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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| /.includepath | ||
| /.project |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,19 +1,18 @@ | ||
| /.RData | ||
| /OrigDensityWebGL.html | ||
| /OrigDensityWebGL_mod.html | ||
| /OrigDensityWebGL_mod.html.log | ||
| /OrigPointsWebGL.html | ||
| /OrigPointsWebGL_mod.html | ||
| /OrigPointsWebGL_mod.html.log | ||
| /add_md5.pl | ||
| /analysis.RData | ||
| /create_3d_source_files.R | ||
| /create_3d_source_files.Rout | ||
| /density.html | ||
| /difference_md5.txt | ||
| /differences_md5_sums.txt | ||
| /index.html | ||
| /rgl.js | ||
| /points.html | ||
| /md5_Density.txt | ||
| /md5_Points.txt | ||
| /OrigDensityWebGL.html | ||
| /OrigDensityWebGL_mod.html | ||
| /OrigDensityWebGL_mod.html.log | ||
| /OrigPointsWebGL.html | ||
| /OrigPointsWebGL_mod.html | ||
| /OrigPointsWebGL_mod.html.log | ||
| /points.html | ||
| /rgl.js |
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| #! /usr/bin/perl -w | ||
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| # Copyright (C) 2016-01-12 Stefan Lang | ||
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| # This program is free software; you can redistribute it | ||
| # and/or modify it under the terms of the GNU General Public License | ||
| # as published by the Free Software Foundation; | ||
| # either version 3 of the License, or (at your option) any later version. | ||
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| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | ||
| # See the GNU General Public License for more details. | ||
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| # You should have received a copy of the GNU General Public License | ||
| # along with this program; if not, see <http://www.gnu.org/licenses/>. | ||
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| =head1 add_md5.pl | ||
| Add the md5 sum over each line to a text file. | ||
| To get further help use 'add_md5.pl -help' at the comman line. | ||
| =cut | ||
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| use Getopt::Long; | ||
| use strict; | ||
| use warnings; | ||
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| use Digest::MD5 qw(md5_hex); | ||
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| use FindBin; | ||
| my $plugin_path = "$FindBin::Bin"; | ||
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| my $VERSION = 'v1.0'; | ||
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| my ( $help, $debug, $database, $infile, $outfile); | ||
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| Getopt::Long::GetOptions( | ||
| "-infile=s" => \$infile, | ||
| "-outfile=s" => \$outfile, | ||
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| "-help" => \$help, | ||
| "-debug" => \$debug | ||
| ); | ||
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| my $warn = ''; | ||
| my $error = ''; | ||
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| unless ( defined $infile) { | ||
| $error .= "the cmd line switch -infile is undefined!\n"; | ||
| } | ||
| unless ( defined $outfile) { | ||
| $error .= "the cmd line switch -outfile is undefined!\n"; | ||
| } | ||
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| if ( $help ){ | ||
| print helpString( ) ; | ||
| exit; | ||
| } | ||
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| if ( $error =~ m/\w/ ){ | ||
| print helpString($error ) ; | ||
| exit; | ||
| } | ||
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| sub helpString { | ||
| my $errorMessage = shift; | ||
| $errorMessage = ' ' unless ( defined $errorMessage); | ||
| return " | ||
| $errorMessage | ||
| command line switches for add_md5.pl | ||
| -infile :<please add some info!> | ||
| -outfile :<please add some info!> | ||
| -help :print this help | ||
| -debug :verbose output | ||
| "; | ||
| } | ||
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| my ( $task_description); | ||
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| $task_description .= 'perl'. $plugin_path .'/add_md5.pl'; | ||
| $task_description .= " -infile $infile" if (defined $infile); | ||
| $task_description .= " -outfile $outfile" if (defined $outfile); | ||
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| open ( LOG , ">$outfile.log") or die $!; | ||
| print LOG $task_description."\n"; | ||
| close ( LOG ); | ||
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| ## Do whatever you want! | ||
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| open ( IN, "<$infile" ) or die $!; | ||
| open ( OUT , ">$outfile" ) or die $!; | ||
| while ( <IN> ) { | ||
| print OUT md5_hex($_).": $_"; | ||
| } | ||
| close (IN); | ||
| close (OUT); | ||
| print "Done\n"; | ||
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| Original file line number | Diff line number | Diff line change |
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| sudo apt-get install libcatalyst-view-tt-perl libcatalyst-plugin-session-store-fastmmap-perl libcatalyst-plugin-session-store-cache-perl libcatalyst-plugin-redirect-perl libcatalyst-plugin-configloader-perl libcatalyst-perl libcatalyst-modules-perl libcatalyst-modules-extra-perl libcatalyst-action-rest-perl dos2unix libhtml-template-perl libnet-ssh2-perl libdatetime-format-mysql-perl libgd-svg-perl libdate-simple-perl pdl | ||
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| mkdir SRC | ||
| cd SRC | ||
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| git clone https://github.com/stela2502/Stefans_Lib_Esentials.git | ||
| cd Stefans_Lib_Esentials/Stefans_Libs_Essentials/ | ||
| make | ||
| sudo make install | ||
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| git clone https://github.com/stela2502/SCExV.git | ||
| cd SCExV/ | ||
| git checkout testing | ||
| cd SCExV/ | ||
| make | ||
| sudo make install | ||
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| ## R | ||
| sudo apt-get install r-base r-base-html r-base-core libcurl4-openssl-dev libssl-dev libssh2-1-dev libx11-dev libglu1-mesa-dev libfreetype6-dev | ||
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| ## within R | ||
| install.packages(c('httr','git2r', 'devtools','Rcpp') ) | ||
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| source("http://bioconductor.org/biocLite.R") | ||
| biocLite("RDRToolbox") | ||
| biocLite("Biobase", 'BiocGenerics') | ||
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| library(devtools) | ||
| install_github('stela2502/RFclust.SGE') | ||
| install_github('RGLab/MAST') | ||
| install_github('stela2502/Rscexv') | ||
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| ## python ZIFA | ||
| sudo apt-get install python-numpy python-matplotlib python-scipy scikits.learn | ||
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| cd SRC | ||
| git clone https://github.com/epierson9/ZIFA | ||
| cd ZIFA | ||
| sudo python setup.py install | ||
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| ## nginx + staman | ||
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| apt-get install nginx-full libdaemon-control-perl starman | ||
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| In the SCexV path: | ||
| sudo perl -I lib script/install.pl -install_path /var/www/html/SCexV/ -server_user www-data -web_root /var/www/html/SCexV/ | ||
| sudo ./myapp.starman.initd get_init_file > /etc/init.d/cat-SCExV | ||
| sudo update-rc.d cat-SCExV defaults | ||
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| create the nginx server information (/etc/nginx/sites-enabled/001_SCExV) to contain: | ||
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| server { | ||
| listen 80; | ||
| server_name localhost; | ||
| root /var/www/html/SCexV/; | ||
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| location / { | ||
| client_max_body_size 40M; | ||
| include /etc/nginx/proxy_params; | ||
| proxy_pass http://unix:/var/www/html/SCexV/SCExV.socket:/; | ||
| } | ||
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| } | ||
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| sudo system nginx restart | ||
| sudo system cat-SCExV start | ||
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| ## apache2 (do not use that!) | ||
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| sudo apt-get install libapache2-mod-perl2 libcatalyst-engine-apache-perl apache2 | ||
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| ## the web interface | ||
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| cpanm Plack | ||
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| cd SRC/SCexV/SCexV/ | ||
| sudo perl -I lib script/install.pl -install_path /var/www/html/SCexV/ -server_user www-data | ||
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| This will print a sample apache2 config file that you can adjust if necessary and put into the sites_eanables directory of your apache config. | ||
| ! make sure that the mod_perl2 mod is loaded ! | ||
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| service restart apache2 | ||
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| You now can access the server under localhost/SCexV/ | ||
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| But you might encounter the same problems as I did - mod_perl seams to not like this application any more :-( | ||
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