Ryan, Please see below
On Wed, Oct 6, 2010 at 16:04, Ryan Schmidt <[email protected]> wrote: > On Oct 6, 2010, at 15:49, Rodolfo Aramayo wrote: > > > Background: > > Perl was installed via Macports. > > Bioperl was installed via CPAN and seems to be installed in a MacPorts > directory. > > I realize I have not yet committed the p5-bioperl port that was submitted, > so you didn't really have a choice, but using CPAN to install into a > MacPorts-owned directory can be problematic. For example, once I do commit > p5-bioperl, if you try to install it, MacPorts will complain that the files > it wants to install are already there and it doesn't know where they came > from. > > I installed Perl and Python using ports and then proceeded to install/activate cpan. Although I was expecting to be using the cpan located in /usr/bin, somehow cpan got installed into my: /opt/local/bin/cpan directory and since then has been working just fine. My active coan is located at: /opt/local/bin If I install anything via cpan, it installs fine. I use git to update bioperl (I need to use the bleeding edge code) and it does it all right. Updated code is properly installed into port directories... > > > I installed p5-dbd-mysql via ports > > My server is running Apple MySQL so even though MySQL was installed as a > dependency of p5-dbd-mysql, it is not being used because I do not know how > to activate the ports one...(see below) > > > > > > Problem: > > Trying to load a database we rtun into the following > > bp_seqfeature_load.pl -c -u "username" -p "password" -a DBI::mysql -d > database data.fasta data.gff > > > > we run into the following error: > > ==== > > DBI connect('Ncrassa_scaffold','rsw3284',...) failed: Can't connect to > local MySQL server through socket '/opt/local/var/run/mysql5/mysqld.sock' > (2) at /opt/local/lib/perl5/site_perl/5.12.1/Bio/DB/SeqFeature/Store/DBI/ > mysql.pm line 217 > > > > -------------------- EXCEPTION -------------------- > > MSG: Can't connect to local MySQL server through socket > '/opt/local/var/run/mysql5/mysqld.sock' (2) > > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init > /opt/local/lib/perl5/site_perl/5.12.1/Bio/DB/SeqFeature/Store/DBI/ > mysql.pm:217 > > STACK Bio::DB::SeqFeature::Store::new > /opt/local/lib/perl5/site_perl/5.12.1/Bio/DB/SeqFeature/Store.pm:386 > > STACK toplevel /opt/local/bin/bp_seqfeature_load.pl:101 > > ==== > > > > MySQL appears to be trying to use '/opt/local/var/run/mysql5/mysqld.sock' > which does not exist. > > > > Solution: I solved this problem by going to directory: > > > > /opt/local/var/run/ > > > > which exists and there I created a directory called mysql5 > > >mkdir -pv mysql5 > > >cd mysql5 > > And a link to the MySQL socket present in /var/mysql > > > > >sudo ln -s /var/mysql/mysql.sock mysqld.sock > > > > and that solved the problem > > > > I believe this is a bug? that might need to be fixed? > > What do you believe the bug is; what should be changed? If the MySQL > daemon's socket is not at the usual MacPorts location of > /opt/local/var/run/mysql5/mysqld.sock but somewhere else, you need to inform > your MySQL client where that is. I believe that's done by editing the my.cnf > file. > To what my.cnf file are you referring to? The one located at: /private/etc/ sends mysql to /var/mysql/mysql.sock Is there a MacPorts my.cnf file? Where is it located? > > > > Regardless, this way I am running p5-dbd-mysql with Apple mysql which it > might not be optimal but allowed me to have the computer ready for class > > Apple MySQL... so you are running Mac OS X Server? Apple does not include > MySQL in the consumer version of Mac OS X. > > > > So how do I switch to the ports MySQL? > > Instructions for using MacPorts MySQL are included in the MAMP how-to > document: > > http://trac.macports.org/wiki/howto/MAMP#mysql > > Thanks for this --R
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