[Scriptome-users] how to make the Command-line ScriptomeExecutables work?

Amir Karger akarger at CGR.Harvard.edu
Tue Jun 26 08:23:45 EDT 2007

Zwieb, Christian wrote:

> I have a bit of trouble to make the command-line Scriptome 
> executables work.
> Scriptome files are here:
> (not sure if they have to be in bin also)
> Christian-Zwiebs-Computer-3:~/programs czwieb$ cd Scriptome
> Christian-Zwiebs-Computer-3:~/programs/Scriptome czwieb$ tree
> .
> |-- ScriptPack
> |-- Scriptome
> |-- bin
> |   |-- ScriptPack
> |   |-- ScriptPack.bat
> |   |-- Scriptome
> |   `-- Scriptome.bat

I would probably leave the Scriptome tools in bin and not bother putting
them in programs/Scriptome. Then put Scriptome/programs/bin in your path
instead of Scriptome/programs. But I doubt this has anything to do with
your problem.

> The HTML-Tree-3.23  module is here:
> Christian-Zwiebs-Computer-3:~/.cpan/build czwieb$ ls
> ExtUtils-CBuilder-0.18      HTML-Tree-3.23              

I think this is your problem.

> Christian-Zwiebs-Computer-3:~ czwieb$ echo $PATH
> /sw/bin:/sw/sbin:/bin:/sbin:/usr/bin:/usr/sbin:~/programs/Scriptome
> Path seems ok.
> because:
> Christian-Zwiebs-Computer-3:~ czwieb$ Scriptome -h
> -bash: /Users/czwieb/programs/Scriptome/Scriptome: 
> /usr/local/bin/perl: bad interpreter: No such file or directory
> I changed "/usr/local/bin/perl" to "usr/bin/env perl" in 
> ScriptPack and Scriptome

Ah. You're not a beginner user, I see.

If anyone else has had a similar problem on UNIX/Mac (You can also get a
"command not found" error) then do a "which perl" and put the result
(e.g., /usr/bin/perl) after the #! on the first line of the
Scriptome/ScriptPack programs. 

> Then:
> Christian-Zwiebs-Computer-3:~ czwieb$ Scriptome -h
> Can't locate HTML/TreeBuilder.pm in @INC (@INC contains: 
> /sw/lib/perl5/5.8.6/darwin-thread-multi-2level 
> /sw/lib/perl5/5.8.6 /sw/lib/perl5 /sw/lib/perl5/darwin 
> /System/Library/Perl/5.8.6/darwin-thread-multi-2level 
> /System/Library/Perl/5.8.6 
> /Library/Perl/5.8.6/darwin-thread-multi-2level 
> /Library/Perl/5.8.6 /Library/Perl 
> /Network/Library/Perl/5.8.6/darwin-thread-multi-2level 
> /Network/Library/Perl/5.8.6 /Network/Library/Perl 
> /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level 
> /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at 
> /Users/czwieb/programs/Scriptome/Scriptome line 15.
> BEGIN failed--compilation aborted at 
> /Users/czwieb/programs/Scriptome/Scriptome line 15.

Aha! @INC does NOT contain ~/.cpan/build (and at any rate, it's going to
look for a directory called HTML, not HTML-Tree-3.2.3). Since it's in
.cpan, I'm assuming you used the CPAN module to download the module. If
so, you need to do a get, a make (plus optionally a test), and an
install (i HTML::Tree), not just a get.

Installing will put directories like HTML/Tree/ (and lots of files
inside them) into places like /Library/Perl/5.8.6/Library/Perl and
elsewhere. If you're lucky, these places will be in your @INC, and
Scriptome/ScriptPack will work once you do this.

Let me know if you run into more issues.


> I am in a jam and grateful for any suggestions.
> Chris
> zwieb at uthct.edu
> MacBook (OS 10.4)
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