This is great! Thank you very much! As you can tell we struggle with Windows questions, so this is very much appreciated.
Cordially, Ted On Sun, Mar 9, 2014 at 4:43 PM, <[email protected]> wrote: > > > 1) To install UMLS-Interface on Windows: > > Instructions source: > 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 > Stage 2 - Install CPAN modules > If you are a newbie (like me), the following link > 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. > 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, 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; > File-Path: http://search.cpan.org/~dland/File-Path-2.09/Path.pm; > 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 install > > Faced some problem in running *nmake test*: > 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 > 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. > > > -- Ted Pedersen http://www.d.umn.edu/~tpederse
