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File Date Author Commit
 DB 2014-06-05 rsanka [r1] Initial commit
 HMM_SCRIPTS_env_var_scripts 2014-06-05 rsanka [r1] Initial commit
 bin 2014-06-05 rsanka [r1] Initial commit
 cgi-bin 2014-06-05 rsanka [r1] Initial commit
 htdocs 2014-06-05 rsanka [r1] Initial commit
 README.txt 2014-06-05 rsanka [r2] Commit of README.

Read Me

SMURF has the following dependencies:
	- Apache2: used (/opt/software/apache2) in cgi-bin/getservers and cgi-bin/getweblogs.
	- LDhmmer-1.5.4: used (/usr/local/packages/LDhmmer-1.5.4) in several hmm files in bin/ directory).
	- hmmsearch tool of HMM-2.3.2: used (/usr/local/bin/hmmsearch) in several scripts in cgi-bin/smurf/pl.
	- Perl: for all perl scripts (cgi-bin/smurf/pl).
	- Perl library CGI: for all cgi scripts (cgi-bin).
	- Sybase OC15: used (/usr/local/packages/sybase) in cgi-bin/smurf/upload.cgi
	- clustalw: used (/usr/local/bin/clustalw) in cgi-bin/smurf/pl/hmm_lib.pl.
	- blastp: used (/usr/local/bin/blastp) in cgi-bin/smurf/pl/hmm_lib.pl.
	- cdbyank: used (/usr/local/bin/cdbyank) in cgi-bin/smurf/pl/hmm_lib.pl.
	- Save and decompress database files in DB and mark location in cgi-bin/smurf/pl/hmm_lib.pl where script refers to them (current set as /usr/local/db/panda/nraa/nraa).
	- Save directory HMM_SCRIPTS_env_var_scripts and mark location in cgi-bin/smurf/upload.cgi where script defines env variable HMM_SCRIPTS (current set as /usr/local/devel/ANNOTATION/hmm/bin).
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