1) To install UMLS-Interface on Windows:
Instructions source:
http://cpansearch.perl.org/src/BTMCINNES/UMLS-Interface-1.39/INSTALL
http://cpansearch.perl.org/src/BTMCINNES/UMLS-Interface-1.39/INSTALL
Stage 1 - Install Perl
I installed 32-bit ActivePerl from here
http://www.activestate.com/activeperl/downloads
http://www.activestate.com/activeperl/downloads
Stage 2 - Install CPAN modules
If you are a newbie (like me), the following link
http://home.ubalt.edu/abento/752/dbi/indexwindows.html
http://home.ubalt.edu/abento/752/dbi/indexwindows.html, can help piece together
info related to Perl, CPAN package, and MySql.
For some users, *ppm* command will not bring up interactive session on command
prompt, but will bring up GUI like here:
http://docs.activestate.com/activeperl/5.10/faq/ActivePerl-faq2.html#ppm_repositories
http://docs.activestate.com/activeperl/5.10/faq/ActivePerl-faq2.html#ppm_repositories.
If using GUI, search for packages using textbox.
After following above, you will have packages DBI, and DBD-mysql installed. For
other packages,
If package is in repository, then installation process is same as above. But if
package is not found in existing repository, then steps to download and install
are:
i. download zipped file from cpan website(***). I prefer saving the extracted
package together with all other packages in the lib directory within the root
Perl installation directory.
ii. cd into package directory and install using following commands:
perl Makefile.PL
nmake
nmake test
nmake install
Windows does not come by default with a c/c++ compiler, nor that it have the
nmake (make in Linux/Unix systems) functionalities. These must be installed
before-hand. I installed Microsoft Visual C++ Express which enables both: 1)
compiling C/C++ via command line; and 2) nmake. After successfully installing
Visual C++, in my experience, neither compiling C/C++ programs nor the nmake
command works unless this:
http://msdn.microsoft.com/en-us/library/f2ccy3wt.aspx
http://msdn.microsoft.com/en-us/library/f2ccy3wt.aspx, is done first in every
newly opened command prompt.
(***) Digest-SHA1: was already present in existing repository; File-Spec:
http://search.cpan.org/~smueller/PathTools-3.40/lib/File/Spec/Functions.pm
http://search.cpan.org/~smueller/PathTools-3.40/lib/File/Spec/Functions.pm;
File-Path: http://search.cpan.org/~dland/File-Path-2.09/Path.pm
http://search.cpan.org/~dland/File-Path-2.09/Path.pm; Text-NSP:
http://search.cpan.org/dist/Text-NSP/ http://search.cpan.org/dist/Text-NSP/
Stage 5 - Load UMLS into MySQL(5.5) related:
Step 2:
Root mysql directory has following configuration file samples: my-huge.ini,
my-large.ini, my-medium.ini, and my-small.ini.
I created a new file called *my.ini* using the Notepad text editor. It's
contents were as below:
# The MySQL server
[mysqld]
port = 3306
socket = /tmp/mysql.sock
key_buffer_size=600M
table_open_cache=300
sort_buffer_size=500M
read_buffer_size=200M
query_cache_limit=3M
query_cache_size=100M
myisam_sort_buffer_size=200M
bulk_insert_buffer_size=100M
join_buffer_size=100M
Step3: Populate the MySQL table using the load scripts
Step G: Modify *my.ini*. It's contents are as below:
# The following options will be passed to all MySQL clients
[client]
user = root
password =
port = 3306
socket = /tmp/mysql.sock
database = umls
# The MySQL server
[mysqld]
port = 3306
socket = /tmp/mysql.sock
key_buffer_size=600M
table_open_cache=300
sort_buffer_size=500M
read_buffer_size=200M
query_cache_limit=3M
query_cache_size=100M
myisam_sort_buffer_size=200M
bulk_insert_buffer_size=100M
join_buffer_size=100M
Stage 6 - Install UMLS-Interface:
From within extracted UMLS-Interface directory, used commands below.
perl Makefile.PL
nmake
nmake test
nmake installFaced some problem in running *nmake test*:
https://groups.yahoo.com/neo/groups/umls-similarity/conversations/messages/358
https://groups.yahoo.com/neo/groups/umls-similarity/conversations/messages/358,
but install was successful.
2) To install UMLS-Similarity on Windows:
Instructions source:
http://cpansearch.perl.org/src/BTMCINNES/UMLS-Similarity-1.35/INSTALL
http://cpansearch.perl.org/src/BTMCINNES/UMLS-Similarity-1.35/INSTALL
From the UMLS-Similarity directory, used commands below.
perl Makefile.PL
nmake
nmake test
nmake
install-------------------------------------------------------------------------------------------------------------------------------
Additional Notes:
1) If any warnings of missing CPAN packages show up when installing
UMLS-Interface or UMLS-Similarity, they can be downloaded from CPAN website and
installed by the same 4-step method as Stage 2.
2) UMLS-Similarity related *nmake test* took about 24 hours to complete.
-------------------------------------------------------------------------------------------------------------------------------
From the forum, Ying's feedback to various questions was especially helpful.
Best wishes.
