questions about Ergatis components installation

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questions about Ergatis components installation

gary_xie
Hi, there, 
I am new on Ergatis, so please bear with some my naive questions. We are currently doing Ergatis components installation and encounter following roadblocks.

1) In order to install and config p_func component, the tigr_roles db needs to be installed and modify path in software.config file. 
[component p_func]
$;TIGR_ROLES_DB_DIR$;=/local/db/by_source/jcvi/tigr_roles

Since the download link for tigr_roles db was not documented,  I did the google search, the closest one i can find is the tigrfam2role.db (unix executable file) inside of the lookup table fold of Manatee download site. Is this the right file? 

2) In order to install and config parse_evidence component ,  TIGRFAMs needs to be installed and downloaded from ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
[component parse_evidence]
$;TIGR_ROLES_DB_DIR$;=/local/db/by_source/jcvi/tigr_roles
$;TIGRFAMS_DIR$;=/local/db/by_source/jcvi/TIGRFAMs/latest

There are a lot of links for version 10, do I need to get them all? 
 is it ok to leave the databases compressed (.gz), or should I unzip them?
For example:  Can the tar files containing SEED and HMM files stay tar files? Or do they all have to be untarred?  And if untarred, all to the same directory? or is there a directory structure.  I couldn't find any good documentation.  

3)Here in a paragraph in software.config file
 ;; This is a collection of HMMs.  "coding_hmm" is a concatenation of
;;  PFams, TIGRFams and select others.
$;HMM_ALL$;=/mnt/staging/db/coding_hmm/coding_hmm.lib.bin
$;HMM_LIB_DB$;=/mnt/staging/db/coding_hmm/coding_hmm.lib.db

Can someone explain where to download coding_hmm.lib.bin and coding_hmm/coding_hmm.lib.db and any instruction on how to install them? 

4) j_ortholog_clusters componment is needed for pangenome pipeline. Where can i download it?

Can someone help me out or point out the right direction...
Thanks,
Gary


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