Commit 2c122609 authored by David Hrbáč's avatar David Hrbáč

Links OK

parent 7b6101dd
Pipeline #5187 passed with stages
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## 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)).
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][a]. 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][b]).
## Starting the Environment
......@@ -233,3 +233,6 @@ mmokrejs@login2~$ gcc-config -l
mmokrejs@login2~$ java-config -L
mmokrejs@login2~$ eselect
```
[a]: https://www.gentoo.org/
[b]: https://wiki.gentoo.org/wiki/Prefix/libc
......@@ -2,7 +2,7 @@
## Access
TEAM is available at the [following address](http://omics.it4i.cz/team/)
TEAM is available at the [following address][a]
!!! note
The address is accessible only via VPN.
......@@ -15,4 +15,6 @@ TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between th
![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.
**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.
[a]: http://omics.it4i.cz/team/
......@@ -2,7 +2,7 @@
## Access
BiERapp is available at the [following address](http://omics.it4i.cz/bierapp/)
BiERapp is available at the [following address][1].
!!! note
The address is accessible only via VPN.
......@@ -15,5 +15,7 @@ BiERapp (28) efficiently helps in the identification of causative variants in fa
![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
**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.
[1]: http://omics.it4i.cz/bierapp/
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