#StackBounty: #14.04 #command-line #apache2 #perl what is Error: Cannot find/read the file ./MASTER_RUN/MASTER_RUN.txt

Bounty: 100

I am trying to install a software which has no support so far.
The software is from here
http://proteomics.ethz.ch/cgi-bin/xquest2_cgi/installation.cgi

and this is what they mentioned to follow

This section describes the installation on Unix based systems. For installation on a single machine, we recommend to use Ubuntu as OS.

a. Install necessary Perl packages

The required Perl packages are listed here: Perl Packages
Install these perl packages on your system (e.g. by using cpan).
Additionally you need to install subversion and dos2unix (on linux systems).
If you use Ubuntu, you can download and execute the install_packages.sh shell script. This script will install all the necessary packages and programs.

Here you can download the install_packages.sh then change the permission which allows you to run it.
I did downloaded that and put it in my desktop. Then I right click on it—> properties and then change the permission. Afterwards. I opened the terminal and set it to the desktop

Cd desktop 
#then
./install_packages.sh  

and these are the inside packages

## apache
sudo apt-get install apache2
sudo apt-get install libapache-session-perl
## other
sudo apt-get install bioperl
sudo apt-get install libberkeleydb-perl
sudo apt-get install libcgi-fast-perl
sudo apt-get install libcgi-session-perl
sudo apt-get install libdata-dumper-concise-perl
sudo apt-get install libdata-dumper-simple-perl
sudo apt-get install libhtml-template-perl
sudo apt-get install libfile-copy-recursive-perl
sudo apt-get install libgd-graph-perl
sudo apt-get install libio-compress-bzip2-perl
sudo apt-get install libio-compress-perl
sudo apt-get install libtemplate-perl
sudo apt-get install libxml-treebuilder-perl
sudo apt-get install libxml-writer-perl
sudo apt-get install libmldbm-perl
sudo apt-get install libstatistics-descriptive-perl
sudo apt-get install libcgi-formbuilder-perl
sudo apt-get install libmail-sender-perl
sudo apt-get install build-essential
"~/Desktop/install_packages.sh" 42L, 1279C 

b. Install xQuest/xProphet

  • Create a directory where xQuest/xProphet will be installed. e.g. /home/xquest/xquest
  • Download the zip or tar folder from the download section. and copy into the installation directory.
  • Unzip the folder. The structure will then be /VERSION/xquest/…
  • change to the /installation folder. Edit the first line of the “install_xquest.sh” script and execute it. Please note: This script executes /cgi/changeheader.pl which changes the header of the cgi files, if your installation path for perl is not /usr/bin/perl you have to edit the script.
  • Add the /xquest/bin directory to your PATH variable, so that the programs can be found.

Here is what i did

sudo mkdir /home/xqxp/
cd /home/xqxp
sudo mkdir xquest

sudo cp /home/user/Desktop/V2_1_1.zip /home/xqxp/xquest/ -r

sudo apt-get install unzip

cd /home/xqxp/xquest/
sudo unzip V2_1_1.zip


# give the permistion to the folder 
sudo chmod -R o+rw /home/xqxp/xquest/V2_1_1/xquest/installation
# you can change the permission by
gksu nautilus

#and then I did
./install_xquant.sh

# add the directory to the profile 
gedit ~/.profile

#then add this 
PATH="$HOME/bin:$HOME/.local/bin:$PATH:/home/xquest/xquest/V2_1_1/xquest/bin" 

Now I follow the structure how to run it http://proteomics.ethz.ch/cgi-bin/xquest2_cgi/howtorun.cgi created a folder in my desktop

cd Desktop/
mkdir testm
cd testm/

I copy and past two files xmm.def and xquest.def to the test folder and I run

runXquest.pl –getdef 

I get this error

Error: Cannot find/read the file ./MASTER_RUN/MASTER_RUN.txt

I googled and I could not find what it is, is there anyone knows about it?

and if I do it like this

runXquest.pl -getdef

I get this error

Current Server: xquestvm
cannot open file /home/xqxp/logs/usage.log No such file or directory at /home/xqxp/xquest/V2_1_1/xquest/bin/../modules/Common.pm line 83.


Get this bounty!!!

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