Commit fa91c5ab authored by Lukáš Krupčík's avatar Lukáš Krupčík
Browse files

test and export pdff

parent 55618f64
Pipeline #1124 passed with stages
in 39 seconds
......@@ -205,4 +205,4 @@ Starting Matlab workers is an expensive process that requires certain amount of
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......@@ -335,7 +335,7 @@ Interpretation
The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team.html) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
![TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.](fig7.png)
![TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.]((../../../img/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 button the diagnostic process starts.
......@@ -347,7 +347,7 @@ Once the file has been uploaded, a panel must be chosen from the Panel list. The
For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:
*![BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.](fig8.png)*
*![BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.](../../../img/fig8.png)*
**Figure 8.** *BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.**
......
......@@ -7,6 +7,19 @@
# bugs: bad internal links
###
if [ "$1" = "-t" ]; then
test="pdfunite"
while read a ; do
test+=" $a"
done < seznam.txt
test+=" test.pdf"
$test
while read a ; do
rm "$i"
done < seznam.txt
fi
if [ "$1" = "-d" ]; then
# remove pdf, md and epub files
STARTTIME=$(date +%s)
......@@ -27,7 +40,7 @@ if [ "$1" = "-d" ]; then
fi
elif [ "$2" = "all" ]; then
echo "$(tput setaf 9)all files deleted$(tput setaf 15)"
if [ -d ./converted ]; then
if [ -d ./docs.it4i ]; then
rm -rf ./converted
fi
if [ -d ./epub ]; then
......@@ -50,12 +63,12 @@ if [ "$1" = "-e" ]; then
# export to pdf/epub
STARTTIME=$(date +%s)
counter=1
count=$(find ./converted -name "*.md" -type f | wc -l)
count=$(find ./docs.it4i -name "*.md" -type f | wc -l)
if [ "$2" = "epub" ]; then
if [ -d ./epub ]; then
rm -rf ./epub
fi
find ./converted -name "*.md" |
find ./docs.it4i -name -name "*.md" |
while read i;
do
a=$(basename "$i")
......@@ -87,7 +100,7 @@ if [ "$1" = "-e" ]; then
if [ -d ./pdf ]; then
rm -rf ./pdf
fi
find ./converted -name "*.md" |
find ./docs.it4i -name "*.md" |
while read i;
do
a=$(basename "$i")
......@@ -104,34 +117,31 @@ if [ "$1" = "-e" ]; then
#job-submission-and-execution.md
if [ $a = "job-submission-and-execution.md" ]; then
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
elif [ $a = "ansys-fluent.md" ]; then
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
elif [ $a = "capacity-computing.md" ]; then
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
elif [ $a = "list_of_modules.md" ]; then
echo "big files..."
else
pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
#pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
pandoc -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf ${a%.*}.md
fi
cd "$c"
done
# new folder for pdf
mkdir pdf;
(while read i;
do
mkdir "./pdf/$i";
done) < ./source/list_folder
# move pdf files to folder pdf
echo "$(tput setaf 11)moved pdf files$(tput setaf 15)";
while read a ; do
mv "./converted/${a%.*}.pdf" "./pdf/${a%.*}.pdf";
done < ./source/list_md_mv
find ./docs.it4i -name "*.pdf" |
while read i;
do
echo "$i" >> seznam.txt
rm "$i"
done
fi
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
......
......@@ -14,7 +14,7 @@
<ul class="repo">
<li class="repo-download">
{% set version = config.extra.version | default("master") %}
<a href="pbspro-documentation/pbspro-programmers-guide.pdf" target="_blank" title="DOWNLOAD PDF VERSION" data-action="download">
<a href="all.pdf" target="_blank" title="DOWNLOAD PDF VERSION" data-action="download">
<i class="icon icon-download"></i> DOWNLOAD PDF VERSION
</a>
</li>
......
......@@ -101,7 +101,7 @@ pages:
- Anselm Cluster Documentation-Software-Numerical Languages:
- Introduction: anselm-cluster-documentation/software/numerical-languages/introduction.md
- R: anselm-cluster-documentation/software/numerical-languages/r.md
- Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md
- Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
- Matlab: anselm-cluster-documentation/software/numerical-languages/matlab.md
- Octave: anselm-cluster-documentation/software/numerical-languages/octave.md
- Anselm Cluster Documentation-Software-Chemistry:
......
./docs.it4i/index.pdf
./docs.it4i/get-started-with-it4innovations/applying-for-resources.pdf
./docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.pdf
./docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.pdf
./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.pdf
./docs.it4i/anselm-cluster-documentation/compute-nodes.pdf
./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.pdf
./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.pdf
./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.pdf
./docs.it4i/anselm-cluster-documentation/introduction.pdf
./docs.it4i/anselm-cluster-documentation/software/compilers.pdf
./docs.it4i/anselm-cluster-documentation/software/gpi2.pdf
./docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.pdf
./docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.pdf
./docs.it4i/anselm-cluster-documentation/software/omics-master/overview.pdf
./docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.pdf
./docs.it4i/anselm-cluster-documentation/software/operating-system.pdf
./docs.it4i/anselm-cluster-documentation/software/kvirtualization.pdf
./docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.pdf
./docs.it4i/anselm-cluster-documentation/software/mpi/mpi.pdf
./docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.pdf
./docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.pdf
./docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/parallel.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.pdf
./docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.pdf
./docs.it4i/anselm-cluster-documentation/software/isv_licenses.pdf
./docs.it4i/anselm-cluster-documentation/software/openfoam.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.pdf
./docs.it4i/anselm-cluster-documentation/software/ansys/ansys.pdf
./docs.it4i/anselm-cluster-documentation/software/java.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/papi.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/cube.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.pdf
./docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.pdf
./docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.pdf
./docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.pdf
./docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.pdf
./docs.it4i/anselm-cluster-documentation/software/paraview.pdf
./docs.it4i/anselm-cluster-documentation/remote-visualization.pdf
./docs.it4i/anselm-cluster-documentation/environment-and-modules.pdf
./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.pdf
./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.pdf
./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.pdf
./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.pdf
./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.pdf
./docs.it4i/anselm-cluster-documentation/network.pdf
./docs.it4i/anselm-cluster-documentation/storage/cesnet-data-storage.pdf
./docs.it4i/anselm-cluster-documentation/storage/storage.pdf
./docs.it4i/anselm-cluster-documentation/prace.pdf
./docs.it4i/anselm-cluster-documentation/hardware-overview.pdf
./docs.it4i/salomon/compute-nodes.pdf
./docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.pdf
./docs.it4i/salomon/accessing-the-cluster/outgoing-connections.pdf
./docs.it4i/salomon/accessing-the-cluster/vpn-access.pdf
./docs.it4i/salomon/introduction.pdf
./docs.it4i/salomon/software/compilers.pdf
./docs.it4i/salomon/software/operating-system.pdf
./docs.it4i/salomon/software/intel-suite/intel-advisor.pdf
./docs.it4i/salomon/software/intel-suite/intel-mkl.pdf
./docs.it4i/salomon/software/intel-suite/intel-debugger.pdf
./docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.pdf
./docs.it4i/salomon/software/intel-suite/intel-tbb.pdf
./docs.it4i/salomon/software/intel-suite/intel-inspector.pdf
./docs.it4i/salomon/software/intel-suite/intel-compilers.pdf
./docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.pdf
./docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.pdf
./docs.it4i/salomon/software/mpi/mpi.pdf
./docs.it4i/salomon/software/mpi/Running_OpenMPI.pdf
./docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.pdf
./docs.it4i/salomon/software/numerical-languages/parallel.pdf
./docs.it4i/salomon/software/numerical-languages/octave.pdf
./docs.it4i/salomon/software/numerical-languages/r.pdf
./docs.it4i/salomon/software/numerical-languages/introduction.pdf
./docs.it4i/salomon/software/numerical-languages/matlab.pdf
./docs.it4i/salomon/software/ansys/setting-license-preferences.pdf
./docs.it4i/salomon/software/ansys/licensing.pdf
./docs.it4i/salomon/software/ansys/ansys-fluent.pdf
./docs.it4i/salomon/software/ansys/ansys-ls-dyna.pdf
./docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.pdf
./docs.it4i/salomon/software/ansys/ansys-cfx.pdf
./docs.it4i/salomon/software/ansys/workbench.pdf
./docs.it4i/salomon/software/ansys/ansys.pdf
./docs.it4i/salomon/software/comsol/comsol-multiphysics.pdf
./docs.it4i/salomon/software/comsol/licensing-and-available-versions.pdf
./docs.it4i/salomon/software/java.pdf
./docs.it4i/salomon/software/debuggers/allinea-ddt.pdf
./docs.it4i/salomon/software/debuggers/allinea-performance-reports.pdf
./docs.it4i/salomon/software/debuggers/aislinn.pdf
./docs.it4i/salomon/software/debuggers/vampir.pdf
./docs.it4i/salomon/software/debuggers/Introduction.pdf
./docs.it4i/salomon/software/debuggers/valgrind.pdf
./docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.pdf
./docs.it4i/salomon/software/debuggers/total-view.pdf
./docs.it4i/salomon/software/chemistry/phono3py.pdf
./docs.it4i/salomon/software/chemistry/molpro.pdf
./docs.it4i/salomon/software/chemistry/nwchem.pdf
./docs.it4i/salomon/software/intel-xeon-phi.pdf
./docs.it4i/salomon/environment-and-modules.pdf
./docs.it4i/salomon/network/7d-enhanced-hypercube.pdf
./docs.it4i/salomon/network/ib-single-plane-topology.pdf
./docs.it4i/salomon/network/network.pdf
./docs.it4i/salomon/resource-allocation-and-job-execution/introduction.pdf
./docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.pdf
./docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.pdf
./docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.pdf
./docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.pdf
./docs.it4i/salomon/storage/cesnet-data-storage.pdf
./docs.it4i/salomon/storage/storage.pdf
./docs.it4i/salomon/prace.pdf
./docs.it4i/salomon/hardware-overview.pdf
./docs.it4i/pbspro-documentation/pbspro-reference-guide.pdf
./docs.it4i/pbspro-documentation/pbspro-programmers-guide.pdf
./docs.it4i/pbspro-documentation/pbspro-users-guide.pdf
./docs.it4i/pbspro-documentation/sitemap.pdf
./docs.it4i/pbspro-documentation/pbspro-quick-start-guide.pdf
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