installing mysql

I am hoping to run a set of scripts that will identify and index olfactory receptors using BLAST and mysql. That means I need to sort out how mysql is installed on noctilio, which should be great fun.

First thing I noticed when I downloaded mysql, is that we have 3 other version of mysql on the server! :)

I knew this was going to cause some problems so I needed to uninstall all versions of MySQL in order to get this working properly. I basically followed this awesome post. Here it is reiterated for Mac OsX Yosemite:

Remove MySQL completely per The Tech Lab

• ps -ax | grep mysql

• stop and kill any MySQL processes
• brew remove mysql
• brew cleanup
• sudo rm /usr/local/mysql
• sudo rm -rf /usr/local/var/mysql
• sudo rm -rf /usr/local/mysql*
• sudo rm ~/Library/LaunchAgents/homebrew.mxcl.mysql.plist
• sudo rm -rf /Library/StartupItems/MySQLCOM
• sudo rm -rf /Library/PreferencePanes/My*
• launchctl unload -w ~/Library/LaunchAgents/homebrew.mxcl.mysql.plist
• edit /etc/hostconfig and remove the line MYSQLCOM=-YES-
• rm -rf ~/Library/PreferencePanes/My*
• sudo rm -rf /Library/Receipts/mysql*
• sudo rm -rf /Library/Receipts/MySQL*
• sudo rm -rf /private/var/db/receipts/*mysql*
• restart your computer just to ensure any MySQL processes are killed
• try to run mysql, it shouldn't work

Brew install MySQL per user Sedorner from this StackOverflow answer

• brew doctor and fix any errors
• brew update
• brew install mysql
• unset TMPDIR
• mysqld -initialize --verbose --user=whoami --basedir="$(brew --prefix mysql)" --datadir=/usr/local/var/mysql --tmpdir=/tmp #note the above command has been edited to replace the deprecated form
• mysql.server start
• run the commands Brew suggests, add MySQL to launchctl so it automatically launches at startup

Okay now to have MySQL start at launch, follow this lovely post. Homebrew can basically set this up for you.

brew tap homebrew/services

Apparently it is no longer supported, so also run these commands:
brew untap homebrew/boneyard brew tap gapple/services

When you run this command, mysql should start:
brew services start mysql

Installing pbh5tools on OSX yosemite

I need to assemble PacBio amplicons of olfactory receptors. One of the main challenges I have been having is that most of the PacBio tools (SMRT-analysis, Celara assembler) focus on assembling whole genomes. Using an approach from Larson, et al. (2014) in BMC Genomics, I am going to do quality filtering using pbh5tools that will filter the reads at a minimum of passes (e.g. 4; though my mean number of passes is quite high for the data (~20)).

To install pbh5tools, I dealt with a series of challenges on Yosemite:
Download from github.

cd pbh5tools-master/

sudo python setup.py install

I ran into this pesky error.

In file included from /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:

/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: 

      "Using deprecated NumPy API, disable it by "          "#defining

      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

#warning "Using deprecated NumPy API, disable it by " \

 ^

In file included from /tmp/easy_install-_W_eCV/h5py-2.5.0/h5py/defs.c:279:

/tmp/easy_install-_W_eCV/h5py-2.5.0/h5py/api_compat.h:27:10: fatal error: 

      'hdf5.h' file not found

#include "hdf5.h"

         ^

1 warning and 1 error generated.

error: Setup script exited with error: command 'cc' failed with exit status 1

First I tries to install hdf5 tool packages and then export the path there, but that wasn't working.

From the setup.py, I see that it needs:
    install_requires=[
        'pbcore >= 0.8.0',
        'numpy >= 1.6.0',
        'h5py >= 1.3.0'
        ]

sudo pip install pbcore

sudo pip install numpy

sudo pip install h5py

Then,

sudo python setup.py install

...

Using /Library/Python/2.7/site-packages

Searching for pysam==0.8.3

Best match: pysam 0.8.3

pysam 0.8.3 is already the active version in easy-install.pth

Using /Library/Python/2.7/site-packages

Finished processing dependencies for pbh5tools==0.8.0

Voila!

I am using modelOmatic to determine which models best fit the sequences, and it include comparisons of codon models. Installing and running modelOmatic. For awhile I thought I was having Yosemite issues but because they are all binaries, everything seems to checking out okay. Lots of "duh" moments were had.

To install on Mac OSX Yosemite:
[1] Download the binaries and move to where you store your programs.

mv ~/Downloads/modelomatic_OSX /usr/local/bin/

[2] Set modelOmatic into your path.

vi .bash_profile  #in your home directory, this opens up your bash profile

#press "i" to edit and then paste this into your .bash_profile

export PATH=/usr/local/bin/modelomatic_OSX:$PATH 

#press ESC, then type "wq!"; restart the terminal

[3] ModelOmatic requires a tree file to run. It can make a NJ tree if you have bioNJ set up. Download the binaries for bioNJ here.

[4] Move the bioNJ into where you store your programs. Set your path. You have to rename your path in lower case so that modelOmatic can read it.

mv ~/Downloads/BIONJ/ /usr/local/bin/ 

mv /usr/local/bin/BIONJ/BIONJ /usr/local/bin/BIONJ/bionj

#add to your path variable
vi .bash_profile

export PATH=/usr/local/bin/BIONJ/BIONJ:$PATH

export PATH=/usr/local/bin/BIONJ:$PATH

The format for input 

./ModelOMatic <data> bionj <output> <genetic_code> fast

I am running it as modelomatic_OSX because it is in my path. 

Using the bionj option tell modelOmatic to make its own tree using bioNJ.

Specify in <output> slot where to put your output folder.

The <genetic_code> has been tricky. It can choke and tell you that you have stop codons if you don't use the correct number:

     0:  Universal code
     1:  Vertebrate mt
     2:  Yeast mt
     3:  Mould mt

     4:  Invertebrate mt
     5:  Ciliate nuclear
     6:  Echinoderm mt
     7:  Euplotid mt

     8:  Alternative yeast nuclear
     9:  Ascidian mt

     10: Blepharisma nuclear

     11: Everything codes (64 character state-space)

My adviser was having trouble but then realized she was using cytb so it actually should have been "1" instead of "0". 

ModelOmatic uses .phylip file. Allegedly can use other formats but I have not tried. However, it actually seems ridiculously flexible in reading a .phylip file.

OR_alignments loloyohe$ modelomatic_OSX Phyllos_OR6_Funct_tAlign.phylip bionj test.txt 1

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: <Phyllos_OR6_Funct_tAlign.phylip>: 35 sequences of length 729 (DataMatrix: 35 x 570)

Checking for sparse (>85% gaps) sequences

Starting with 35 ... after removal there are 35 sequences

Creating start tree ... 

Assertion failed: (0), function Error, file tools.cxx, line 235.

Unrecognised codon: AGA for data codon position 241 in sequence 1...Abort trap: 6

We had stop codons. Okay, so I translated the sequences, looked for where the stop codons were, and then I replaced them in the original .phylip file using "---".  Note in the future that all .phylip sequence files in /Volumes/Yango/Hayden_ORs/OR_alignments have the stop codon replaced, while the .nex files have the original sequence alignments. Lets try to get it running...

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR4_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR4_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR4_Funct_tAlign.phylip>: 127 sequences of length 753 (DataMatrix: 127 x 666)

Checking for sparse (>85% gaps) sequences

Starting with 127 ... after removal there are 127 sequences

Creating start tree ...  estimated using bionj (1.15646s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (3.56514s)

NT Done  (10.6517s)

AA Done  (71.2184s).........

Codon Done  (232.733s)

Outputting results to <Phyllos_OR4_Funct_tAlign_mOm_results.txt>

Successful exit

####now for the others

modelomatic_OSX /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR6_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR6_Funct_tAlign_mOm_results.txt 0 fast

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR10_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR10_Funct_tAlign_mOm_results.txt 0 fast

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR51_Funct_tAlign_mOm_results.txt 0 fast

Had a hiccup with this data:

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR2_13_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR2_13_Funct_tAlign_mOm_results.txt 0 normal

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR2_13_Funct_tAlign.phylip>: 264 sequences of length 1530 (DataMatrix: 264 x 943)

Checking for sparse (>85% gaps) sequences

Starting with 264 ... after removal there are 264 sequences

Creating start tree ...  estimated using bionj (4.68751s)

Optimisation settings: normal 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

Broken Prob(): -0.000104812

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR137_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR137_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR137_Funct_tAlign.phylip>: 452 sequences of length 804 (DataMatrix: 452 x 766)

Checking for sparse (>85% gaps) sequences

Starting with 452 ... after removal there are 452 sequences

Creating start tree ...  estimated using bionj (4.7425s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (8.05337s)

NT Done  (44.7082s)

Broken Prob(): -40.8111

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR52_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR52_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip>: 152 sequences of length 750 (DataMatrix: 152 x 712)

Checking for sparse (>85% gaps) sequences

Starting with 152 ... after removal there are 152 sequences

Creating start tree ...  estimated using bionj (1.32059s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (4.69988s)

NT Done  (13.8241s)

AA Done  (85.6409s).........

...

Broken Prob(): -2.64535e+41

I think the problem is in running the "fast" option with large datasets. When I use "trimfast" and "normal", they both work. 

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt 0 trimfast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip>: 152 sequences of length 750 (DataMatrix: 152 x 712)

Checking for sparse (>85% gaps) sequences

Starting with 152 ... after removal there are 152 sequences

Creating start tree ...  estimated using bionj (1.58694s)

Optimisation settings: fast trim=10

TRIMMING: Tree contains 152 sequences (>TrimTree=10) ...

          Loose optimisation of start tree under JC ... done

          Obtaining greedy start tree with 10 sequences ... done

          Reinitialising objects for trimmed data ... done

          New files available: data = </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt.trim.data>; tree = </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt.trim.tree>

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (1.08313s)

NT Done  (1.18703s)

AA Done  (6.64464s).........

Codon Done  (24.4936s)

Outputting results to </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt>

Successful exit

However, word of caution. The "trimfast" option gives a vastly different result:

Normal it is! With fewer parameters, its best just to wait it out.

installing garli on yosemite

sudo gem update --system



brew install open-mpi --cc=gcc-4.9 --build-from-source




brew remove ncl garli



brew install ncl garli --cc=gcc-4.9 --build-from-source

#installing Fasta_reader (needed to run script for stats on Trinity assembly)
#first need to install npm
brew install node
vi server.js
#paste the following
var http = require('http'); http.createServer(function (req, res) { res.writeHead(200, {'Content-Type': 'text/plain'}); res.end('Hello World\n'); }).listen(8124, "127.0.0.1"); console.log('Server running at http://127.0.0.1:8124/');
#ESC wq!

#to check if it works
node server.js

npm install fastareader

WOOPS! nevermind! All of this stuff is already installed with Trinity. To run TrinityStats.pl, it cannot be run alone. You must navigate to the directory in which it is found.

###################

#   Ar_jam MOE    #

###################

#combine data from Lanes 1 & 2

cat Arjam_MOE* >> DR_004_Arjam_MOE_assembled.fasta

sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_004_Arjam_MOE_assembled.fasta

################################

## Counts of transcripts, etc.

################################

Total trinity transcripts: 140189

Total trinity components: 63956

Percent GC: 55.16

########################################

Stats based on ALL transcript contigs:

########################################

Contig N10: 4088

Contig N20: 3085

Contig N30: 2434

Contig N40: 1927

Contig N50: 1502

Median contig length: 426

Average contig: 826.50

Total assembled bases: 115865619

#####################################################

## Stats based on ONLY LONGEST ISOFORM per COMPONENT:

#####################################################

Contig N10: 3860

Contig N20: 2862

Contig N30: 2212

Contig N40: 1726

Contig N50: 1310

Median contig length: 440

Average contig: 793.55

Total assembled bases: 50752060 

###################

#   Ar_jam VNO    #

###################

#combine data from Lanes 1 & 2

cat Arjam_VNO* >> DR_011_Arjam_VNO_assembled.fasta

sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_011_Arjam_VNO_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 138142
Total trinity components: 61477
Percent GC: 55.51

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4735
Contig N20: 3550
Contig N30: 2822
Contig N40: 2240
Contig N50: 1741

Median contig length: 455
Average contig: 920.11
Total assembled bases: 127106357

#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3855
Contig N20: 2871
Contig N30: 2270
Contig N40: 1814
Contig N50: 1436

Median contig length: 467
Average contig: 848.36

Total assembled bases: 52154403

###################

#   Mo_red MOE    #

###################

#combine data from Lanes 1 & 2

cat Mored_MOE* >> DR_013_Mored_MOE_assembled.fasta

sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_013_Mored_MOE_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 245573
Total trinity components: 100799
Percent GC: 56.14

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 5311
Contig N20: 4036
Contig N30: 3304
Contig N40: 2703
Contig N50: 2118

Median contig length: 406
Average contig: 960.45
Total assembled bases: 235861464

#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 4140
Contig N20: 2880
Contig N30: 2105
Contig N40: 1512
Contig N50: 1053

Median contig length: 377
Average contig: 685.78

Total assembled bases: 69126334

###################

#   Mo_red VNO    #

###################

#combine data from Lanes 1 & 2

cat Mored_VNO* >> DR_013_Mored_VNO_assembled.fasta

sudo perl $TRINITY_HOME/util/TrinityStats.pl DR_013_Mored_VNO_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 163233
Total trinity components: 70319
Percent GC: 55.74

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4648
Contig N20: 3450
Contig N30: 2778
Contig N40: 2186
Contig N50: 1709

Median contig length: 430
Average contig: 883.37
Total assembled bases: 144195048

#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3865
Contig N20: 2811
Contig N30: 2110
Contig N40: 1605
Contig N50: 1187

Median contig length: 427
Average contig: 754.88

Total assembled bases: 53082440

###################

#   Mo_bla MOE    #

###################

cat Mobl_MOE* >> DR_091_Mobl_MOE_assembled.fasta

sudo perl $TRINITY_HOME/util/TrinityStats.pl DR_091_Mobl_MOE_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 249551
Total trinity components: 115871
Percent GC: 54.01

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4786
Contig N20: 3549
Contig N30: 2741
Contig N40: 2123
Contig N50: 1598

Median contig length: 335
Average contig: 763.67
Total assembled bases: 190573978

#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3761
Contig N20: 2670
Contig N30: 1971
Contig N40: 1426
Contig N50: 989

Median contig length: 344
Average contig: 636.73

Total assembled bases: 73778325

Okay we have FINALLY updated our operating system.

Apparently Mavericks already has commandline tools installed so it is not necessary to install again. However, there are some issues if you install Homebrew and the gcc compiler not being linked. So starting from scratch, here is what do do.

#install homebrew

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

#check to see your comp is ready to brew

brew doctor

#i had several errors/warnings (errors indicated in orange)

/usr/bin comes before /usr/local/bin

export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

/usr/local/lib/gcc is not writable.

sudo chown -R laurelyohe /usr/local

brew install homebrew/science/bowtie

brew install apple-gcc42

brew install samtools

brew install trinity

Okay, everything seems good to go. Now I am unzipping the transcriptome output from trimmomatic. 

#installing bamm

brew tap macroevolution/bamm
brew install bamm

#it worked

Installing FASTA on a Mac:

-ORA says it requires * FASTA r56 distribution. I did not see this on the server but installed the current version (which is 36). Maybe it's a typo in the readme?

Anyways, this one was a little dicier than HMMER:

Start by going to: ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/
#cd to the /src file:
cd src
#make the file (you have to type in the path to the make folder in fasta)
#highlighted in pink is what you change to make it work on your comp

make -f ~/Scripts/fasta-36.3.6b/make/Makefile.os_x86 all

#now see if it works

 ~/Scripts/fasta-36.3.6b/bin/fasta36 -q ~/Scripts/fasta-36.3.6b/seq/mgstm1.aa ~/Scripts/fasta-36.3.6b/seq/prot_test.lseg

#depending on the version of fasta you downloaded, the command will be different (e.g. fasta35 

#instead of fasta36)

Installing *HMMER v3

Download and unzip the version (from this program with a communist logo: http://hmmer.janelia.org/)

Navigate to the directory where you have moved your downloaded hmmer.. file and type the following commands into the terminal (in bold):

cd hmmer-3.1b1-macosx # move into new directory

./configure #configure

make #build

make check #run the automated tests

make install #install

Smoothest installation ever (assuming you have make)...

Going to install the Olfactory Receptor family Assigner (http://search.cpan.org/~ceratites/ora-1.9.1/lib/Bio/ORA.pm#SEE_ALSO)

Downloaded the .gz.tar

Install Bioperl.

#need to find out version of perl
perl -v
# it is v.5.16.2

#woops of course you have to install fink
http://www.finkproject.org/download/index.php?phpLang=en

#of course there is no fink installation for macs OS > 10.8
# http://www.bioperl.org/wiki/Installing_BioPerl_on_Mac_OSX
#following general installation on unix
# http://www.bioperl.org/wiki/Installing_BioPerl_on_Unix

#first install CPAN

perl -MCPAN -e shell #answer a bunch of questions--try to select automate

#CPAN interface will install
cpan>install Bundle::CPAN #a bunch of installing lines happen
#takes several minutes and you have to answer questions in between

cpan>q #quits the CPAN interface

To get the most updated version of BioPerl (which I'm sure I'll regret down the line), install it via cpan (assuming you got cpan working as well).

>perl -MCPAN -e shell

cpan>d /bioperl/
Reading '/home/francisco/.cpan/Metadata'
  Database was generated on Wed, 19 Mar 2014 13:17:02 GMT
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CJFIELDS/BioPerl-1.6.923.tar.gz
Distribution    CJFIELDS/BioPerl-DB-1.006900.tar.gz
Distribution    CJFIELDS/BioPerl-Network-1.006902.tar.gz
Distribution    CJFIELDS/BioPerl-Run-1.006900.tar.gz



cpan>install CJFIELDS/BioPerl-1.6.923.tar.gz 
#now a million things will happen and you should run the tests to make
#sure that it worked

Now you have to set up a local module. For some reason this cpan thing seems to work better and they are begging you to use it. What I have highlighted in pink is what you should change for your home directory.

>perl -e shell -MCPAN
cpan>o conf makepl_arg PREFIX=/Users/loloyohe/My_Local_Perl_Modules
cpan>o conf mbuildpl_arg "--prefix /Users/loloyohe/My_Local_Perl_Modules"
cpan>o conf commit

Should be done now!
Test to see if it worked:

Quit cpan and type in your terminal:

>perl -MBio::Seq -e 0

If there are no errors, you have installed it correctly :)