Genbank updates: Difference between revisions

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(change procedure due to switch to git)
Line 11: Line 11:
           ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs
           ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs
           ~/kent/src/hg/makeDb/genbank/etc/rr.dbs
           ~/kent/src/hg/makeDb/genbank/etc/rr.dbs
       please remove the name, don't comment it out, cvs keeps the file edit history.
       and commit.  Please remove the name, don't comment it out, git keeps the file edit history.
    -> cvs update in this directory (cvs up -dP /cluster/data/genbank/etc)
     -> ssh hgwbeta
     -> ssh hgwbeta
     -> cd /genbank/etc
     -> cd ~/kent/src/hg/makeDb/genbank
     -> cvs update /genbank/etc on hgwbeta (cvs up -dP)
     -> git pull
    -> make etc-update-rr
     -> cd to /cluster/data/genbank/data/ftp/${assembly}  
     -> cd to /cluster/data/genbank/data/ftp/${assembly}  
     -> remove /cluster/data/genbank/data/ftp/${assembly}  
     -> remove /cluster/data/genbank/data/ftp/${assembly}  

Revision as of 00:46, 16 June 2010

To disable genbank updates to an assembly:

In addition to removing the assembly name from the hgwbeta.dbs and rr.dbs files, the files here need to be removed:

/cluster/data/genbank/data/ftp/

Otherwise the genbank files will keep reappearing.

So, to disable a genome:

   -> on hgwdev remove the assembly name from these files: 
          ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs
          ~/kent/src/hg/makeDb/genbank/etc/rr.dbs
      and commit.  Please remove the name, don't comment it out, git keeps the file edit history.
   -> ssh hgwbeta
   -> cd ~/kent/src/hg/makeDb/genbank
   -> git pull
   -> make etc-update-rr
   -> cd to /cluster/data/genbank/data/ftp/${assembly} 
   -> remove /cluster/data/genbank/data/ftp/${assembly} 
   -> remove files on hgdownload by sending a push request to drop this directory and its contents:
          /usr/local/apache/htdocs/goldenPath/${assembly}