bioperl on mac
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bioperl on mac
by Katherine Wendelsdorf
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Dear one who knows,
I have a macbook with Leopard OSX and I am having trouble running scripts that call for bioperl modules. Here is my history: Using Fink I installed bioperl-pm586 version 1.5.2-4 and bioperl-run-pm586 version 1.5.2-1. when I type >which bioperl-pm586 in to the command line I get nothing. Spotlight says that the path is /sw/share/bioperl-pm586. The same goes for bioperl-run-pm586. 1. I tried to run test2.pl script that was literally copied and pasted from the HOWTO manual, but it wouldnt run. The two attached docs are the script I tried to run and the output (which is nonexistant). I read something that said to "go in to" Bioperl to execute a command. I could not enter the bioperl directory when it was in the sw/shared directory so I copied the bioperl folder to the Desktop just so I could try executing the script inside bioperl. Where am I going wrong here? Should I place these folders (bioperl-pm586 and bioperl-run-pm586) somewhere else on my computer? Shoudl they be in the same directory as perl (usr/bin/perl)? 2. How do I know what modules are included in the bioperl-pm586 I downloaded? Specifically I want to use Bio::SeqIO. 3. What is the best way to download/install new modules as I need them? Any answers you coudl give me for any of these questions would be greatly appreciated! Thank you so much, kind volunteer! -Kate Last login: Wed Jan 23 20:00:40 on console hc6521e39:~ katherinewendelsdorf$ perl -MCPAN -e "install Bio::SeqIO > " CPAN: Storable loaded ok Going to read /Users/katherinewendelsdorf/.cpan/Metadata Database was generated on Sun, 20 Jan 2008 23:37:55 GMT CPAN: LWP::UserAgent loaded ok Fetching with LWP: /authors/01mailrc.txt.gz LWP failed with code[400] message[URL must be absolute] Fetching with LWP: ftp://cpan-du.viaverio.com/pub/CPAN/authors/01mailrc.txt.gz Going to read /Users/katherinewendelsdorf/.cpan/sources/authors/01mailrc.txt.gz CPAN: Compress::Zlib loaded ok Fetching with LWP: /modules/02packages.details.txt.gz LWP failed with code[400] message[URL must be absolute] Fetching with LWP: ftp://cpan-du.viaverio.com/pub/CPAN/modules/02packages.details.txt.gz Going to read /Users/katherinewendelsdorf/.cpan/sources/modules/02packages.details.txt.gz Database was generated on Wed, 23 Jan 2008 23:30:57 GMT There's a new CPAN.pm version (v1.9205) available! [Current version is v1.7602] You might want to try install Bundle::CPAN reload cpan without quitting the current session. It should be a seamless upgrade while we are running... Fetching with LWP: /modules/03modlist.data.gz LWP failed with code[400] message[URL must be absolute] Fetching with LWP: ftp://cpan-du.viaverio.com/pub/CPAN/modules/03modlist.data.gz Going to read /Users/katherinewendelsdorf/.cpan/sources/modules/03modlist.data.gz Going to write /Users/katherinewendelsdorf/.cpan/Metadata Warning: Cannot install Bio::SeqIO, don't know what it is. Try the command i /Bio::SeqIO/ to find objects with matching identifiers. hc6521e39:~ katherinewendelsdorf$ i /Bio::SeqIO -bash: i: command not found hc6521e39:~ katherinewendelsdorf$ i /Bio::SeqIO/ -bash: i: command not found hc6521e39:~ katherinewendelsdorf$ perl -MCPAN -e "install bioperl-live::Bio::SeqIO" CPAN: Storable loaded ok Going to read /Users/katherinewendelsdorf/.cpan/Metadata Database was generated on Wed, 23 Jan 2008 23:30:57 GMT Warning: Cannot install 0, don't know what it is. Try the command i /0/ to find objects with matching identifiers. hc6521e39:~ katherinewendelsdorf$ which bioperl hc6521e39:~ katherinewendelsdorf$ which bioperl-pm586 hc6521e39:~ katherinewendelsdorf$ which perl /usr/bin/perl hc6521e39:~ katherinewendelsdorf$ which bioperl-run-pm586 hc6521e39:~ katherinewendelsdorf$ perl Desktop/test2.pl hc6521e39:~ katherinewendelsdorf$ perl Desktop/test2.pl Can't open perl script "Desktop/test2.pl": No such file or directory hc6521e39:~ katherinewendelsdorf$ cd Desktop/bioperl-pm586/ hc6521e39:bioperl-pm586 katherinewendelsdorf$ perl test2.pl hc6521e39:bioperl-pm586 katherinewendelsdorf$ #! /usr/bin/perl -w use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); print $seq_obj->seq; _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bioperl on mac
by Brian Osborne-2
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Katherine,
Perl keeps the addresses of all the module directories in its @INC array. What do you see when you do: perl -e 'print @INC' ? If '/sw/share/bioperl-pm586' is not in @INC then you need to put it there, perhaps by adding something like: setenv PERL5LIB ${PERL5LIB}:/sw/share/bioperl-pm586 to the .tcshrc file in your home directory (if you use tcsh that is, most use bash, .bashrc, and 'set' these days). You asked some other questions, the general answer is that all the modules you'll need are in the 2 packages you've installed, and you don't need to move them from /sw. Brian O. On Jan 24, 2008, at 1:19 PM, Katherine Wendelsdorf wrote: > Dear one who knows, > > I have a macbook with Leopard OSX and I am having trouble running > scripts > that call for bioperl modules. > > Here is my history: Using Fink I installed bioperl-pm586 version > 1.5.2-4 > and bioperl-run-pm586 version 1.5.2-1. when I type >which bioperl- > pm586 in > to the command line I get nothing. Spotlight says that the path is > /sw/share/bioperl-pm586. The same goes for bioperl-run-pm586. > > 1. I tried to run test2.pl script that was literally copied and pasted > from the HOWTO manual, but it wouldnt run. The two attached docs are > the > script I tried to run and the output (which is nonexistant). I read > something that said to "go in to" Bioperl to execute a command. I > could > not enter the bioperl directory when it was in the sw/shared > directory so > I copied the bioperl folder to the Desktop just so I could try > executing > the script inside bioperl. Where am I going wrong here? > > Should I place these folders (bioperl-pm586 and bioperl-run-pm586) > somewhere else on my computer? Shoudl they be in the same directory as > perl (usr/bin/perl)? > > 2. How do I know what modules are included in the bioperl-pm586 I > downloaded? Specifically I want to use Bio::SeqIO. > > 3. What is the best way to download/install new modules as I need > them? > > > Any answers you coudl give me for any of these questions would be > greatly > appreciated! > > Thank you so much, kind volunteer! > - > Kate > <test.txt><test2.pl>_______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bioperl on mac
by Jason Stajich-3
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Usually this is done by fink by adding a line to your .tcshrc (if you
are running that shell) or .bash_profile or .bashrc. On my machine I have this at the top of my .bash_profile file: test -r /sw/bin/init.sh && . /sw/bin/init.sh if that is not there you need to add it to insure that all the fink tools are setup properly. On Jan 26, 2008, at 8:14 AM, Brian Osborne wrote: > Katherine, > > Perl keeps the addresses of all the module directories in its @INC > array. What do you see when you do: > > perl -e 'print @INC' > > ? > > If '/sw/share/bioperl-pm586' is not in @INC then you need to put it > there, perhaps by adding something like: > > setenv PERL5LIB ${PERL5LIB}:/sw/share/bioperl-pm586 > > to the .tcshrc file in your home directory (if you use tcsh that > is, most use bash, .bashrc, and 'set' these days). > > You asked some other questions, the general answer is that all the > modules you'll need are in the 2 packages you've installed, and you > don't need to move them from /sw. > > > Brian O. > > > On Jan 24, 2008, at 1:19 PM, Katherine Wendelsdorf wrote: > >> Dear one who knows, >> >> I have a macbook with Leopard OSX and I am having trouble running >> scripts >> that call for bioperl modules. >> >> Here is my history: Using Fink I installed bioperl-pm586 version >> 1.5.2-4 >> and bioperl-run-pm586 version 1.5.2-1. when I type >which bioperl- >> pm586 in >> to the command line I get nothing. Spotlight says that the path is >> /sw/share/bioperl-pm586. The same goes for bioperl-run-pm586. >> >> 1. I tried to run test2.pl script that was literally copied and >> pasted >> from the HOWTO manual, but it wouldnt run. The two attached docs >> are the >> script I tried to run and the output (which is nonexistant). I read >> something that said to "go in to" Bioperl to execute a command. I >> could >> not enter the bioperl directory when it was in the sw/shared >> directory so >> I copied the bioperl folder to the Desktop just so I could try >> executing >> the script inside bioperl. Where am I going wrong here? >> >> Should I place these folders (bioperl-pm586 and bioperl-run-pm586) >> somewhere else on my computer? Shoudl they be in the same >> directory as >> perl (usr/bin/perl)? >> >> 2. How do I know what modules are included in the bioperl-pm586 I >> downloaded? Specifically I want to use Bio::SeqIO. >> >> 3. What is the best way to download/install new modules as I need >> them? >> >> >> Any answers you coudl give me for any of these questions would be >> greatly >> appreciated! >> >> Thank you so much, kind volunteer! >> - >> Kate<test.txt><test2.pl>_____________________________________________ >> __ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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problem of bioperl on mac
by MADSGENE
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I installed the bioperl-pm586 version 1.5.2-4 in my macbook(MAC OS X version 10.5.6) using fink. I also found it in /sw/share/bioperl-pm586. However I failed to get it when I typed "which". When I typed >perl -e 'print @INC', it displayed /sw/lib/perl5/5.8.6/darwin-thread-multi-21evel...but no information about bioperl-pm586. I took the suggstion and added "setenv PERL5LIB ${PERL5LIB}:/sw/share/bioperl-pm586 " into .bashrc, it still did not work. I am grateful to you if anyone could help me out. I note there are two .bashrc files, one is in root and the other in home. If your suggestion is to modify these files, please let me know which one. Regards Xia Wang |
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Re: problem of bioperl on mac
by Dave Messina-3
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I'm not familiar with how fink sets up BioPerl, but 'which' typically works
only for executables that are in your PATH. Since BioPerl is a collection of perl modules, I wouldn't expect it to show up with 'which' even when properly installed. There is a scripts directory that comes with BioPerl and may be in that /sw/share/bioperl-pm586 directory. If you want those scripts to appear when you 'which', then /sw/share/bioperl-pm586/scripts must be in your PATH environmental variable. Dave PS - A later and much better version of BioPerl (1.6) is available now, and it's easy to install with CPAN. Really no need to fink it. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: problem of bioperl on mac
by MADSGENE
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Hi bioperlers,
Thanks for all responses. I removed the bioperl and reinstalled it by fink. It works. Regards Xia
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Re: problem of bioperl on mac
by Kevin Brown-8
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And for those that are interested, here's what version of bioperl are
available via fink for various levels of OSX http://pdb.finkproject.org/pdb/package.php/bioperl-pm586 > -----Original Message----- > From: bioperl-l-bounces@... > [mailto:bioperl-l-bounces@...] On Behalf Of MADSGENE > Sent: Wednesday, March 04, 2009 1:52 PM > To: Bioperl-l@... > Subject: Re: [Bioperl-l] problem of bioperl on mac > > > Hi bioperlers, > > Thanks for all responses. > I removed the bioperl and reinstalled it by fink. It works. > > Regards > > Xia > > > > > > MADSGENE wrote: > > > > > > I installed the bioperl-pm586 version 1.5.2-4 in my macbook(MAC OS X > > version 10.5.6) using fink. I also found it in > /sw/share/bioperl-pm586. > > However I failed to get it when I typed "which". When I > typed >perl -e > > 'print @INC', it displayed > > /sw/lib/perl5/5.8.6/darwin-thread-multi-21evel...but no > information about > > bioperl-pm586. I took the suggstion and added "setenv PERL5LIB > > ${PERL5LIB}:/sw/share/bioperl-pm586 " into .bashrc, it > still did not work. > > > > I am grateful to you if anyone could help me out. > > I note there are two .bashrc files, one is in root and the > other in home. > > If your suggestion is to modify these files, please let me > know which one. > > > > Regards > > > > Xia Wang > > > > > > > > > > -- > View this message in context: > http://www.nabble.com/bioperl-on-mac-tp15101357p22339072.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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