diff --git a/docs.it4i/anselm-cluster-documentation/prace.md b/docs.it4i/anselm-cluster-documentation/prace.md
index 74520cdd222c823197295e242c7aa34e942983b8..c48fc3e226262b265d2e7ba4761519540960d1a7 100644
--- a/docs.it4i/anselm-cluster-documentation/prace.md
+++ b/docs.it4i/anselm-cluster-documentation/prace.md
@@ -209,7 +209,7 @@ For production runs always use scratch file systems, either the global shared or
All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation](environment-and-modules/).
-PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production).
+PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/prace-common-production-environment/).
```bash
$ module load prace
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index e09cd64a3f7724af581315d1e3a936b84faa381f..4daa5a06639b74d38891844805ef87f93fe1aa4c 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -62,7 +62,7 @@ Be sure to log in with an X window forwarding enabled. This could mean using th
$ ssh -X username@anselm.it4i.cz
```
-Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)
From the login node an interactive session **with X windows forwarding** (-X option) can be started by following command:
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index 8cdcd2b8e57550ccc2a5baeedc71835950121aee..3be05fe85a496fb88fa8cabf153b8b715a481100 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -25,7 +25,7 @@ You can start using PETSc on Anselm by loading the PETSc module. Module names ob
module load petsc/3.4.4-icc-impi-mkl-opt
```
-where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](http://www.mcs.anl.gov/petsc/features/threads.html).
+where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](https://www.mcs.anl.gov/petsc/miscellaneous/petscthreads.html).
External libraries
------------------
@@ -57,6 +57,6 @@ All these libraries can be used also alone, without PETSc. Their static or share
- [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
- [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
- preconditioners & multigrid
- - [Hypre](http://acts.nersc.gov/hypre/)
+ - [Hypre](http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
- [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
- [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
index 0fbdc214f727d55f454f844dfde02b9c2eca226d..47f3e6478f15d6070bb28df14ee3b2e3226eed31 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
@@ -3,7 +3,7 @@ Diagnostic component (TEAM)
### Access
-TEAM is available at the following address: <http://omics.it4i.cz/team/>
+TEAM is available at the [following address](http://omics.it4i.cz/team/)
!!! Note "Note"
The address is accessible only via VPN.
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
index f8434816050ab7935f240c4d386a08a3230c2b09..2b3be2f52d915af055444920373ade4de68bc1d2 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
@@ -291,9 +291,9 @@ The pipeline calls the following tools:
sequence data.
- [gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
-- [hpg-aligner](http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:downloads), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: *Burrows-Wheeler Transform* (BWT) to speed-up mapping high-quality reads, and *Smith-Waterman*> (SW) to increase sensitivity when reads cannot be mapped using BWT.
+- [hpg-aligner](https://github.com/opencb-hpg/hpg-aligner), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: *Burrows-Wheeler Transform* (BWT) to speed-up mapping high-quality reads, and *Smith-Waterman*> (SW) to increase sensitivity when reads cannot be mapped using BWT.
- [hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
-- [hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
+- [hpg-variant](http://docs.bioinfo.cipf.es/projects/hpg-variant/wiki), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
- [picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
- [samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
- [snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
index 8b5cb8cf6ae3cdf00649ea640ec417920d3ad76c..3c2c24cd07fb3e995fb86ed7798f2131fb853e91 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
@@ -3,7 +3,7 @@ Prioritization component (BiERapp)
### Access
-BiERapp is available at the following address: <http://omics.it4i.cz/bierapp/>
+BiERapp is available at the [following address](http://omics.it4i.cz/bierapp/)
!!! Note "Note"
The address is accessible onlyvia VPN.
diff --git a/docs.it4i/anselm-cluster-documentation/storage.md b/docs.it4i/anselm-cluster-documentation/storage.md
index d67279a8ae66cfc36af743d7db9850758961643f..3cbb15a1de47b6369872c91a8948666fb77e12f3 100644
--- a/docs.it4i/anselm-cluster-documentation/storage.md
+++ b/docs.it4i/anselm-cluster-documentation/storage.md
@@ -334,7 +334,7 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
-The service is documented at <https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
+The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
index 833117661666ba6377780cfd0767bc6e308ccd03..3c6b877ca9821559517f89bf2459fd83b009fcb5 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -42,7 +42,7 @@ In order to display graphical user interface GUI of various software tools, you
X Server on OS X
----------------
-Mac OS users need to install [XQuartz server](http://xquartz.org).
+Mac OS users need to install [XQuartz server](https://www.xquartz.org).
X Server on Windows
-------------------
diff --git a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index e3b3e374fa6ea3a483618d76f7e019cdde3ceaa4..cced0979db40caa02b4c27afb9f1fb66ebced3db 100644
--- a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -25,7 +25,7 @@ Q: Which X.509 certificates are recognised by IT4Innovations?
Q: How do I get a User Certificate that can be used with IT4Innovations?
------------------------------------------------------------------------
-To get a certificate, you must make a request to your local, IGTF approved, Certificate Authority (CA). Usually you then must visit, in person, your nearest Registration Authority (RA) to verify your affiliation and identity (photo identification is required). Usually, you will then be emailed details on how to retrieve your certificate, although procedures can vary between CAs. If you are in Europe, you can locate [your trusted CA](http://www.eugridpma.org/members/worldmap).
+To get a certificate, you must make a request to your local, IGTF approved, Certificate Authority (CA). Usually you then must visit, in person, your nearest Registration Authority (RA) to verify your affiliation and identity (photo identification is required). Usually, you will then be emailed details on how to retrieve your certificate, although procedures can vary between CAs. If you are in Europe, you can locate [your trusted CA](www.eugridpma.org/members/worldmap).
In some countries certificates can also be retrieved using the TERENA Certificate Service, see the FAQ below for the link.
@@ -146,7 +146,7 @@ Most grid services require the use of your certificate; however, the format of y
If employing the PRACE version of GSISSH-term (also a Java Web Start Application), you may use either the PEM or p12 formats. Note that this service automatically installs up-to-date PRACE CA certificates.
-If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information, please visit [UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE)
+If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information, please visit [UNICORE6 in PRACE](www.prace-ri.eu/UNICORE6-in-PRACE)
If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5, then the certificates can be in either p12 or PEM format and must reside in the "$HOME/.globus" directory for Linux and Mac users or %HOMEPATH%.globus for Windows users. (Windows users will have to use the DOS command ’cmd’ to create a directory which starts with a ’.’). Further, user certificates should be named either "usercred.p12" or "usercert.pem" and "userkey.pem", and the CA certificates must be kept in a pre-specified directory as follows. For Linux and Mac users, this directory is either $HOME/.globus/certificates or /etc/grid-security/certificates. For Windows users, this directory is %HOMEPATH%.globuscertificates. (If you are using GSISSH-Term from prace-ri.eu then you do not have to create the .globus directory nor install CA certificates to use this tool alone).
diff --git a/docs.it4i/salomon/prace.md b/docs.it4i/salomon/prace.md
index f64d7a31b60fb8cdc05c7b2e6b1c22dd4b9d0fae..facda414a0c72b7ebe6e0a43a2c1590f8723c06a 100644
--- a/docs.it4i/salomon/prace.md
+++ b/docs.it4i/salomon/prace.md
@@ -221,7 +221,7 @@ For production runs always use scratch file systems. The available file systems
All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation](environment-and-modules/).
-PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production).
+PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/prace-common-production-environment/).
```bash
$ module load prace
diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md
index 9bd7ced93f1ec946a86e598d975cbbb35b7b552f..d1b8ade6ec1bf50d430d9f34d790609111fd283c 100644
--- a/docs.it4i/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md
@@ -1,7 +1,7 @@
ANSYS CFX
=========
-[ANSYS CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX) software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.
+[ANSYS CFX](http://www.ansys.com/products/fluids/ansys-cfx) software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.
To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index 4d8aa00357dd32dd82262acb921683df5f25fbd2..0ebec531d8ef8dfe30eceedf6045d2d80916c719 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md
@@ -1,7 +1,7 @@
ANSYS Fluent
============
-[ANSYS Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
+[ANSYS Fluent](http://www.ansys.com/products/fluids/ansys-fluent)
software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.
1. Common way to run Fluent over pbs file
diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
index c2ce777868c34566878c2c7b20d520ddb45bee14..9284e151c7d723d883c55eabf0a38c133ba9e613 100644
--- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
@@ -1,7 +1,7 @@
ANSYS LS-DYNA
=============
-**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
+**[ANSYSLS-DYNA](http://www.ansys.com/products/structures/ansys-ls-dyna)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.
diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
index 939a599b92f29b07e8f4836d604753c20e57592a..9c05b279128303104d281a508f02cd5202471570 100644
--- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,7 +1,7 @@
ANSYS MAPDL
===========
-**[ANSYS Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
+**[ANSYS Multiphysics](http://www.ansys.com/products/multiphysics)**
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.
diff --git a/docs.it4i/salomon/software/debuggers/allinea-ddt.md b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
index 0693e6504c24fb5a2c6b69a76500f9ec36f4ed64..4badb0582736df26d3128dd160c2c9617cb799fe 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
@@ -62,7 +62,7 @@ Be sure to log in with an X window forwarding enabled. This could mean using th
$ ssh -X username@anselm.it4i.cz
```
-Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)
From the login node an interactive session **with X windows forwarding** (-X option) can be started by following command:
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index c15ea2ec39fe110508afb90a75c8149bc523c991..dfd53fb6d6e6a44d56262c2cb751e221f998e0ad 100644
--- a/docs.it4i/salomon/storage.md
+++ b/docs.it4i/salomon/storage.md
@@ -337,7 +337,7 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
-The service is documented at <https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
+The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.