ALPHA

Step 1 for Unix PubCrawler:
Downloading and Testing.

Please follow these instructions carefully and report problems to pubcrawlerREMOVECAPShelp@gmail.com. Also have a look at the PubCrawler FAQ .

Downloading

1. Check if you have Perl - version 5 running on your system by typing the following command into one of your (x-)terminals:

perl -v
You should get a message like This is perl, version 5...
If you don't: install the latest version of Perl. This is freeware.

2. With the following command check if you have all necessary Perl-modules installed:

perl -MLWP -MHTML::Parser -e 42
An error message (Can't locate LWP.pm in @INC...) indicates that some of the required modules could not be found. If you are not experienced with Unix and Perl, you should download a PubCrawler package with precompiled libraries (see next step), otherwise install these modules manually (see instructions for installing Perl-modules) - they are freely available.

3. Please choose one of the following links to download the package that meets your requirements:
Packages available for downloading
(press 'Shift'-key and click on link)
PubCrawler with precompiled libraries (~ 160 kB)
available for the following platforms:

Linux 2.x on Intel x86
DEC_OSF1 on Alpha
SunOS 5.5.1 on Sun
FreeBSD 2.2.7 on Intel x86
Linux 2.x on Alpha
PubCrawler source code (~ 43 kB)
(requires installed modules or external command line browser):

PubCrawler's source files for Unix
Upgraders: Please read the README file!

Tip: If you don't know what your platform is, enter the command uname -a . If yours is not supported, try one of the other packages or send an email including your system specifications to PubCrawler.

NOTE: It is recommended to download the PubCrawler package into your home directory and extract it from there, especially if you are getting a package with precompiled libraries (want to know why?).

4. If you have used PubCrawler before, save a backup copy of your configuration file before extracting the PubCrawler components by entering

gzip -cd pubcrawler_src.tgz | tar xovf -
or
gzip -cd pubcrawler_<platform>.tgz | tar xovf -
This will extract the files pubcrawler.pl and pubcrawler.config into a new directory called 'PubCrawler'.
If you have downloaded a package with precompiled libraries a subdirectory 'PubCrawler/lib' will be created which holds the additional modules.
NOTE: Previous files with the same name will be overwritten!

5. Change to the new directory

cd PubCrawler
and make sure the Perl-script is executable:
chmod +x pubcrawler.pl

Testing

6. Try to run PubCrawler by entering:

pubcrawler.pl -h
This should produce a pubcrawler help message. If you see something like
bash: .../pubcrawler.pl: No such file or directory
you have to edit the first line of the program by changing the path to the location of your perl-executable (find out where it resides by entering the command which perl).
Please see the README file for more help if you are using a package with precompiled libraries!

7. Run the program in "check-mode":

pubcrawler.pl -check
  • The messages appearing in your terminal will tell you if everything is OK, or if there are any problems.

    • 8. If you got no errors, run the program again without the -check option but in verbose mode:

    pubcrawler.pl -v
  • You should see a lot of text appearing in your terminal, describing communications between the program and NCBI. When PubCrawler has finished running it will tell you so. This might take a few minutes.

    • 9. View the output by opening the file "pubcrawler_output.html" with Netscape (File -> Open -> Page in Navigator).  You should see the results of the set of searches specified in the file "pubcrawler.config" that is distributed with the program.

    If it looks OK, go onto step BETA


    10. If it's not working, look in terminal window for error messages.  There is probably something wrong with your network, or you need to specify a proxy.  If the check-mode (point 7 above) did not report any errors, see PubCrawler's Technical Description for suggestions about how to manually configure the network settings.


    For your information....
    The PubCrawler for Unix package contains:
  • pubcrawler.config, a configuration file (contains details of the searches to be made)
  • pubcrawler.pl, the Perl source code

    •  
  • After the program has been run, three more files will appear in the PubCrawler working directory:
  • pubcrawler_output.html, the web page with the results
  • pubcrawler_log.html a web page logging what happened when the program ran
  • pubcrawler.db, a database of PubMed and GenBank entries that have been met (and when)
    		•


    Last modified at $Date: 2018/05/25 12:12:10 $