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

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 downloaded that and put it in my desktop. Then I right-click on it, select "Properties" and then change the permission. Afterwards, I opened the terminal and set it to the desktop.

cd desktop 

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 

[...] necessary packages and programs.

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

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

#then add this 

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 testm folder and I run or I don't copy them because the -getdef suppose to do this

runXquest.pl –getdef 

I get this error:

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

And if I do:

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.

What else I should do to install xQuest/xProphet?

  • Nope. But there's a troubleshooting section here – Elder Geek Feb 28 '17 at 21:14
  • @Elder Geek thanks, I did my best on the troubleshooting but they have never mentioned anything about it . I get other errors that the also did not mention .:-( – Moh Feb 28 '17 at 21:19
  • Well, if that's the case you should help us help you by edit your post mentioning the other errors you did not mention. Doing so may prevent this question being closed as unclear what you are asking. – Elder Geek Feb 28 '17 at 21:22
  • 1
    @Elder Geek I gave a detailed explanation of each step I followed above – Moh Feb 28 '17 at 21:54
  • Would you be so kind as to actually list the Perl packages or include the link to the list and include the process you used to install them and the results of same? Thank you for helping us help you! – Elder Geek Feb 28 '17 at 22:03

From your question:

 # 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

Though when the path was created:

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

edit the ~/.profile again,modifying the path:


Logout of your session and back into it. And try the process again.

| improve this answer | |
  • thanks for the message but this is not the problem. it was my typo !!! – Moh Mar 4 '17 at 20:10

At the beginning of your post, did you leave out this step, or omit it?

cd desktop 



Should be:

cd desktop


chmod +x install_packages.sh

| improve this answer | |
  • thanks steve, I did it in both ways, right click give execution and permission right to the install_packages.sh and also chmod , this is also not the case – Moh Mar 5 '17 at 14:41

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