diff --git a/README.md b/README.md
index 85140f71fe5569fb06ffba91506a2bb288c3d45e..763b337046f7587faa334d723e749ca43420532e 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-Převod html dokumentace do md formátu (version 0.47) - BETA
+Převod html dokumentace do md formátu (version 0.51) - BETA
===========================================================
VĂ˝sledkem projektu by mÄ›l bĂ˝t skript pro staĹľenĂ a pĹ™evod stávajĂcĂ dokumentace na docs.it4i.cz do md formátu
@@ -13,6 +13,13 @@ VĂ˝sledkem projektu by mÄ›l bĂ˝t skript pro staĹľenĂ a pĹ™evod stávajĂcĂ dok
Pro svou práci si naklonujete Gitem repozitář do svĂ©ho pracovnĂho adresáře.
+| Ăškon | OrientaÄŤnĂ ÄŤas |
+|--------|--------|
+|StaĹľenĂ|~1m|
+|Převod|~16m|
+|Export pdf|~12m|
+|Export epub|~16s|
+
### Vývoj
| Verze | čas | změny |
|--------|--------|---|
@@ -20,13 +27,13 @@ Pro svou práci si naklonujete Gitem repozitář do svĂ©ho pracovnĂho adresář
|0.4|24m56s|oprava obrázků + optimalizace|
|0.45|7m56s|optimalizace|
|0.47|11m7s|přidánà filtrů pro opravu a nahrazenà tabulek, vylepšenà filtrace, ...|
-|0.5|?|...|
+|0.51|16m37s|export do pdf, export do epub, filtry, ...|
+
>**Problémy**
> * internĂ a externĂ odkazy
> * formátovánà tabulek
-> * ~~doba převodu 24min~~
> * formátovánà kódů
### Funkce skriptu
@@ -41,4 +48,24 @@ Konverze html do md
```bash
html_md.sh -c
-```
\ No newline at end of file
+```
+
+Export do pdf
+
+```bash
+html_md.sh -e pdf
+```
+
+Export do epub
+
+```bash
+html_md.sh -e epub
+```
+
+Smazánà souborů
+
+```bash
+html_md.sh -d md
+html_md.sh -d pdf
+html_md.sh -d epub
+```
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index 5ed6a2e02f658e0c6d708c997a3af3037d09fa78..c9658ea20320bea1399068cb30bd80c23baaec26 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -98,7 +98,7 @@ but just select the corresponding item.
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on
the lock icon.
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 9aa01f36a93882730bdc50345f80ba2182b710ca..9c992325d431d7bf5774b50a5db61889eee8e142 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -166,9 +166,9 @@ qviz**. The queue has following properties:
<col width="12%" />
<col width="12%" />
<col width="12%" />
- |queue |active project<th align="left">project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
| --- | --- |
- |<strong>qviz              </strong> Visualization queue\<td align="left">yes<td align="left">none required<td align="left">2<td align="left">4<td align="left">><em>150</em><td align="left">no<td align="left">1 hour / 2 hours |
+ |<strong>qviz              </strong> Visualization queue\ |yes |none required |2 |4 |><em>150</em> |no |1 hour / 2 hours |
Currently when accessing the node, each user gets 4 cores of a CPU
allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity.
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index 65982348664bcbdf922d02280a25ae64fd08b5d6..34cab0ac07e1507dc797235af541a56c5939ed4d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -24,13 +24,13 @@ resources. Following table provides the queue partitioning overview:Â Â
<col width="12%" />
<col width="12%" />
<col width="12%" />
- |queue |active project<th align="left">project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
| --- | --- |
- |<strong>qexp</strong>Express queue |no<td align="left">none required<td align="left">2 reserved, 31 totalincluding MIC, GPU and FAT nodes |1<td align="left">><em>150</em><td align="left">no<td align="left">1h |
- |<strong>qprod</strong>Production queue |yes |> 0<td align="left">><em>178 nodes w/o accelerator</em>\ |16<td align="left">0<td align="left">no<td align="left">24/48h |
- |<strong>qlong</strong>Long queue\ |yes<td align="left">> 0<td align="left">60 nodes w/o accelerator<td align="left">16<td align="left">0<td align="left">no<td align="left">72/144h |
- |<strong>qnvidia, qmic, qfat</strong>Dedicated queues\ |yes<td align="left"><p>> 0\<td align="left">23 total qnvidia4 total qmic2 total qfat |16<td align="left">><em>200</em><td align="left">yes<td align="left">24/48h |
- |<strong>qfree</strong>Free resource queue |yes<td align="left">none required<td align="left">178 w/o accelerator<td align="left">16<td align="left">-1024<td align="left">no<td align="left">12h |
+ |<strong>qexp</strong>Express queue |no |none required |2 reserved, 31 totalincluding MIC, GPU and FAT nodes |1 |><em>150</em> |no |1h |
+ |<strong>qprod</strong>Production queue |yes |> 0 |><em>178 nodes w/o accelerator</em>\ |16 |0 |no |24/48h |
+ |<strong>qlong</strong>Long queue\ |yes |> 0 |60 nodes w/o accelerator |16 |0 |no |72/144h |
+ |<strong>qnvidia, qmic, qfat</strong>Dedicated queues\ |yes |<p>> 0\ |23 total qnvidia4 total qmic2 total qfat |16 |><em>200</em> |yes |24/48h |
+ |<strong>qfree</strong>Free resource queue |yes |none required |178 w/o accelerator |16 |-1024 |no |12h |
The qfree queue is not free of charge**. [Normal
accounting](resources-allocation-policy.html#resources-accounting-policy)
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index 2f8a9f488ea2e9d7c421a850c8ce20cb5188491f..e6ee9de61d5fad509934dc6785d9b51cd7bf7144 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -206,7 +206,7 @@ CFD license in user preferences. To make this change anslic_admin
utility should be run
```
-/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin
+/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
```
ANSLIC_ADMIN Utility will be run
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+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -134,7 +134,7 @@ LiveLink™* *for MATLAB®^
>>COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
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--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -17,7 +17,7 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
Usage
-----
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index 0000000000000000000000000000000000000000..c354a709c95a0b286d31338b68fd534e79ea35bb
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
index 482f5f423885149d1af81d26dc95bb674f7f02db..a2a1335bc2d7a4c89fbec1a364ed6ef08c20ac1f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -102,11 +102,11 @@ use:
|Application |List of provided features |
| --- | --- |
- |ansys<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '</code></pre> |
- |comsol<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '</code></pre> |
- |comsol-edu<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '</code></pre> |
- |matlab<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '</code></pre> |
- |matlab-edu<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '</code></pre> |
+ |ansys |<pre><code>$ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '</code></pre> |
+ |comsol |<pre><code>$ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '</code></pre> |
+ |comsol-edu |<pre><code>$ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '</code></pre> |
+ |matlab |<pre><code>$ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '</code></pre> |
+ |matlab-edu |<pre><code>$ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '</code></pre> |
Â
@@ -115,18 +115,18 @@ Example of PBS Pro resource name, based on APP and FEATURE name:
<col width="33%" />
<col width="33%" />
<col width="33%" />
- |Application |Feature<th align="left">PBS Pro resource name |
+ |Application |Feature |PBS Pro resource name |
| --- | --- |
- |ansys<td align="left">acfd<td align="left">feature__ansys__acfd |
- |ansys<td align="left">aa_r<td align="left">feature__ansys__aa_r |
- |comsol<td align="left">COMSOL<td align="left">feature__comsol__COMSOL |
- |comsol<td align="left">HEATTRANSFER<td align="left">feature__comsol__HEATTRANSFER |
- |comsol-edu<td align="left">COMSOLBATCH<td align="left">feature__comsol-edu__COMSOLBATCH |
- |comsol-edu<td align="left">STRUCTURALMECHANICS<td align="left">feature__comsol-edu__STRUCTURALMECHANICS |
- |matlab<td align="left">MATLAB<td align="left">feature__matlab__MATLAB |
- |matlab<td align="left">Image_Toolbox<td align="left">feature__matlab__Image_Toolbox |
- |matlab-edu<td align="left">MATLAB_Distrib_Comp_Engine<td align="left">feature__matlab-edu__MATLAB_Distrib_Comp_Engine |
- |matlab-edu<td align="left">Image_Acquisition_Toolbox<td align="left">feature__matlab-edu__Image_Acquisition_Toolbox\ |
+ |ansys |acfd |feature__ansys__acfd |
+ |ansys |aa_r |feature__ansys__aa_r |
+ |comsol |COMSOL |feature__comsol__COMSOL |
+ |comsol |HEATTRANSFER |feature__comsol__HEATTRANSFER |
+ |comsol-edu |COMSOLBATCH |feature__comsol-edu__COMSOLBATCH |
+ |comsol-edu |STRUCTURALMECHANICS |feature__comsol-edu__STRUCTURALMECHANICS |
+ |matlab |MATLAB |feature__matlab__MATLAB |
+ |matlab |Image_Toolbox |feature__matlab__Image_Toolbox |
+ |matlab-edu |MATLAB_Distrib_Comp_Engine |feature__matlab-edu__MATLAB_Distrib_Comp_Engine |
+ |matlab-edu |Image_Acquisition_Toolbox |feature__matlab-edu__Image_Acquisition_Toolbox\ |
Be aware, that the resource names in PBS Pro are CASE SENSITIVE!**
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index d258ce19e82f89c02c6162b89d15dc4babaeae41..1e6126a2fd6294c4972b6b84e737c4b3638316a4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -233,10 +233,10 @@ Some options have changed in OpenMPI version 1.8.
|version 1.6.5 |version 1.8.1 |
| --- | --- |
- |--bind-to-none<td align="left">--bind-to none |
- |--bind-to-core<td align="left">--bind-to core |
- |--bind-to-socket<td align="left">--bind-to socket |
- |-bysocket<td align="left">--map-by socket |
- |-bycore<td align="left">--map-by core |
- |-pernode<td align="left">--map-by ppr:1:node\ |
+ |--bind-to-none |--bind-to none |
+ |--bind-to-core |--bind-to core |
+ |--bind-to-socket |--bind-to socket |
+ |-bysocket |--map-by socket |
+ |-bycore |--map-by core |
+ |-pernode |--map-by ppr:1:node\ |
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.pdf
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index 768ba0045ec18e7d8c792c2039694a10c92fe56b..d865beb6b5792af8b52f974d2de0b83b53bec853 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -10,11 +10,11 @@ The Anselm cluster provides several implementations of the MPI library:
|MPI Library |Thread support |
| --- | --- |
- |The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong>\<td align="left"><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED |
- |The <strong>Intel MPI 4.1</strong><td align="left">Full thread support up to MPI_THREAD_MULTIPLE |
- |The <a href="http://www.open-mpi.org/" <strong>OpenMPI 1.6.5</strong></a><td align="left">Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
- |The OpenMPI 1.8.1<td align="left">Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support |
- |The <strong><strong>mpich2 1.9</strong></strong><td align="left">Full thread support up to <strong></strong> MPI_THREAD_MULTIPLE, BLCR c/r support |
+ |The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong>\ |<strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED |
+ |The <strong>Intel MPI 4.1</strong> |Full thread support up to MPI_THREAD_MULTIPLE |
+ |The <a href="http://www.open-mpi.org/" <strong>OpenMPI 1.6.5</strong></a> |Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
+ |The OpenMPI 1.8.1 |Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support |
+ |The <strong><strong>mpich2 1.9</strong></strong> |Full thread support up to <strong></strong> MPI_THREAD_MULTIPLE, BLCR c/r support |
MPI libraries are activated via the environment modules.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.pdf
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index 05072c5eefd8157063797cecdf6707cf3c5e3f34..b36e1df414473cb2252b5d22842b0b6314d914e1 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -22,16 +22,16 @@ gnu** compilers. These are available via modules:
<col width="25%" />
<col width="25%" />
<col width="25%" />
- |Version |Parallelization<th align="left">module<th align="left">linker options |
+ |Version |Parallelization |module<th align="left">linker options |
| --- | --- |
- |FFTW3 gcc3.3.3 |pthread, OpenMP<td align="left">fftw3/3.3.3-gcc<td align="left">-lfftw3, -lfftw3_threads-lfftw3_omp |
- |FFTW3 icc3.3.3\ |pthread, OpenMP<td align="left">fftw3<td align="left">-lfftw3, -lfftw3_threads-lfftw3_omp |
- |FFTW2 gcc2.1.5\ |pthread<td align="left">fftw2/2.1.5-gcc<td align="left">-lfftw, -lfftw_threads |
- |FFTW2 icc2.1.5 |pthread<td align="left">fftw2<td align="left">-lfftw, -lfftw_threads |
- |FFTW3 gcc3.3.3 |OpenMPI<td align="left">fftw-mpi3/3.3.3-gcc<td align="left">-lfftw3_mpi |
- |FFTW3 icc3.3.3 |Intel MPI<td align="left">fftw3-mpi<td align="left">-lfftw3_mpi |
- |FFTW2 gcc2.1.5 |OpenMPI<td align="left">fftw2-mpi/2.1.5-gcc<td align="left">-lfftw_mpi |
- |FFTW2 gcc2.1.5 |IntelMPI<td align="left">fftw2-mpi/2.1.5-gcc<td align="left">-lfftw_mpi |
+ |FFTW3 gcc3.3.3 |pthread, OpenMP |fftw3/3.3.3-gcc |-lfftw3, -lfftw3_threads-lfftw3_omp |
+ |FFTW3 icc3.3.3\ |pthread, OpenMP |fftw3 |-lfftw3, -lfftw3_threads-lfftw3_omp |
+ |FFTW2 gcc2.1.5\ |pthread |fftw2/2.1.5-gcc |-lfftw, -lfftw_threads |
+ |FFTW2 icc2.1.5 |pthread |fftw2 |-lfftw, -lfftw_threads |
+ |FFTW3 gcc3.3.3 |OpenMPI |fftw-mpi3/3.3.3-gcc |-lfftw3_mpi |
+ |FFTW3 icc3.3.3 |Intel MPI |fftw3-mpi |-lfftw3_mpi |
+ |FFTW2 gcc2.1.5 |OpenMPI |fftw2-mpi/2.1.5-gcc |-lfftw_mpi |
+ |FFTW2 gcc2.1.5 |IntelMPI |fftw2-mpi/2.1.5-gcc |-lfftw_mpi |
$ module load fftw3
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index 6e2bb61a7a479ed4a8b7bb120f0554929b07dd59..fe336aa4fb107845ec1e35c9af485b5be160ea27 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -19,22 +19,15 @@ Versions **1.8.11** and **1.8.13** of HDF5 library are available on
Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and
gnu** compilers. These are available via modules:
-<table style="width:100%;">
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
- |Version |Parallelization<th align="left">module<th align="left">C linker options<th align="left">C++ linker options<th align="left">Fortran linker options |
+ |Version |Parallelization |module<th align="left">C linker options<th align="left">C++ linker options<th align="left">Fortran linker options |
| --- | --- |
- |HDF5 icc serial<td align="left">pthread<td align="left">hdf5/1.8.11<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">$HDF5_INC $HDF5_CPP_LIB<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc parallel MPI\<td align="left">pthread, IntelMPI<td align="left">hdf5-parallel/1.8.11<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">Not supported<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc serial<td align="left">pthread<td align="left">hdf5/1.8.13<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">$HDF5_INC $HDF5_CPP_LIB<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc parallel MPI\<td align="left">pthread, IntelMPI<td align="left">hdf5-parallel/1.8.13<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">Not supported<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI\<td align="left">pthread, OpenMPI 1.6.5, gcc 4.8.1<td align="left">hdf5-parallel/1.8.11-gcc<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">Not supported<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI\<td align="left">pthread, OpenMPI 1.6.5, gcc 4.8.1<td align="left">hdf5-parallel/1.8.13-gcc<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">Not supported<td align="left">$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI\<td align="left">pthread, OpenMPI 1.8.1, gcc 4.9.0<td align="left">hdf5-parallel/1.8.13-gcc49<td align="left">$HDF5_INC $HDF5_SHLIB<td align="left">Not supported<td align="left">$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 icc serial |pthread |hdf5/1.8.11 |$HDF5_INC $HDF5_SHLIB |$HDF5_INC $HDF5_CPP_LIB |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 icc parallel MPI\ |pthread, IntelMPI |hdf5-parallel/1.8.11 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 icc serial |pthread |hdf5/1.8.13 |$HDF5_INC $HDF5_SHLIB |$HDF5_INC $HDF5_CPP_LIB |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 icc parallel MPI\ |pthread, IntelMPI |hdf5-parallel/1.8.13 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 gcc parallel MPI\ |pthread, OpenMPI 1.6.5, gcc 4.8.1 |hdf5-parallel/1.8.11-gcc |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 gcc parallel MPI\ |pthread, OpenMPI 1.6.5, gcc 4.8.1 |hdf5-parallel/1.8.13-gcc |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
+ |HDF5 gcc parallel MPI\ |pthread, OpenMPI 1.8.1, gcc 4.9.0 |hdf5-parallel/1.8.13-gcc49 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
Â
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index 0000000000000000000000000000000000000000..c2521e95e7dfeb906eb08f6ad81a98b7cf9640be
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
index 7bf179e1636f0df462c93f733122d2b539f2530d..1d64ec161c43715dafac51e30c7b5d4aff3b902d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
@@ -34,7 +34,7 @@ mutations can be added or discarded to adjust panel definitions.Â
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.](fig5.png.1 "fig5.png")
+increases.](fig5.png)
Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.pdf
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index 0000000000000000000000000000000000000000..a504d54c24de83f1a1ded039af661887cc62333d
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig7.png b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig7.png
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index 0000000000000000000000000000000000000000..dc4952d10d945e633ffcf2aed1317fba55f55cef
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index 620f85b1c01beeb45404a317c3e417d5dceaf425..aa82e9852509460a0a5b4b533696c67a8f64acae 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -27,7 +27,7 @@ secondary (alignment) data files are stored in IT4I sequence DB and
uploaded to the discovery (candidate priorization) or diagnostic
component where they can be analysed directly by the user that produced
them, depending of the experimental design carried
-out.](images/fig1.png "Fig 1")
+out.](fig1.png)
*Figure 1.*** *OMICS MASTER solution overview. Data is produced in the
external labs and comes to IT4I (represented by the blue dashed line).
@@ -77,7 +77,7 @@ the future.
#### Quality control, preprocessing and statistics for FASTQ
-Component:**> Hpg-Fastq & FastQC.
+ FastQC& FastQC.
These steps are carried out over the original FASTQ file with optimized
scripts and includes the following steps: sequence cleansing, estimation
@@ -135,18 +135,18 @@ corresponding information is unavailable. Â
<col width="33%" />
<col width="33%" />
<col width="33%" />
- |<strong>No.</strong>\<td align="left"><p><strong>Name</strong>\<td align="left"><p><strong>Description</strong></p> |
- |1\<td align="left"><p>QNAME\<td align="left"><p>Query NAME of the read or the read pair</p> |
- |2\<td align="left"><p>FLAG\<td align="left"><p>Bitwise FLAG (pairing,strand,mate strand,etc.)</p> |
- |3\<td align="left"><p>RNAMEÂ \<td align="left"><p>Reference sequence NAME</p> |
- |4\<td align="left"><p>POS \<td align="left"><p>1-Based  leftmost POSition of clipped alignment</p> |
- |5\<td align="left"><p>MAPQÂ \<td align="left"><p>MAPping Quality (Phred-scaled)</p> |
- |6\<td align="left"><p>CIGARÂ \<td align="left"><p>Extended CIGAR string (operations:MIDNSHP)</p> |
- |7\<td align="left"><p>MRNMÂ \<td align="left"><p>Mate REference NaMe ('=' if same RNAME)</p> |
- |8\<td align="left"><p>MPOSÂ \<td align="left"><p>1-Based leftmost Mate POSition</p> |
- |9\<td align="left"><p>ISIZEÂ \<td align="left"><p>Inferred Insert SIZEÂ </p> |
- |10\<td align="left"><p>SEQÂ \<td align="left"><p>Query SEQuence on the same strand as the reference</p> |
- |11\<td align="left"><p>QUALÂ \<td align="left"><p>Query QUALity (ASCII-33=Phred base quality)</p> |
+ |<strong>No.</strong>\ |<p><strong>Name</strong>\ |<p><strong>Description</strong></p> |
+ |1\ |<p>QNAME\ |<p>Query NAME of the read or the read pair</p> |
+ |2\ |<p>FLAG\ |<p>Bitwise FLAG (pairing,strand,mate strand,etc.)</p> |
+ |3\ |<p>RNAMEÂ \ |<p>Reference sequence NAME</p> |
+ |4\ |<p>POS \ |<p>1-Based  leftmost POSition of clipped alignment</p> |
+ |5\ |<p>MAPQÂ \ |<p>MAPping Quality (Phred-scaled)</p> |
+ |6\ |<p>CIGARÂ \ |<p>Extended CIGAR string (operations:MIDNSHP)</p> |
+ |7\ |<p>MRNMÂ \ |<p>Mate REference NaMe ('=' if same RNAME)</p> |
+ |8\ |<p>MPOSÂ \ |<p>1-Based leftmost Mate POSition</p> |
+ |9\ |<p>ISIZEÂ \ |<p>Inferred Insert SIZEÂ </p> |
+ |10\ |<p>SEQÂ \ |<p>Query SEQuence on the same strand as the reference</p> |
+ |11\ |<p>QUALÂ \ |<p>Query QUALity (ASCII-33=Phred base quality)</p> |
>
@@ -174,7 +174,7 @@ to position 9, and the first five to position 29 on the reverse strand.
The hard clipping operation H indicates that the clipped sequence is not
present in the sequence field. The NM tag gives the number of
mismatches. Read r004 is aligned across an intron, indicated by the N
-operation.](fig3.png "fig3.png")
+operation.](fig3.png)
*
Figure 3.*** *SAM format file. The â€@SQ’ line in the header section
gives the order of reference sequences. Notably, r001 is the name of a
@@ -209,13 +209,13 @@ Component:** Hpg-Fastq & FastQC. Some features:
- Filtering: by number of errors, number of hits, …
- Comparator: stats, intersection, ...
-Input:** BAM file.
+Input:** BAM** file.**
-Output:** BAM file plus an HTML file containing statistics.Â
+Output:** BAM file plus an HTML file containing statistics.**
#### Variant Calling
-Component:** GATK.
+Component:** GATK.**
Identification of single nucleotide variants and indels on the
alignments is performed using the Genome Analysis Toolkit (GATK). GATK
@@ -224,11 +224,11 @@ 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.
-Input:** BAM
+Input:** BAM**
-Output:** VCF
+Output:** VCF**
-Variant Call Format (VCF)**
+**Variant Call Format (VCF)**
>VCF (3)^> is a standardized format for storing the
most prevalent types of sequence variation, including SNPs, indels and
@@ -359,7 +359,7 @@ CellBase imports miRNA from miRBase (8)^; curated and non-curated miRNA
targets from miRecords (9)^, >miRTarBase ^(10)^>,
TargetScan(11)^> and microRNA.org ^(12)^> and
CpG islands and conserved regions from the UCSC database
-(13)^>.>Â </span>
+(13)^>.>
**Functional annotation**
@@ -378,7 +378,7 @@ phenotypically annotated SNPs were imported from NHRI GWAS Catalog
(21)^>, UniProt ^(7)^> and OMIM
(22)^>; mutations from COSMICÂ ^(23)^> and
structural variations from Ensembl
-(6)^>.>Â </span>
+(6)^>.>
**Systems biology**
@@ -568,7 +568,7 @@ should use the next command:
per-position format.</span>
- >><span>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
variant annotation and effect
- prediction toolbox.</span></span>
+ prediction toolbox.
This listing show which tools are used in each step of the pipeline :
@@ -616,7 +616,7 @@ Internet thus avoiding any problem of data privacy or confidentiality.
>
+starts.](fig7.png)
*Figure 7***. *TEAM upload panel.* *Once the file has been uploaded, a
panel must be chosen from the Panel **** list. Then, pressing the Run
@@ -640,7 +640,7 @@ can be customized by adding new genes (action F) or removing undesired
genes (action G). New disease mutations can be added independently or
associated to an already existing disease term (action E). Disease terms
can be removed by simply dragging themback (action
-H).](images/fig7x.png "fig7x.png")
+H).](fig7x.png)
*Figure 7.*** *The panel manager. The elements used to define a panel
are (**A**) disease terms, (**B**) diagnostic mutations and (**C**)
@@ -660,7 +660,7 @@ BierApp by using the following form:
**
+](fig8.png)*
**Figure 8.*** *BierApp VCF upload panel. It is recommended to choose
a name for the job as well as a description.**
@@ -679,7 +679,7 @@ context provided by an embedded version of >the Genome Maps Tool
If a variant has an associated phenotype we could see it in the last
column. In this case, the variant 7:132481242 C>T is associated to
the phenotype: large intestine
-tumor.](images/fig9.png "fig9.png")**
+tumor.](fig9.png)
***Figure 9.*** *This picture shows all the information associated to
the variants. If a variant has an associated phenotype we could see it
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.pdf
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--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
@@ -32,7 +32,7 @@ Project. in which more than 800 exomes have been analyzed.
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.](fig6.png.1 "fig6.png")
+genomic coordinates.](fig6.png)
*Figure 6***. *Web interface to the prioritization tool.* *This
figure*Â *shows the interface of the web tool for candidate gene
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+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
@@ -39,7 +39,7 @@ key into authorized_keys file for authentication with your own private
- Wait.
- 
+ 
- Enter a *comment* for your key using formatÂ
'username@organization.example.com'.
@@ -48,7 +48,7 @@ key into authorized_keys file for authentication with your own private
Save your new private key `in "*.ppk" `format with *Save private
key* button.
- 
+ 
- Save the public key with *Save public key* button.
You can copy public key out of the â€Public key for pasting into
@@ -59,7 +59,7 @@ key into authorized_keys file for authentication with your own private
- Export private key in OpenSSH format "id_rsa" using Conversion
-> Export OpenSSH key
- 
+ 
- Now you can insert additional public key into authorized_keys file
for authentication with your own private >key.
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@@ -81,16 +81,9 @@ SGI UV 2000
For large memory computations a special SMP/NUMA SGI UV 2000 server is
available:
-<table style="width:100%;">
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
-<col width="16%" />
- |Node |Count<th align="left">Processor<th align="left">Cores<th align="left">Memory<th align="left">Extra HW |
+ |Node |Count |Processor<th align="left">Cores<th align="left">Memory<th align="left">Extra HW |
| --- | --- |
- |UV2000<td align="left">1<td align="left">14x Intel Xeon E5-4627v2, 3.3GHz, 8cores<td align="left">112<td align="left">3328GB DDR3@1866MHz<td align="left">2x 400GB local SSD1x NVIDIA GM200(GeForce GTX TITAN X),12GB RAM\ |
+ |UV2000 |1 |14x Intel Xeon E5-4627v2, 3.3GHz, 8cores |112 |3328GB DDR3@1866MHz |2x 400GB local SSD1x NVIDIA GM200(GeForce GTX TITAN X),12GB RAM\ |
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index 89332118d2d99847aa05562904e65215f85d0e54..9453f57ebf292c984fc155cfa6fdd62d4e1acff1 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -25,15 +25,15 @@ resources. Following table provides the queue partitioning overview:
<col width="12%" />
<col width="12%" />
<col width="12%" />
- |queue |active project<th align="left">project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
| --- | --- |
- |<strong>qexp</strong>Express queue |no<td align="left">none required<td align="left">32 nodes, max 8 per user<td align="left">24<td align="left">>150<td align="left">no<td align="left">1 / 1h |
- |<strong>qprod</strong>Production queue |yes |> 0<td align="left">>1006 nodes, max 86 per job\<td align="left">24<td align="left">0<td align="left">no<td align="left">24 / 48h |
- |<strong>qlong</strong>Long queue |yes<td align="left">> 0<td align="left">256 nodes, max 40 per job, only non-accelerated nodes allowed<td align="left">24<td align="left">0<td align="left">no<td align="left">72 / 144h |
- |<strong>qmpp</strong>Massive parallel queue |yes<td align="left">> 0<td align="left">1006 nodes<td align="left">24<td align="left">0<td align="left">yes<td align="left">2 / 4h |
- |<strong>qfat</strong>UV2000 queue |yes<td align="left">> 0\<td align="left">1 (uv1)<td align="left">8<td align="left">0<td align="left">yes<td align="left">24 / 48h |
- |<strong>qfree</strong>Free resource queue |yes<td align="left">none required<td align="left">752 nodes, max 86 per job<td align="left">24<td align="left">-1024<td align="left">no<td align="left">12 / 12h |
- |<strong><strong>qviz</strong></strong>Visualization queue |yes<td align="left">none required<td align="left">2 (with NVIDIA Quadro K5000)<td align="left">4<td align="left">150<td align="left">no<td align="left">1 / 2h |
+ |<strong>qexp</strong>Express queue |no |none required |32 nodes, max 8 per user |24 |>150 |no |1 / 1h |
+ |<strong>qprod</strong>Production queue |yes |> 0 |>1006 nodes, max 86 per job\ |24 |0 |no |24 / 48h |
+ |<strong>qlong</strong>Long queue |yes |> 0 |256 nodes, max 40 per job, only non-accelerated nodes allowed |24 |0 |no |72 / 144h |
+ |<strong>qmpp</strong>Massive parallel queue |yes |> 0 |1006 nodes |24 |0 |yes |2 / 4h |
+ |<strong>qfat</strong>UV2000 queue |yes |> 0\ |1 (uv1) |8 |0 |yes |24 / 48h |
+ |<strong>qfree</strong>Free resource queue |yes |none required |752 nodes, max 86 per job |24 |-1024 |no |12 / 12h |
+ |<strong><strong>qviz</strong></strong>Visualization queue |yes |none required |2 (with NVIDIA Quadro K5000) |4 |150 |no |1 / 2h |
Â
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+++ b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
@@ -17,11 +17,11 @@ Launch the ANSLIC_ADMIN utility in a graphical environment:
ANSLIC_ADMIN Utility will be run
-
+
-
+[](Fluent_Licence_2.jpg)
-
+
Â
@@ -30,5 +30,5 @@ the bottom of the list.
Â
-
+
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@@ -134,7 +134,7 @@ LiveLink™* *for MATLAB®^
>>COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
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@@ -17,7 +17,7 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
Usage
-----
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@@ -7,7 +7,7 @@ functionality to collect traces, you need to use a trace collection tool
(such as [Score-P](score-p.html)) first to collect the
traces.
-
+
----------------------------------------------------------------------------------------------------------------------------------------------
Installed versions
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index 0000000000000000000000000000000000000000..748f3f3a447dc8e35695bab0df6a24931ea105cf
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diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index b62dfc24675687fe536cd51074cc87e72facfb8f..9a76d02d5e7868b66462d6549d9e286eada26ba8 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -232,10 +232,10 @@ Some options have changed in OpenMPI version 1.8.
|version 1.6.5 |version 1.8.1 |
| --- | --- |
- |--bind-to-none<td align="left">--bind-to none |
- |--bind-to-core<td align="left">--bind-to core |
- |--bind-to-socket<td align="left">--bind-to socket |
- |-bysocket<td align="left">--map-by socket |
- |-bycore<td align="left">--map-by core |
- |-pernode<td align="left">--map-by ppr:1:node\ |
+ |--bind-to-none |--bind-to none |
+ |--bind-to-core |--bind-to core |
+ |--bind-to-socket |--bind-to socket |
+ |-bysocket |--map-by socket |
+ |-bycore |--map-by core |
+ |-pernode |--map-by ppr:1:node\ |
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.pdf b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..a8b9ccf6afa9bf0e7eebba3aac60fb4f12a59d52
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diff --git a/converted/docs.it4i.cz/salomon/storage/storage.epub b/converted/docs.it4i.cz/salomon/storage/storage.epub
new file mode 100644
index 0000000000000000000000000000000000000000..e845ce80e8cc58e6364e5d99acdd6dc7d4ddbd0d
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diff --git a/converted/docs.it4i.cz/salomon/storage/storage.pdf b/converted/docs.it4i.cz/salomon/storage/storage.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..0894339d01903ba808dea03a9fd7b1edbb04eab9
Binary files /dev/null and b/converted/docs.it4i.cz/salomon/storage/storage.pdf differ
diff --git a/html_md.sh b/html_md.sh
index 4e69e470f57c8a283e68a0d001cc31c2bbf7e9c5..c81f705fe8be4ac683e9990b811aad57b2078cee 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -2,11 +2,68 @@
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
-# version: 0.47
-# change: repair tables, optimalization
-# bugs: bad links for other files, formatting bugs, bad bash and other code (formatting)...
+# version: 0.51
+# change: export pdf, epub
+# bugs: bad internal links
###
+if [ "$1" = "-e" ]; then
+ # export to pdf/epub
+ STARTTIME=$(date +%s)
+ counter=1
+ count=$(find ./converted -name "*.md" -type f | wc -l)
+ if [ "$2" = "epub" ]; then
+ find ./converted -name "*.md" |
+ while read i;
+ do
+ a=$(basename "$i")
+ b=$(dirname "$i")
+ c=$(pwd)
+
+ echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$a => $(tput setaf 13)${a%.*}.epub$(tput setaf 15)"
+ counter=$((counter+1))
+ cd "$b"
+ #if [ $a = "job-submission-and-execution.md" ]; then
+ #!double subscripts problem !!!!!!
+ #wkhtmltopdf job-submission-and-execution.md job-submission-and-execution.pdf
+ #else
+ pandoc ${a%.*}.md -o ${a%.*}.epub
+ #fi
+ cd "$c"
+ done
+ fi
+ if [ "$2" = "pdf" ]; then
+ find ./converted -name "*.md" |
+ while read i;
+ do
+ a=$(basename "$i")
+ b=$(dirname "$i")
+ c=$(pwd)
+
+ echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$a => $(tput setaf 13)${a%.*}.pdf$(tput setaf 15)"
+ #echo "$b"
+ counter=$((counter+1))
+ cd "$b"
+ if [ $a = "job-submission-and-execution.md" ]; then
+ #!double subscripts problem !!!!!!
+ wkhtmltopdf job-submission-and-execution.md job-submission-and-execution.pdf
+ else
+ pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
+ fi
+ cd "$c"
+ done
+ fi
+ ENDTIME=$(date +%s)
+ echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
+fi
+if [ "$1" = "-d" ]; then
+ find . -name "*."$2 |
+ while read i;
+ do
+ echo "$(tput setaf 9)$i deleted$(tput setaf 15)"
+ rm "$i"
+ done
+fi
if [ "$1" = "-w" ]; then
# download html pages
STARTTIME=$(date +%s)
@@ -22,6 +79,10 @@ if [ "$1" = "-w" ]; then
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig8.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig9.png
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
@@ -147,7 +208,7 @@ if [ "$1" = "-c" ]; then
find ./docs.it4i.cz -name "*.md" -type f> ./info/list_md;
find ./docs.it4i.cz -type d | sort > ./info/list_folder;
- count=$(find . -name "*.md" -type f | wc -l)
+ count=$(find ./docs.it4i.cz -name "*.md" -type f | wc -l)
if [ $count -eq 150 ]; then
rm -rf ./converted
@@ -175,6 +236,9 @@ if [ "$1" = "-c" ]; then
cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
cp ./docs.it4i.cz/virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
+ cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg ./converted/docs.it4i.cz/salomon/accessing-the-cluster/anyconnecticon.jpg
+ cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg ./converted/docs.it4i.cz/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg
+ cp ./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png ./converted/docs.it4i.cz/salomon/software/debuggers/TightVNC_login.png
# listall files and folder /converted
find ./converted -name "*.png" -type f > ./info/list_image_converted;
diff --git a/source/formatting b/source/formatting
index a644a853ad4ba16733d73a9fa53306318e5dcd08..cea3e3b9bad821c94cca84283188c26730635477 100644
--- a/source/formatting
+++ b/source/formatting
@@ -37,3 +37,13 @@ nodes.****&nodes.
### Compute Nodes Summary********&### Compute Nodes Summary
<p><a href="x-window-system/cygwin-and-x11-forwarding.html" If no able to forward X11 using PuTTY to CygwinX</a>&[If no able to forward X11 using PuTTY to CygwinX](x-window-system/cygwin-and-x11-forwarding.html)
<p><a href="http://x.cygwin.com/" Install Cygwin</a>&[Install Cygwin](http://x.cygwin.com/)
+Component:**> Hpg-Fastq & FastQC&Component:**> Hpg-Fastq & FastQC**
+Input:** BAM file.&Input:** BAM file.**
+Output:** BAM file plus an HTML file containing statistics. &Output:** BAM file plus an HTML file containing statistics.**
+Component:** GATK.&Component:** GATK.**
+Input:** BAM&Input:** BAM**
+Output:** VCF&Output:** VCF**
+Variant Call Format (VCF)**&**Variant Call Format (VCF)**
+</span></span>&
+/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin&/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
+<td align="left">& |
diff --git a/source/list_image_mv b/source/list_image_mv
index dfceea15b76c3c930520d611bd32cd18eb7a84a1..4a28b7e38acd26bed95716d251b146f5f9396882 100644
--- a/source/list_image_mv
+++ b/source/list_image_mv
@@ -11,7 +11,7 @@
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwinX11forwarding.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/XWinlistentcp.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_004V.png
-./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/20150312_143443.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_003V.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PageantV.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_001V.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_host_Salomon.png
@@ -47,6 +47,7 @@
./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_download_2.png
./docs.it4i.cz/salomon/accessing-the-cluster/vpn_contacting_https.png
./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_install_4.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig7.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vncviewer.png
./docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png
./docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png
@@ -66,9 +67,12 @@
./docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png
./docs.it4i.cz/anselm-cluster-documentation/quality1.png
./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig1.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig8.png
./docs.it4i.cz/salomon/software/debuggers/report.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpnuiV.png
./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig4.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig7x.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig9.png
./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg
./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_4.jpg
./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_1.jpg
@@ -81,8 +85,8 @@
./docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg
./docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg
./docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg
-./docs.it4i.cz/anselm-cluster-documentation/firstrun.jpg
-./docs.it4i.cz/anselm-cluster-documentation/successfullconnection.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/firstrun.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/successfullconnection.jpg
./docs.it4i.cz/salomon/sgi-c1104-gp1.jpeg
./docs.it4i.cz/salomon/salomon-1.jpeg
./docs.it4i.cz/salomon/hardware-overview-1/uv-2000.jpeg
diff --git a/source/repairIMG b/source/repairIMG
index c5bbd4ab3468c5c7a642a1a1c28ce921c7cfa968..7bc3a16235a6e0a0e686fd9c4e0474501b4065d1 100644
--- a/source/repairIMG
+++ b/source/repairIMG
@@ -19,7 +19,7 @@ connection](../anyconnecticon.jpg "Successfull connection")&&
&
&
+profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")&
&
**&&
@@ -55,10 +55,10 @@ Preferences](gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.pn
[](PuttyKeygeneratorV.png)&
[](PuttyKeygenerator_001V.png)&
[](PuttyKeygenerator_002V.png)&
- [](20150312_143443.png)&
- [](PuttyKeygenerator_004V.png)&
+ [](20150312_143443.png)&
+ [](PuttyKeygenerator_004V.png)&
[](PuttyKeygenerator_005V.png)&
- [](PuttyKeygenerator_006V.png)&
+ [](PuttyKeygenerator_006V.png)&
[](../vpn_web_login.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&
@@ -90,20 +90,20 @@ Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images
[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)&
[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)&
-[](Fluent_Licence_1.jpg)&
-[](Fluent_Licence_2.jpg)&
-[](Fluent_Licence_3.jpg)&
-[](Fluent_Licence_4.jpg)&
+[](Fluent_Licence_1.jpg)&
+[](Fluent_Licence_2.jpg)&
+[](Fluent_Licence_3.jpg)&
+[](Fluent_Licence_4.jpg)&
&
&
[{.image-inline width="451"&
height="513"}](ddt1.png)&Â
&
-[](vtune-amplifier)&
+[](vtune-amplifier)&
[](totalview1.png)&
[](totalview2.png)&
-&
+&
&
![The Authorization chain for access and utilization of computational&
@@ -112,3 +112,12 @@ Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorizatio
screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&
[](gnome-terminal.png)&
[](gnome-compute-nodes-over-vnc.png)&
+&
+genomic coordinates.](fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png)
+out.](images/fig1.png "Fig 1")&out.](ig1.png)
+operation.](fig3.png "fig3.png")&operation.](fig3.png)
+starts.](images/fig7.png "fig7.png")&starts.](fig7.png)
+H).](images/fig7x.png "fig7x.png")&H).](fig7x.png)
+](images/fig8.png "fig8.png")*&](fig8.png)*
+tumor.](images/fig9.png "fig9.png")**&tumor.](fig9.png)
+increases.](fig5.png.1 "fig5.png")&increases.](fig5.png)
diff --git a/source/replace b/source/replace
index 9d6743dbfd2be78e283d6a547285cb85147bcf0c..a95df81e42d694997a5e586e71a9b7630ecc0196 100644
--- a/source/replace
+++ b/source/replace
@@ -125,3 +125,4 @@ class="WYSIWYG_LINK">&
class="visualHighlight">&
{.spip_in&
.external&
+Â </span>&
diff --git a/source/tab b/source/tab
index 65a1098fdb2a84e10a5fb91f0b1964ab5325a000..bec6eca8f5bc1ba6a48cd28c2a1c38babbcf13ef 100644
--- a/source/tab
+++ b/source/tab
@@ -23,3 +23,6 @@
)\&)
.\&.
<p>&
+<table style="width:100%;">&\\
+<col width="16%" />&\\
+<th align="left">& |