primer3-2.3.7
+sci-biology/prinseq-lite-0.20.4
+sci-biology/proda-1.0
+sci-biology/pybedtools-0.6.9
+sci-biology/pysam-0.9.0
+sci-biology/pysamstats-0.24.2
+sci-biology/quast-2.3
+sci-biology/quorum-1.0.0
+sci-biology/reaper-15348
+sci-biology/repeatmasker-libraries-20150807
+sci-biology/reptile-1.1
+sci-biology/samstat-20130708
+sci-biology/samtools-0.1.20-r2
+sci-biology/samtools-1.3-r1
+sci-biology/scaffold_builder-20131122-r1
+sci-biology/scan_for_matches-20121220
+sci-biology/screed-0.7.1
+sci-biology/scythe-0.992
+sci-biology/seqan-2.1.1
+sci-biology/seqtools-4.34.5
+sci-biology/sff_dump-1.04
+sci-biology/sgp2-1.1
+sci-biology/shrimp-2.2.3
+sci-biology/sickle-9999
+sci-biology/smalt-0.7.6
+sci-biology/snpomatic-9999
+sci-biology/ssaha2-bin-2.5.5
+sci-biology/stampy-1.0.28
+sci-biology/stringtie-1.2.2
+sci-biology/subread-1.4.6
+sci-biology/swissknife-1.72
+sci-biology/tagdust-20101028
+sci-biology/tclust-110625
+sci-biology/tigr-foundation-libs-2.0-r1
+sci-biology/trans-abyss-1.4.8
+sci-biology/trf-4.07b
+sci-biology/uchime-4.2.40
+sci-biology/velvet-1.2.10
+sci-biology/velvetk-20120606
+sci-biology/zmsort-110625
+```
+
+```bash
+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
+sci-libs/cbflib-0.9.3.3
+sci-libs/ccolamd-2.8.0
+sci-libs/cholmod-2.1.2
+sci-libs/coinor-cbc-2.8.9
+sci-libs/coinor-cgl-0.58.6
+sci-libs/coinor-clp-1.15.6-r1
+sci-libs/coinor-dylp-1.9.4
+sci-libs/coinor-osi-0.106.6
+sci-libs/coinor-utils-2.9.11
+sci-libs/coinor-vol-1.4.4
+sci-libs/colamd-2.8.0
+sci-libs/cxsparse-3.1.2
+sci-libs/dcmtk-3.6.0
+sci-libs/gsl-2.1
+sci-libs/hdf5-1.8.15_p1
+sci-libs/htslib-1.3
+sci-libs/io_lib-1.14.7
+sci-libs/lapack-reference-3.6.0-r1
+sci-libs/lemon-1.3-r2
+sci-libs/libmaus2-9999
+sci-libs/qrupdate-1.1.2-r1
+sci-libs/scikits-0.1-r1
+sci-libs/suitesparseconfig-4.2.1
+sci-libs/umfpack-5.6.2
+mmokrejs@login2 ~ $
 
+	error-correctors
+	aligners
+	clusterers
+	assemblers
+	scaffolders
+	motif searching
+	ORF/gene prediction/genome annotation
+	genotype/haplotype/popullation genetics
+	phylogenetics
+	transcriptome analysis
+	utilities
+	GUI
+	libraries
+```
 
 Classification of applications
 ------------------------------
 
-[gentoo_apps_on_anselm.xls](src/gentoo_apps_on_anselm.xls)
+|Applications for bioinformatics at IT4I	|
+|---|---|
+|error-correctors|6|
+|aligners|20|
+|clusterers|5|
+|assemblers|9|
+|scaffolders|6|
+|motif searching|6|
+|ORF/gene prediction/genome annotation|13|
+|genotype/haplotype/popullation genetics|3|
+|phylogenetics|1|
+|transcriptome analysis|2|
+|utilities|15|
+|GUI|3|
+|libraries|4|
+|**Total**|**93**|
+
+![graphs](../img/bio-graphs.png)
 
 
 Other applications available through Gentoo Linux

docs.it4i/software/orca.md

+ORCA
+====
+
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
+
+Making orca available
+---------------------
+
+The following module command makes the latest version of orca available to your session
+
+```bash
+$ module load ORCA/3_0_3-linux_x86-64
+```
+
+**Dependency**
+
+```bash
+$ module list
+Currently Loaded Modulefiles:
+  1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
+  2) GCC/4.9.3-binutils-2.25
+  3) binutils/2.25-GCC-4.9.3-binutils-2.25
+  4) GNU/4.9.3-2.25
+  5) icc/2015.3.187-GNU-4.9.3-2.25
+  6) ifort/2015.3.187-GNU-4.9.3-2.25
+  7) iccifort/2015.3.187-GNU-4.9.3-2.25
+  8) numactl/2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
+  9) hwloc/1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
+  10) OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
+  11) ORCA/3_0_3-linux_x86-64
+```
+
+Example single core job
+-----------------------
+
+Create a file called orca_serial.inp that contains the following orca commands
+
+```
+# My first ORCA calculation :-)
+#
+# Taken from the Orca manual
+# https://orcaforum.cec.mpg.de/OrcaManual.pdf
+! HF SVP
+* xyz 0 1
+  C 0 0 0
+  O 0 0 1.13
+*
+```
+
+Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
+
+```bash
+!/bin/bash
+
+module load ORCA/3_0_3-linux_x86-64
+orca orca_serial.inp
+```
+
+Submit the job to the queue with the command
+
+```bash
+$ qsub -q qexp -I -l select=1
+qsub: waiting for job 196821.isrv5 to start
+qsub: job 196821.isrv5 ready
+[username@r37u04n944 ~]$ ./submit_serial.sh
+
+
+                                 *****************
+                                 * O   R   C   A *
+                                 *****************
+
+           --- An Ab Initio, DFT and Semiempirical electronic structure package ---
+
+                  #######################################################
+                  #                        -***-                        #
+                  #  Department of molecular theory and spectroscopy    #
+                  #              Directorship: Frank Neese              #
+                  # Max Planck Institute for Chemical Energy Conversion #
+                  #                  D-45470 Muelheim/Ruhr              #
+                  #                       Germany                       #
+                  #                                                     #
+                  #                  All rights reserved                #
+                  #                        -***-                        #
+                  #######################################################
+
+...
+
+                             ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
+[username@r37u04n944 orca]$ logout
+
+qsub: job 196821.isrv5 completed
+```
+
+Register as a user
+------------------
+
+You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
+
+Documentation
+-------------
+
+A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
+

docs.it4i/src/.~lock.gentoo_apps_on_anselm.xls#

+,kru0052,kru0052,24.01.2017 06:58,file:///home/kru0052/.config/libreoffice/4;
\ No newline at end of file

mkdocs.yml

@@ -53,7 +53,7 @@ pages:
         - ANSYS MAPDL: anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
         - LS-DYNA: anselm-cluster-documentation/software/ansys/ls-dyna.md
       - 'Bioinformatics':
-        - Bioinformatics Applications: anselm-cluster-documentation/software/bio-gentoo.md
+        - Bioinformatics Applications: software/bio-gentoo.md
       - 'Debuggers':
         - Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
         - Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -70,6 +70,7 @@ pages:
       - 'Chemistry':
         - Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
         - NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
+        - ORCA: software/orca.md
       - COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
       - Compilers: anselm-cluster-documentation/software/compilers.md
       - GPI-2: anselm-cluster-documentation/software/gpi2.md
@@ -138,10 +139,13 @@ pages:
         - Workbench: salomon/software/ansys/workbench.md
         - Setting License Preferences: salomon/software/ansys/licensing.md
         - Licensing and Available Versions: salomon/software/ansys/setting-license-preferences.md
+      - 'Bioinformatics':
+        - Bioinformatics Applications: software/bio-gentoo.md
       - 'Chemistry':
         - Molpro: salomon/software/chemistry/molpro.md
         - NWChem: salomon/software/chemistry/nwchem.md
         - Phono3py: salomon/software/chemistry/phono3py.md
+        - ORCA: software/orca.md
       - Compilers: salomon/software/compilers.md
       - 'COMSOL':
         - COMSOL: salomon/software/comsol/comsol-multiphysics.md