epaule

split off the gffdb step to have its own command-line switch

remove creation of symbolic link and tests for files in GFF directory which is no longer created

added exceptions for length checks for two segmental_duplications which have lengths of more than 100Kb

revised minimum size for remanei make_wormrna.pl

chdir to $ftp directory to avoid problems with accessing the automounted /nfs/disk69/ftp/pub directory

only load ensembl_protein_info.ace for elegans -homol

flipped the reference strand for CIGAR lines based on Lincoln's email.

moved ensembl_protein_info to the homol section

check for existance of the swiss_id2gene hash element

added Feature to Feature connection

split data_sets into misc_data_sets and homol_data_sets

get -misc and -homol switches working correctly for non-elegans species

quietened the wget output

commented out the colours, so that the polar bear country gang can colour it on the website

don't dump the wibbles during the dump step (we need only to update them when the genomes change)

that should be enought o cover Tier I/II with build/currentdb/ftp-server options

Modified output path to CGC as requested by geneace curator.

Split_from and Dead and Made_into_transposon won't give an error now

script to check forum registrants and email them to check validity

reverted gnw person to mt3

makes mysql gff databases for Todd

Minor tweak

Dont throw an error if there are no flanking sequences - there are two features that cant be mapped

welcome back mt3

removed md9

Updated mysql database and port.

geneace_check.pl

Updated mysql database and port.

fixed bug in output of post-translational modification which was not restricting output to only experiments defining that peptide

added some error checks

added promoter and regulatory_region

added a $db->close ... just to be on the safe side

... and removed the last few ensembldir bits

set the new feature sizes to -1

hadcoded the ensembl paths :-(

set the new feature sizes to 1

added genome sequence error and transcription start and end sites

Added new Features and misc_autoace_methods to list of files to be loaded into curation databases post split.

that is a config template for a mysql server running only the myisam engine using a socket (you can't access it, except if you can read/write to the socket itself ... nope, no TCP connections)

so, should work now

removed superfluous "rm $file"

change the startup to be more like batch_kill.pl

upped the maxsize for C.elegans

I don't know where the files end up in the end ... but the script finally works now.

initial commit of the postprocessing script

moved the process_gff file from git to CVS

find the LSF module even if not in path

added md5sums for Todd

script to create blast databases fro Todd

corrected the SO term for transcription_start_site to "TSS"