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. _Amir > > I am in a jam and grateful for any suggestions. > > Chris > zwieb at uthct.edu > MacBook (OS 10.4) > _______________________________________________ > Scriptome-users mailing list > Scriptome-users at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/scriptome-users > Unsubscribe by sending mail (subject and content don't matter) to: > Scriptome-users-unsubscribe at bioinformatics.org >