fix

docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md

@@ -16,7 +16,7 @@ We recommned you to download "**A Windows installer for everything except PuTTYt
 ## PuTTY - How to Connect to the IT4Innovations Cluster
 
 * Run PuTTY
-* Enter Host name and Save session fields with [Login address](shell-and-data-access.md) and browse Connection -  SSH - Auth menu. The _Host Name_ input may be in the format **"username@clustername.it4i.cz"** so you don't have to type your login each time.In this example we will connect to the Salomon cluster using **"salomon.it4i.cz"**.
+* Enter Host name and Save session fields with login address and browse Connection -  SSH - Auth menu. The _Host Name_ input may be in the format **"username@clustername.it4i.cz"** so you don't have to type your login each time.In this example we will connect to the Salomon cluster using **"salomon.it4i.cz"**.
 
 ![](../../../img/PuTTY_host_Salomon.png)
 

docs.it4i/salomon/compute-nodes.md

@@ -28,7 +28,7 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
 
 ![cn_mic](../img/cn_mic-1.jpg)
 
-![(source Silicon Graphics International Corp.)](img/sgi-c1104-gp1.jpeg)
+![(source Silicon Graphics International Corp.)](../img/sgi-c1104-gp1.jpeg)
 
 ![cn_mic](../img/cn_mic.jpg)
 

docs.it4i/salomon/shell-and-data-access.md

@@ -15,7 +15,7 @@ The Salomon cluster is accessed by SSH protocol via login nodes login1, login2,
 | login3.salomon.it4i.cz | 22   | ssh      | login3                                |
 | login4.salomon.it4i.cz | 22   | ssh      | login4                                |
 
-The authentication is by the [private key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
+The authentication is by the [private key](../general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
 
 !!! note
     Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
@@ -44,7 +44,7 @@ If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to
 local $ chmod 600 /path/to/id_rsa
 ```
 
-On **Windows**, use [PuTTY ssh client](general/accessing-the-clusters/shell-access-and-data-transfer/putty.md).
+On **Windows**, use [PuTTY ssh client](../general/accessing-the-clusters/shell-access-and-data-transfer/putty.md).
 
 After logging in, you will see the command prompt:
 

docs.it4i/salomon/visualization.md

@@ -80,7 +80,7 @@ Remote visualization with NICE DCV software is availabe on two nodes.
 
 **Run VPN client** [VPN IT4Innovations](https://vpn.it4i.cz/user) (user-computer)
 
-**Login to Salomon via PuTTY** [salomon](salomon.it4i.cz) (user-computer)
+**Login to Salomon via PuTTY** (user-computer)
 
 ```console
 $ ssh salomon.it4i.cz
@@ -140,7 +140,7 @@ $ ssh -i ~/salomon_key -TN -f user@vizserv2.salomon.it4i.cz -L 5902:localhost:59
 
 **Run VPN client** [VPN IT4Innovations](https://vpn.it4i.cz/user) (user-computer)
 
-**Login to Salomon** [salomon](salomon.it4i.cz) (user-computer)
+**Login to Salomon** (user-computer)
 
 ```console
 $ ssh salomon.it4i.cz

docs.it4i/software/bio/bioinformatics.md

@@ -222,7 +222,7 @@ sci-libs/umfpack-5.6.2
 | libraries                               | 4      |
 | **Total**                               | **93** |
 
-![graphs](../img/bio-graphs.png)
+![graphs](../../img/bio-graphs.png)
 
 ## Other Applications Available Through Gentoo Linux
 

docs.it4i/software/bio/omics-master/diagnostic-component-team.md

@@ -13,6 +13,6 @@ VCF files are scanned by this diagnostic tool for known diagnostic disease-assoc
 
 TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions.
 
-![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](../../img/fig5.png)
+![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](../../../img/fig5.png)
 
 ** Figure 5. **Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.

docs.it4i/software/bio/omics-master/priorization-component-bierapp.md

@@ -13,7 +13,7 @@ BiERapp is available at the [following address](http://omics.it4i.cz/bierapp/)
 
 BiERapp (28) efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research, in Rare Diseases (CIBERER) and the Medical Genome Project. in which more than 800 exomes have been analyzed.
 
-![Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.](img/fig6.png)
+![Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.](../../../img/fig6.png)
 
 ** Figure 6 **. Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene
 prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.

docs.it4i/software/chemistry/phono3py.md

@@ -155,7 +155,7 @@ one finds which grid points needed to be calculated, for instance using followin
 $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write-gamma --gp="0 1 2
 ```
 
-one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see [gofree-cond1.sh](software/chemistry/gofree-cond1.sh)
+one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see [gofree-cond1.sh](gofree-cond1.sh)
 
 ```console
 $ qsub gofree-cond1.sh