HISTORY

TAG: mirror_wget-6-0-26-?
DATE: 11/19/2025
wts2-1684/sprt-18/Test new GO Central Load
	new file: current.geneontology.org.goload
        new file: current.geneontology.org.uniprotload
	deleted:  snapshot.geneontology.org.goload
	deleted:  snapshot.geneontology.org.uniprotload

TAG: mirror_wget-6-0-26-4
TAG: mirror_wget-6-0-26-3
DATE: 12/03/2025
wts2-1766/sprt-146/Weekly Mirror www.ebi.ac.uk.arrayexpress.json
comment www.ebi.ac.uk.arrayexpress.json out of packagelist.weekly
        modified:   packagelist.weekly
        deleted:    www.ebi.ac.uk.arrayexpress.json

TAG: mirror_wget-6-0-26-2
DATE: 09/18/2025
wts2-1725/sprt-59/inconsistencies between MGI GPI and GOA_mouse GPI
added ftp.ebi.ac.uk.goload to packagelist.weekly

TAG: mirror_wget-6-0-26-1
DATE: 07/25/2025
wts2-1555/e4g-314/Cross-references changes in UniProt
        new file:   www.uniprot.org.gcrp
        modified:   packagelist.weekly

TAG: mirror_wget-6-0-25-10
DATE: 06/18/2025
        deleted:    ftp.ebi.ac.uk.arrayexpress
        modified:   packagelist.daily

TAG: mirror_wget-6-0-25-9
DATE: 06/18/2025
move GO mirror from daily to weekly
        modified:   packagelist.daily
        modified:   packagelist.weekly

TAG: mirror_wget-6-0-25-8
DATE: 05/20/2025
remove -t 10; use default of 20
        modified:   raw.githubusercontent.com.diseaseontology
        modified:   raw.githubusercontent.com.evidenceontology
        modified:   raw.githubusercontent.com.mp_hp
        modified:   raw.githubusercontent.com.sequenceontology

TAG: mirror_wget-6-0-25-7
DATE: 04/22/2025
wts2-1647/e4g-220/Retire neXtProt from MGI
#	modified:   packagelist.weekly
#	deleted:    download.nextprot.org   

TAG: mirror_wget-6-0-25-6
DATE: 04/18/2025
e4g-215 femover - IMSR file interaction
#	get IMSR files for the mover

TAG: mirror_wget-6-0-25-5
TAG: mirror_wget-6-0-25-4
DATE: 03/31/2025
wts2-562/e4g-207/mapping RNA central ids to MGI genes (TR13445)
#	new file: ftp.ebi.ac.uk.gornacentral

TAG: mirror_wget-6-0-25-3
TAG: mirror_wget-6-0-25-2
TAG: mirror_wget-6-0-25-1
DATE: 02/04/2025, 03/25/2025
e4g-127/Process Alliance File to Load SNP_ConsensusSnp_Marker
#	modified:   alliancegenome.org.variants

TAG: mirror_wget-6-0-24-5
DATE: 12/03/2024
as part of the wts2-1109/e4g-13/postgres upgrade/IT training
removed "remote_user=anonymous
removed "remote_password=mgscron@informatics.jax.org"
#	deleted:    ftp.informatics.jax.org.imsr

TAG: mirror_wget-6-0-24-4
DATE: 12/02/2024
wts2-1585/e4g-88/Jax Pheno Strain Info Curl Issue
#	new file:   phenome.jax.org
#       modified:   packagelist.weekly

TAG: mirror_wget-6-0-24-3
DATE: 11/19/2024
wts2-1580/e4g-77/mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
#       deleted:    bhmgiimsr01.jax.org.imsr_allStrains
#       new file:   bhmgiimsr02lp.jax.org.imsr_allStrains
#       modified:   packagelist.weekly

TAG: mirror_wget-6-0-24-2
DATE: 08/29/2024
wts2-1528/fl2-951/Add NCBI regulatory regions/biological_region to MGIreg.gff3 file
#       new file:   ftp.ncbi.nih.gov.regulator

TAG: mirror_wget-6-0-24-1
DATE: 08/26/2024
wts2-1540/fl2-955/added --no-check-certificate
#       modified:   data.glygen.org

TAG: mirror_wget-6-0-23-3
DATE: 04/09/2024
remove unused go files
#       modified:   packagelist.daily

TAG: mirror_wget-6-0-23-2
TAG: mirror_wget-6-0-23-1
DATE: 03/29/2024
wts2-1155/GOC taking over GOA mouse, GOA human, etc.
wts2-575/fl2-743/Add GlyGen links to MGI gene detail pages (TR13475)
#       new file:   data.glygen.org
#       new file:   snapshot.geneontology.org.goload
#
#       modified:   ftp.ebi.ac.uk.goload
#       modified:   ftp.ebi.ac.uk.interpro
#       modified:   packagelist.daily
#       modified:   packagelist.weekly
#       modified:   purl.obolibrary.org.hp.obo
#
#       renamed:    ftp.geneontology.org.external2go -> snapshot.geneontology.org.uniprotload
#       
#       deleted:    bhmgiimsrtest-01lt.jax.org.imsr_allStrains
#       deleted:    cgd.jax.org
#       deleted:    ftp.geneontology.org.goload
#       deleted:    research.bioinformatics.udel.edu
#       deleted:    snapshot.geneontology.org.goload.noctua
#

TAG: mirror_wget-6-0-22-19
DATE: 11/14/2023
STAFF: dbm
CHANGES:
Remove cgd.jax.org: retired genmapload

TAG: mirror_wget-6-0-22-18
DATE: 10/20/2023
STAFF: sc
CHANGES: updated www.gentar.org.es_cell
The targetedalleleload was turned off/archived on 10/19/23
 We continue to download the file for qc reports

TAG: mirror_wget-6-0-22-17
DATE: 06/27/2023
STAFF: dbm
CHANGES:
www.findmice.org.imsrwi: ignore robots.txt file that causes 404 error

TAG: mirror_wget-6-0-22-16
DATE: 05/12/2023
STAFF: lec
CHANGES:
wts2-1095/fl2-149/Mouse models of human disease report (1)
wts2-1120/fl2-204/Mouse models of human disease report (2)
bhmgiimsrtest-01lt.jax.org.imsr_allStrains

TAG: mirror_wget-6-0-22-15
TAG: mirror_wget-6-0-22-14
DATE: 05/03/2023
STAFF: sc
CHANGES: fl2-315 - download alliance human coord file. New package
    alliancegenome.org.human_coordload
rm ftp.ncbi.nih.gov.mapview (old human coord package)

TAG: mirror_wget-6-0-22-13
DATE: 04/11/2023
STAFF: dbm
CHANGES:
1) purl.obolibrary.org.ma.obo: retired package
2) purl.obolibrary.org.mod.obo: retired package
3) www.genetraps.org.igtc: retired package
4) www.gensat.org.EntrezGeneIds: retired package
5) www.sequenceontology.org.current_release.obo: retired package
fl2-278 clean-up

TAG: mirror_wget-6-0-22-12
DATE: 03/24/2023
STAFF: lec
CHANGES:
wts2-1143/fl2-258/snapshot.geneontology.org.goload.noctua

TAG: mirror_wget-6-0-22-11
DATE: 02/21/2023
STAFF: lec
CHANGES:
wts2-1125/fl2-220/Modify the Noctua load to only include the noctua_mgi file. 

TAG: mirror_wget-6-0-22-10
TAG: mirror_wget-6-0-22-9
STAFF: sc
CHANGES: wts2-1037
    ftp.ensembl.org.mouse_regulatory - updated the hardcoded filename to a wildcard - date suffix 
    changes with each release. Also, this was never added to packagelist.weekly

TAG: mirror_wget-6-0-22-8
DATE: 11/29/2022
STAFF: sc
CHANGES: www.gentar.org.crispr - changed url to mgi_initial_crispr
This is for the new 9 col file provided by Robert

TAG: mirror_wget-6-0-22-7
DATE: 11/14/2022
STAFF: sc
CHANGES: http://wts.informatics.jax.org/searches/tr.detail.cgi?TR_Nr=11893
Return Human Gene-Associated Diseases from HMDC Pheno Queries
Added raw.githubusercontent.com.mp_hp and listed it in packagelist.weekly

TAG: mirror_wget-6-0-22-6
DATE: 10/13/2022
STAFF: sc
CHANGES: wts2-412 Skip load processing if input files do not exist (TR12754) 
ftp.geneontology.org.goload - set do_deletes=false
download_package - report when deleting local files

TAG: mirror_wget-6-0-22-5
DATE: 09/30/2022
STAFF: sc
CHANGES: wts2-558
* remove www.mousephenotyping.reports mirror
* added:
  * www.gentar.org.mgi_crispr
  * www.gentar.org.mgi_modification
  * www.gentar.org.mgi_es_cell
  * www.gentar.org.mgi_phenotyping
 

TAG: mirror_wget-6-0-22-4
DATE: 09/20/2022
STAFF: dbm
CHANGES:
wts2-982/Update Xenbase link

TAG: mirror_wget-6-0-22-3
DATE: 08/31/2022
STAFF: dbm
CHANGES:
wts2-969/Update EBI FTP link for InterPro files

TAG: mirror_wget-6-0-22-2
TAG: mirror_wget-6-0-22-1
TAG: mirror_wget-6-0-21-3
DATE: 07/21/2022, 07/25/2022, 08/01/2022
STAFF: lec
CHANGES:
wts2-646/ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen : keep

TAG: mirror_wget-6-0-21-2
DATE: 07/07/2022
STAFF: dbm
CHANGES:
1) www.uniprot.org.pirsfload: new URL to get the input file

TAG: mirror_wget-6-0-21-1
DATE: 07/05/2022
STAFF: lec
CHANGES:
wts2-921/TSS_Region (SO:0001240) is obsolete

TAG: mirror_wget-6-0-19-1
DATE: 04/12/2022
STAFF: lec
CHANGES:
wts2-808/New OMIM load API key/modify OMIM load/data.omim.org.omim

TAG: mirror_wget-6-0-18-2
TAG: mirror_wget-6-0-18-1
DATE: 03/08/2022
STAFF: lec
CHANGES:
wts2-813/Load ENSEMBL and VISTA Regulatory Elements/ftp.ensembl.org.mouse_regulatory
ftp.ncbi.nih.gov.entrez_gene/re-added mim2gene_medgen:

TAG: mirror_wget-6-0-17-6
DATE: 12/30/2021
STAFF: sc
CHANGES:
1) remove mygene.info.wikipedia
2) remove mygene.info.wikipedia from pakagelist.weekly

TAG: mirror_wget-6-0-17-5
DATE: 10/18/2021
STAFF: dbm
CHANGES:
1) ftp.nextprot.org.nextprot: removed - ftp site is no longer available
2) download.nextprot.org: new package
3) packagelist.weekly: replaced nextprot package file name

TAG: mirror_wget-6-0-17-4
DATE: 10/15/2021
STAFF: dbm
CHANGES:
1) data.omim.org.omim: revert certificate change because Mike updated the certificate on our servers to allow the connection

TAG: mirror_wget-6-0-17-3
DATE: 10/14/2021
STAFF: dbm
CHANGES:
1) data.omim.org.omim: added "--no-check-certificate" option to wget call
                       because the mirror was failing certification

TAG: mirror_wget-6-0-17-2
DATE: 06/16/2021
STAFF: sc
CHANGES: removed ftp.proteininformationresource.org.pirsfload and call in
    packagelist.weekly

TAG: mirror_wget-6-0-17-1
DATE: 06/10/2021
STAFF: sc
CHANGES: WTS2-620 - new package file for pirsfload www.uniprot.org.pirsfload
        need to remove ftp.proteininformationresource.org.pirsfload
        once load is tested

TAG: mirror_wget-6-0-16-19
TAG: mirror_wget-6-0-16-18
DATE: 05/04/2021
STAFF: dbm
CHANGES:
1) removed: ftp.pir.georgetown.edu.pirsfload
2) added: ftp.proteininformationresource.org.pirsfload
3) modified: packagelist.weekly with new package name

TAG: mirror_wget-6-0-16-17
DATE: 04/27/2021
STAFF: lec
CHANGES:
wts2-606/Human gene COV report has mouse genes
alliancegenome.org.humandisease

TAG: mirror_wget-6-0-16-16
DATE: 04/26/2021
STAFF: dbm
CHANGES:
1) removed ftp.ncbi.nih.gov.unigene
2) removed ftp.ncbi.nih.gov.unists

TAG: mirror_wget-6-0-16-15
DATE: 04/16/2021
STAFF: sc
CHANGES: TR11349
1) deleted ftp.ensembl.org.mouse_gff3.v92
2) updated ftp.ensembl.org.mouse_gff3

TAG: mirror_wget-6-0-16-14
DATE: 04/12/2021
STAFF: sc
CHANGES: TR13484 retire mirroring of genbank & refseq release files
# deleted:    ftp.ncbi.nih.gov.gbRel
# deleted:    ftp.ncbi.nih.gov.refseqVertebrate
# deleted:    packagelist.refseq.release
# modified:   packagelist.genbank.release, removed ftp.ncbi.nih.gov.gbRel

TAG: mirror_wget-6-0-16-13
DATE: 04/06/2021
TAFF: sc
CHANGES: TR13349 - Build39 project
alliancegenome.org.humandisease - new for public covid human disease rpt
alliancegenome.org.orthology - updated with static url

TAG: mirror_wget-6-0-16-12
DATE: 04/05/2021
STAFF: dbm
CHANGES: TR13481
1) alliancegenome.org.gene_descriptions: New package for GO text load
2) packagelist.daily: Added new package

TAG: mirror_wget-6-0-16-11
DATE: 03/19/2021
STAFF: sc
CHANGES: tr13349 - remove ftp.ncbi.nih.gov.homologene
it is not being called by any of the  packagelist scripts
see tag mirror_wget-6-0-12-8

TAG: mirror_wget-6-0-16-10
DATE: 03/04/2021
STAFF: lec
CHANGES:
TR13471/Changes to Proper places to get GO mapping files
ftp.geneontology.org.external2go

TAG: mirror_wget-6-0-16-9
DATE: 02/24/2021
STAFF: dbm
CHANGES:
1) ftp.hgu.mrc.ac.uk.emage: removed - obsolete
2) packagelist.daily: remove ftp.hgu.mrc.ac.uk.emage

TAG: mirror_wget-6-0-16-8
DATE: 02/23/2021
STAFF: dbm
CHANGES: TR13468
1) compbio.charite.de.phenotype_annotation: removed - obsolete
2) purl.obolibrary.org.phenotype.hpoa: new
3) packagelist.weekly: updated with new package name

TAG: mirror_wget-6-0-16-7
DATE: 01/27/2021
STAFF: sc
CHANGES: Added package to download Alliance Homology
        Added package to weekly package list

TAG: mirror_wget-6-0-16-6
DATE: 09/28/2020
STAFF: sc
CHANGES: packagelist.weekly - moved sprot and trembl
    packages to end of list. See comment at top of the
    file

TAG: mirror_wget-6-0-16-5
DATE: 09/28/2020
STAFF: sc
CHANGES:
TR13235 www.ebi.ac.uk.arrayexpress.json

TAG: mirror_wget-6-0-16-4
DATE: 09/22/2020
STAFF: lec
CHANGES:
TR13390/raw.githubusercontent.com.diseaseontology : change "master" to "main"

TAG: mirror_wget-6-0-16-3
DATE: 09/01/2020
STAFF: lec
CHANGES: TR13272/GO meeting/CalTech/tasks to-do
remove: purl.obolibrary.org.ro

TAG: mirror_wget-6-0-16-2
DATE: 08/31/2020
STAFF: sc
CHANGES: B39 assembly mirror 

TAG: mirror_wget-6-0-16-1
DATE: 08/25/2020
STAFF: lec
CHANGES: TR13272/GO meeting/CalTech/tasks to-do
add: purl.obolibrary.org.ro

TAG: mirror_wget-6-0-15-3
DATE: 05/04/2020
STAFF: lec
CHANGES: TR13299
remove: purl.obolibrary.org.pr.obo
add: purl.obolibrary.org.pr

TAG: mirror_wget-6-0-15-1
DATE: 03/02/2020
STAFF: sc
CHANGES: TR13275
1)  compbio.charite.de.phenotype_annotation - changed file path at source

TAG: mirror_wget-6-0-14-9
DATE: 12/17/2019
STAFF: dbm
CHANGES:
1) update compbio.charite.de.phenotype_annotation with new file path

TAG: mirror_wget-6-0-14-8
DATE: 11/13/2019
STAFF: dbm
CHANGES:
1) Remove pir.georgetown.edu.proisoform package (obsolete)
2) Remove pir.georgetown.edu.proisoform from packagelist.daily

TAG: mirror_wget-6-0-14-7
TAG: mirror_wget-6-0-14-6
TAG: mirror_wget-6-0-14-5
DATE: 09/23/2019
STAFF: sc
CHANGES: typo in ftp.ncbi.nih.gov.refseqVertebrate
    causing download of extraneous files
download_files - For refseq, first rm/make directory (to start fresh) 
    then download

TAG: mirror_wget-6-0-14-4
DATE: 08/19/2019
STAFF: lec
CHANGES: TR13132
data.omim.org.omim : change to "https"

TAG: mirror_wget-6-0-14-3
DATE: 06/04/2019
STAFF: lec
CHANGES: TR13052
remove: research.bioinformatics.udel.edu
replaced with: proconsortium.org
changed: purl.obolibrary.org.pr.obo

TAG: mirror_wget-6-0-14-2
DATE: 04/22/2019
STAFF: sc
CHANGES:
TR13065 - update to mirror refseq vertebrate instead of entire
    release

TAG: mirror_wget-6-0-14-1
DATE: 04/11/2019
STAFF: lec
CHANGES: TR13081
* remove dmdd.org.uk.htmpload
* remove from packagelist.weekly

TAG: mirror_wget-6-0-13-13
DATE: 04/03/2019
STAFF: sc
CHANGES: TR13065 - moving from refseq complete release
to vertebrate only. Changes:
* remove ftp.ncbi.nih.gov.refseqRel
* add ftp.ncbi.nih.gov.refseqVertebrate
* update packagelist.refseq.release

TAG: mirror_wget-6-0-13-12
TAG: mirror_wget-6-0-13-11
DATE: 03/26/2019
STAFF: sc
CHANGES: TR13059 - new URL/filename

TAG: mirror_wget-6-0-13-10
DATE: 03/13/2019
STAFF: sc
CHANGES: TR13054 - new omim/hpo annotload file
updated: compbio.charite.de.phenotype_annotation

TAG: mirror_wget-6-0-13-9
TAG: mirror_wget-6-0-13-8
DATE: 01/30/2019
STAFF: lec
CHANGES: 
TR13011/noctua
TR13029/CFP/goc
obsolete: build.berkeleybop.org.gpad.goload
obsolete: build.berkeleybop.org.goload
added CFP to this new package
new : snapshot.geneontology.org.goload.noctua

TAG: mirror_wget-6-0-13-7
TAG: mirror_wget-6-0-13-6
TAG: mirror_wget-6-0-13-5
DATE: 01/28/2019
STAFF: lec
CHANGES: 
TR13011
obsolete: build.berkeleybop.org.gpad.goload
new : snapshot.geneontology.org.goload.noctua
put the obsoleted package back in due to GO/input issues.

TAG: mirror_wget-6-0-13-4
DATE: 1/3/2019
STAFF: dbm
CHANGES: 
1) packagelist.daily: removed www.gensat.org.EntrezGeneIds because the gensat
                      site is not operational (per Connie)
TAG: mirror_wget-6-0-13-3
DATE: 12/11/2018
STAFF: dbm
CHANGES: 
added "/custom" to URL in www.genenames.org.hgnc to get hgnc.tsv file

TAG: mirror_wget-6-0-13-2
DATE: 12/05/2018
STAFF: jsb
CHANGES: 
added raw.githubusercontent.com.sequenceontology (SO vocab) for DADT release;
added it to packagelist.weekly

TAG: mirror_wget-6-0-13-1
DATE: 11/30/2018
STAFF: sc
CHANGES: www.ebi.ac.uk.impc.json - add back in LOCAL_DIR=$REMOTE_SITE
so file is downloaded to the proper place for the impc htmpload to find
it. TR12994

TAG: mirror_wget-6-0-12-10
DATE: 09/13/2018
STAFF: lec
CHANGES:
TR12955/purl.obolibrary.org.go-basic.obo changes

TAG: mirror_wget-6-0-12-9
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.hgu.mrc.ac.uk.emage from packagelist.daily

TAG: mirror_wget-6-0-12-8
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.ncbi.nih.gov.homologene from packagelist.weekly

TAG: mirror_wget-6-0-12-7
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.ncbi.nih.gov.mapview from packagelist.weekly

TAG: mirror_wget-6-0-12-6
TAG: mirror_wget-6-0-12-5
DATE: 08/29/2018
STAFF: sc
CHANGES: TR12044 - New HGNC biomart call
www.genenames.org.hgnc - updated biomart url

TAG: mirror_wget-6-0-12-4
DATE: 08/15/2018
STAFF: lec
CHANGES: TR12918/change in goload/gorefgen (PAINT)
add snapshot.geneontology.org.goload
remove paint from ftp.geneontology.org.goload

TAG: mirror_wget-6-0-12-3
DATE: 07/12/2018
STAFF: sc
CHANGES: TR12115
add new crispr file to www.mousephenotype.org.reports

TAG: mirror_wget-6-0-12-2
DATE: 05/10/2018
STAFF: sc
CHANGES: TR12734 - saved ftp.ensembl.org.mouse_gff3 as ftp.ensembl.org.mouse_gff3.v91
 updated ftp.ensembl.org.mouse_gff3 to v92

TAG: mirror_wget-6-0-12-1
DATE: 04/26/2018
STAFF: lec  
CHANGES: TR12834/new GO qualifiers & pr.gpad file 
build.berkeleybop.org.gpad.goload : new url, add pr.gpad

TAG: mirror_wget-6-0-11-11
DATE: 04/05/2018
STAFF: sc
CHANGES: TR12734 Added ftp.ensembl.org.mouse_gff3 and packagelist.gff3.release

TAG: mirror_wget-6-0-11-10
DATE: 03/28/2018
STAFF: lec
CHANGES: 
add '--no-check-certificate' to purl.obolibrary.org.pr.obo

TAG: mirror_wget-6-0-11-9
DATE: 03/19/2018
STAFF: lec
CHANGES: TR12827/PRO_mgi.txt
mv ftp.pir.georgetown.edu.proload to https://research.bioinformatics.udel.edu

TAG: mirror_wget-6-0-11-8
DATE: 03/15/2018
STAFF: sc
CHANGES: TR12817
www.mousephenotype.org.reports - add --no-check-certificate

TAG: mirror_wget-6-0-11-7
DATE: 03/05/2018
STAFF: lec
CHANGES:
moved into packagelist.daily
purl.obolibrary.org.pr.obo
pir.georgetown.edu.proisoform

TAG: mirror_wget-6-0-11-6
DATE: 03/01/2018
STAFF:
CHANGES: TR12802
 rm ftp.sanger.ac.uk.vega_cdna ftp.sanger.ac.uk.vega_gtf ftp.sanger.ac.uk.vega_ncrna ftp.sanger.ac.uk.vega_prot

TAG: mirror_wget-6-0-11-5
TAG: mirror_wget-6-0-11-4
DATE: 02/05/2018, 03/01/2018
STAFF: lec
CHANGES:
1) TR12783
purl.obolibrary.org.pr.obo : new
ftp.pir.georgetown.edu.proisoform : obsolete

TAG: mirror_wget-6-0-11-3
DATE: 12/11/2017
STAFF: dbm
CHANGES:
1) dmdd.org.uk.htmpload: Updated remote path to file

TAG: mirror_wget-6-0-11-2
DATE: 11/13/2017
STAFF: sc
CHANGES: TR12662/GMC Project
1) remove ontologies.berkeleybop.org.uberon - we will use the already downloaded obo 
   file instead.

TAG: mirror_wget-6-0-11-1
DATE: 11/09/2017
STAFF: sc
CHANGES: TR12662/GMC Project
1) added new package: ontologies.berkeleybop.org.uberon to packagelist.daily

TAG: mirror_wget-6-0-10-2
DATE: 07/10/2017
STAFF: dbm
CHANGES:
1) run_mirror.sh: New script to download package lists
2) run_mirror_logged.sh: New wrapper for downloading/logging in radar
3) packagelist.daily: New daily package list
4) packagelist.weekly: New weekly package list
5) packagelist.weekly.logged: New weekly logged package list
6) packagelist.genbank.release: New Genbank release package list
7) packagelist.refseq.release: New Refseq release package list
8) ftp.ncbi.nih.gov.refseqRel: Removed release*.removed-records.gz
9) dailycron.sh, weeklycron.sh, weeklycron-logged.sh,
       genbankRel.sh, refseqRel.sh, check_mirror_logs.sh: Retired

TAG: mirror_wget-6-0-10-1
DATE: 06/08/2017
STAFF: sc
CHANGES: TR12083 seqdeleter fix
1) add ftp.ncbi.nih.gov.refseq_deletes to dailycron.sh

TAG: mirror_wget-6-0-9-2
DATE: 04/06/2017
STAFF: lec
CHANGES: TR12504/IMPC/lacZ
new file:   www.ebi.ac.uk.impc_lacz_alz.json
new file:   www.ebi.ac.uk.impc_lacz_elz.json

TAG: mirror_wget-6-0-9-1
DATE: 04/04/2017
STAFF: sc
CHANGES: Merge tr12488 to trunk

TAG: mirror_wget-tr12488-2
DATE: 03/23/2017
STAFF: lnh
CHANGES:scrum bob contigs epic
1) removed ftp.ncbi.nih.gov.gbGenomicRel and gbGenomicRel.sh -
   restored gb release contig files in ftp.ncbi.nih.gov.gbRel 
2) removed ftp.ncbi.nih.gov.refseqGenomicRel and refseqGenomicRel.sh -
   Added RefSeq genomic files in ftp.ncbi.nih.gov.refseqGenomicRel

DATE: 03/22/2017
STAFF: sc
CHANGES:scrum bob contigs epic
1) removed gb release contig files from ftp.ncbi.nih.gov.gbRel created 
    ftp.ncbi.nih.gov.gbGenomicRel
2) new:
    ftp.ncbi.nih.gov.gbGenomicRel - genbank genomic release package file
    ftp.ncbi.nih.gov.refseqGenomicRel - refseq genomic release package file
    genbankGenomicRel.sh - run adhoc genbank genomic mirror
    refseqGenomicRel.sh - run adhoc refseq genomic mirror

TAG: mirror_wget-tr12488-1
DATE: 03/14/2017
STAFF: sc
CHANGES:scrum bob contigs epic
1) add contig non-cums to ftp.ncbi.nih.gov.gbNC
2) add contig release files to ftp.ncbi.nih.gov.gbRel

TAG: no tag needed
DATE: 02/28/2017
STAFF: lec
CHANGES: 
1) TR12504/www.ebi.ac.uk.impc_lacz.json

TAG: mirror_wget-6-0-7-4
DATE: 02/07/2017
STAFF: lec
CHANGES: 
1) added ftp.pir.georgetown.edu.proisoform to weeklycron.sh

TAG: mirror_wget-6-0-7-3
DATE: 01/26/2017
STAFF: lec
CHANGES: 
1) www.ebi.ac.uk.impc_lacz.json fix

TAG: mirror_wget-6-0-7-2
DATE: 01/20/2017
STAFF: lec
CHANGES: 
TR12447/DMDD phenotype data load
1) dmdd.org.uk.htmpload
2) weeklycron.sh

TAG: mirror_wget-6-0-7-1
DATE: 1/4/2017
STAFF: dbm
CHANGES: 
1) emnet.informatics.jax.org.imsr_allStrains: removed package
2) bhmgiimsr01.jax.org.imsr_allStrains: added package
3) weeklycron.sh: replaced emnet package with bhmgiimsr01 package

TAG: mirror_wget-6-0-6-??
DATE: 01/03/2017
STAFF: lec
CHANGES: 
1) TR12427/Disease Ontology (DO)
raw.githubusercontent.com.diseaseontology

TAG: mirror_wget-6-0-6-11
DATE: 12/19/2016
STAFF: lec
CHANGES: 
1) TR12486/raw.githubusercontent.com.evidenceontology
purl.obolibrary.org.eco.obo/removed/obsolete

TAG: mirror_wget-6-0-6-10
DATE: 12/08/2016
STAFF: lec
CHANGES: 
1) TR12474/build.berkeleybop.org.goload
remote directory changed

TAG: mirror_wget-6-0-6-9
DATE: 12/01/2016
STAFF: lec
CHANGES: 
1) TR12468/build.berkeleybop.org.gpad.goload
remote directory changed

TAG: mirror_wget-6-0-6-8
DATE: 11/28/2016
STAFF: lec
CHANGES: 
1) weeklycron.sh : added pir.georgetown.edu.proisoform

TAG: mirror_wget-6-0-6-7
DATE: 11/10/2016
STAFF: lec
CHANGES: 
1) ftp.ncbi.nih.gov.homologene/pub.HomologGene/current/homologene.data
has not been updated since 5/6/2014
removing from dailycron.sh

TAG: mirror_wget-6-0-6-6
DATE: 10/25/2016
STAFF: lec
CHANGES: 
1) purl.obolibrary.org.cl-basic.obo
moved from dailycron.sh to weeklycron.sh

TAG: mirror_wget-6-0-6-4
DATE: 10/05/2016
STAFF: lec
CHANGES: TR12427/DO (Disease Ontology)
1) raw.githubusercontent.com.diseaseontology
2) weeklycron.sh : added DO

TAG: mirror_wget-6-0-6-3
DATE: 09/27/2016
STAFF: sc
CHANGES: TR12370 - GXD HT project
* www.ebi.ac.uk.arrayexpress.json - updated to fetch four years of data

TAG: mirror_wget-6-0-6-2
TAG: mirror_wget-6-0-6-1
DATE: 09/08/2016
STAFF: lec
CHANGES: TR12349/TR12345/gone-dor + more/gpad, 
TR12378/adding isoforms
remove human from ftp.geneontology.org.goload

build.berkeleybop.org.goload
build.berkeleybop.org.gpad.goload
ftp.ebi.ac.uk.goload
ftp.geneontology.org.goload

TAG: mirror_wget-6-0-5-7
DATE: 08/03/2016
STAFF: lec
CHANGES: TR12345/gpad, TR12378/adding isoforms
new: ftp.ebi.ac.uk.goload : add goa_human.gaf.gz, goa_human_isoform.gaf.gz

TAG: mirror_wget-6-0-5-6
TAG: mirror_wget-6-0-5-5
DATE: 08/01/2016
STAFF: lec
CHANGES: TR12345/gpad, TR12378/adding isoforms
ftp.ebi.ac.uk.goload : add goa_mouse_isoform.gaf.gz
build.berkeleybop.org.gpad.goload : added for goload/goamousenoctua

TAG: mirror_wget-6-0-5-4
DATE: 07/13/2016
STAFF: lec
CHANGES:
1) ftp.ebi.ac.uk.goload
there is not HISTORY for 6-0-5-1, 2, 3?

TAG: mirror_wget-6-0-4-15
TAG: mirror_wget-6-0-4-14
DATE: 07/01/2016
STAFF: lnh
CHANGES:
1) ftp.ncbi.nih.gov.gbRel: Converted it to new format
2) ftp.ncbi.nih.gov.refseqRel: Converted it to new format
3) Added wrapper scripts genbankRel.sh and refseqRel.sh 
   to run Genbank release and Refseq release packages

TAG: mirror_wget-tr12317-1
DATE: 05/11/2016
STAFF: sc
CHANGES: updated URL to exclude MGP and EUPH' www.ebi.ac.uk.impc.json

TAG: mirror_wget-tr12317-BP
DATE: 05/11/2016
STAFF: sc
CHANGES: Branch Point Tag TR12317 IMPC ri data

TAG: mirror_wget-6-0-4-13
TAG: mirror_wget-6-0-4-12
TAG: mirror_wget-6-0-4-11
DATE: 06/28/2016
STAFF: lnh
CHANGES:
1) www.genenames.org.hgnc: Added a new variable 'is_xml_query'
2) download_package: Added a check for 'is_xml_query' variable 
3) weeklycron.sh: Scheduled the www.genenames.org.hgnc package 

TAG: mirror_wget-6-0-4-10
DATE: 06/28/2016
STAFF: lec
CHANGES:

for new proisoformload:
1) ftp.pir.georgetown.edu.proisoform
2) pir.georgetown.edu.proisoform

for proload/documentation
rename:
ftp.pir.georgetown.edu.pro_ids
to
ftp.pir.georgetown.edu.proload
and moved to weeklycron.sh

for pirsfload:
rename:
ftp.pir.georgetown.edu.iproclass
to:
ftp.pir.georgetown.edu.pirsfload
and moved to weeklycron.sh

TAG: mirror_wget-6-0-4-9
DATE: 06/16/2016
STAFF: dbm
CHANGES:
1) ftp.ebi.ac.uk.interpro: remote directory changed from "Current" to "current"

TAG: mirror_wget-6-0-4-8
TAG: mirror_wget-6-0-4-7
TAG: mirror_wget-6-0-4-6
DATE: 06/14/2016, 06/16/2016
STAFF: lec
CHANGES: TR12340/GOA file name changes
1) ftp.geneontology.org.gene-associations  -> ftp.geneontology.org.goload
2) ftp.geneontology.org.gene-associations.paint  -> ftp.geneontology.org.goload
3) dailycron2.sh merged into dailycron.sh

TAG: mirror_wget-6-0-4-5
TAG: mirror_wget-6-0-4-4
TAG: mirror_wget-6-0-4-3
TAG: mirror_wget-6-0-4-2
DATE: 06/01/2016
STAFF: lec
CHANGES: 

removed from dailycron.sh (obsolete):
www.sequenceontology.org.current_release.obo
www.genetrap.igtc
purl.obolibrary.org.emap.obo purl.obolibrary.org.ma.obo purl.obolibrary.org.mod.obo

removed from dailycron.sh/weeklycron.sh : on demand only:
ftp.ncbi.nih.gov.unigene

removed:
purl.obolibrary.org.emap.obo

TAG: mirror_wget-6-0-4-1
DATE: 05/31/2016
STAFF: lec
CHANGES: TR12340/GOA file name changes
1) ftp.geneontology.org.gene-associations 
2) ftp.ebi.ac.uk.goa
3) removing ANNOTATIONS variable
4) adding github repository name (load name) to "comment" variable

TAG: mirror_wget-6-0-3-7
DATE: 04/19/2016
STAFF: lnh
CHANGES: TR 12327
1) dailycron.sh: Added ftp.sanger.ac.uk.vega_ncrna package

TAG: mirror_wget-6-0-3-6
DATE: 04/18/2016
STAFF: lnh
CHANGES: TR 12327
1) mirror_lock: Removed step that sources th Configuration 
2) ftp.sanger.ac.uk.vega_ncrna: Added VEGA ncrna package

TAG: mirror_wget-6-0-3-5
DATE: 04/15/2016
STAFF: lnh
CHANGES:
1) check_mirror_logs.sh: Added support the email recipient modification - EMAIL_TO
1) Configuration.default: Added the email recipient variable - EMAIL_TO

TAG: mirror_wget-6-0-3-4
DATE: 04/15/2016
STAFF: lnh
CHANGES: 
1) Configuration.default: Added setting path and sourcing master config 
2) All the wrapper script: dailycron* weeklycron* - 
   removed sourcing of live mgiconfig master.config script

TAG: mirror_wget-6-0-3-3
DATE: 04/14/2016
STAFF: lnh
CHANGES: TR12266 - Retire mirror_ftp
1) Added an Install script to create the Configuration file
2) Configuration.default:
    Moved the DATADOWNLOADS and MIRRORLOG setting in the Configuration file
3) download_package script: Removed the host server restriction

TAG: mirror_wget-6-0-3-2
DATE: 04/13/2016
STAFF: lnh
CHANGES: TR12266 - Retire mirror_ftp
1) Migrated all mirror_ftp packages to mirror_wget
2) Converted mirror_wget daily and weekly packages to the new format
3) Wrote mirror_check_log script and scheduled it to be called by
   daily and weekly mirrors wrapper scripts
4) Converted all the wraper scripts to sh shell
5) Removed obsolete packages as needed

TAG: mirror_wget-6-0-3-1
DATE: 03/31/2016
STAFF: lec
CHANGES: TR12273/IMPC load (htmpload)
1) www.mousephenotype.org : add new imits report (mp2_load_phenotyping_colonies_report.tsv)
2) remove : ikmc.vm.bytemark.co.uk

TAG: mirror_wget-6-0-2-10
DATE: 3/08/2016
STAFF: sc
CHANGES: TR12273/IMPC load (htmpload)
1) www.mousephenotype.org : add new imits report (mp2_load_phenotyping_colonies_report.tsv)
2) remove : ikmc.vm.bytemark.co.uk

TAG: mirror_wget-6-0-2-10
DATE: 3/08/2016
STAFF: sc
CHANGES: TR12267
2) added:  purl.obolibrary7.org using wget to ht -O option so local filepath 
   does not reflect the redirect path from the site. replaces i
   purl.obolibrary8.org (as I skipped 8 inadvertently)
2) updated weeklycron.csh to reflect above

TAG: mirror_wget-6-0-2-8
DATE: 3/07/2016
STAFF: sc
CHANGES: TR12267 - this is a BAD tag

TAG: mirror_wget-6-0-2-8
DATE: 3/04/2016
STAFF: sc
CHANGES: TR12267
1) added: compbio.charite.de and purl.obolibrary8.org
2) added above to weeklycron.csh

TAG: mirror_wget-6-0-2-7
DATE: 2/25/2016
STAFF: lnh
CHANGES: TR12225
1)ftp.ebi.ac.uk_goa: Added support to download GPAD and GPI files 
     in addition to the GAF file

TAG: mirror_wget-6-0-2-6
DATE: 2/09/2016
STAFF: sc
CHANGES: TR12026 entering IMPC lacZ data into GXD
1) www.ebi.ac.uk2 - added embryonic LacZ to URL

TAG: mirror_wget-6-0-2-5
DATE: 2/2/2016
STAFF: dbm
CHANGES: TR12163
1) data.omim.org: New - get omim.txt from new location
2) weeklycron.csh: Added data.omim.org package

TAG: mirror_wget-6-0-2-4
DATE: 2/01/2016
STAFF: sc
CHANGES: TR12026 entering IMPC lacZ data into GXD
1. added www.ebi.ac.uk2 - to adhoc mirror the lacZ datafile. This 
   is NOT included in any of the wrapper scripts

TAG: mirror_wget-6-0-2-3
DATE: 1/19/2016
STAFF: dbm
CHANGES:
1) ftp.xenbase.org: Overwrite log files so previous errors don't persist

TAG: mirror_wget-6-0-2-2
TAG: mirror_wget-6-0-2-1
DATE: 12/11/2015
STAFF: 
CHANGES:
1) TR12070/12011:added ikmc.vm.bytemark.co.uk for imits

TAG: mirror_wget-6-0-1-2
DATE: 11/27/2015
STAFF: 
CHANGES: TR12148
1) added mygene.info package
2) added mygene.info to weeklycron.csh

TAG: mirror_wget-6-0-1-1
DATE: 11/2/2015
STAFF: lec
CHANGES:
1) TR12070/add purl.obolibrary6.org/uberon.obo file

TAG: mirror_wget-6-0-0-4
DATE: 09/17/2015
STAFF: lec
CHANGES:
1) TR12011/12070/www.mousephenotype.org
2) obsolete: www.sanger.ac.uk5

TAG: mirror_wget-6-0-0-3
DATE: 09/11/2015
STAFF: lec
CHANGES:
1) TR12011/12070/www.mousephenotype.org
2) obsolete:
www.i-dcc.org2
www.i-dcc.org3
www.i-dcc.org_imits
make sure '/data/downloads/www.i-dcc.org' is also removed

TAG: mirror_wget-6-0-0-2
DATE: 09/09/2015
STAFF: lec
CHANGES:
1) TR12011/12070/www.mousephenotype.org

TAG: mirror_wget-6-0-0-1
DATE: 07/24/2015
STAFF: lec
CHANGES:
1) TR11750/postgres

DATE: 07/07/2015
STAFF: kstone
CHANGES:
1) moving ftp.ebi.ac.uk from mirror_ftp
2) moving radar-dependent scripts of ftp.ncbi.nih.gov from mirror_ftp

TAG: mirror_wget-5-2-1-20
TAG: mirror_wget-5-2-1-19
TAG: mirror_wget-5-2-1-18
DATE: 05/06/2015
STAFF: lec
CHANGES: 
obsolete:
1) www.i-dcc.org4
2) www.i-dcc.org1
3) func.med.harvard.edu
4) www.europhenome.org

TAG: mirror_wget-5-2-1-17
TAG: mirror_wget-5-2-1-16
DATE: 02/25/2015
STAFF: sc
CHANGES: TR11888 - added ftp.xenbase.org

TAG: mirror_wget-5-2-1-15
DATE: 02/23/2015
STAFF: lnh
CHANGES:
1) added lock_dir to ftp.ncbi.nih.gbRel

TAG: mirror_wget-5-2-1-14
TAG: mirror_wget-5-2-1-13
DATE: 01/29/2015
STAFF: lnh 
CHANGES:- TR11918 
1)    ftp.ncbi.nih.gov.refseqRel: Changed the mirror download base directory from release/vertebrate_mammalian to release/complete
2)    Created a new directory called complete under ${DATADOWNLOADS}/refseq/
3)    ftp.ncbi.nih.gov.refseqRel : Added a step to also download the release*.removed-records.gz file
4)    ftp.ncbi.nih.gov.refseqRel: Added step to download the release number file

TAG: mirror_wget-5-2-1-12
DATE: 01/28/2015
STAFF: lnh
CHANGES:
1) added mirror_lock to ftp.ncbi.nih.gbRel
2) added the update day check to ftp.ncbi.nih.gbRel 

TAG: mirror_wget-5-2-1-11
DATE: 01/28/2015
STAFF: sc
CHANGES: 
1) renamed www.zfin.* to zfin.*
2) weeklycron.csh - updated per above 

TAG: mirror_wget-5-2-1-10
DATE: 01/07/2015
STAFF: sc
CHANGES: TR11887
1) renamed geisha.arizona.edu --> geisha.arizona.expr.edu
2) added geisha.arizona.orthos.edu
3) added both to weeklycron.csh

TAG: mirror_wget-5-2-1-9
DATE: 01/07/2015
STAFF: sc
CHANGES: Update to look for/create uniprot lock file in parent directory
  (/data/downloads/uniprot), because this is where seqdb_engine places read
   locks, rather than trembl and swissprot directories
  (/data/downloads/uniprot/trembl /data/downloads/uniprot/swissprot)

TAG: mirror_wget-5-2-1-8
DATE: 01/07/2015
STAFF: sc
CHANGES: TR11721 - Establish gene-based links to ZFIN expression data
1) renamed www.zfin.org to www.zfin.xpat.org
2) added www.zfin.gene.org and www.zfin.mouse_ortho.org
3) weeklycron.csh - added above three files

TAG: mirror_wget-5-2-1-7
DATE: 01/05/2014
STAFF: sc
CHANGES: bug in ftp.ebi.ac.uk. Removed rm* from swissprot and trembl AFTER
the lock files created.

TAG: mirror_wget-5-2-1-6
DATE: 12/30/2014
STAFF: dbm
CHANGES:
1) Removed packages for files that are no longer used: www.genenames.org,
   www.sanger.ac.uk2, www.sanger.ac.uk3, www.sanger.ac.uk4
2) dailycron.csh: removed www.genenames.org
3) weeklytasks.csh: removed www.sanger.ac.uk packages

TAG: mirror_wget-5-2-1-5
DATE: 12/23/2014
STAFF: dbm
CHANGES:
1) check_mirror_logs.csh: use "-i" to ignore case with grep commands

TAG: mirror_wget-5-2-1-4
DATE: 12/18/2014
STAFF: sc
CHANGES: TR11886 - M&M project
1) Added www.genenames_hgnc.org to get HGNC human/mouse homologies and
    added to weeklytasks.csh

TAG: mirror_wget-5-2-1-3
DATE: 12/17/2014
STAFF: kstone
CHANGES: Adding allStrains.csv report from IMSR

TAG: mirror_wget-5-2-1-2
TAG: mirror_wget-5-2-1-1
DATE: 12/03/2014
STAFF: sc
CHANGES: merge tr11674 branch to trunk

TAG: mirror_wget-5-2-0-6
DATE: 10/14/2014
STAFF: dbm
CHANGES:
1) added check_mirror_logs.csh - copy of script from mirror_ftp

TAG: mirror_wget-5-2-0-5
DATE: 10/13/2014
STAFF: sc
CHANGES: TR11796
1) added ftp.ebi.ac.uk to weeklycron.csh

TAG: mirror_wget-5-2-0-4
DATE: 10/?/2014
STAFF: sc
CHANGES: TR11796
1) added ftp.ebi.ac.uk to mirror swissprot/trembl sequences; uses lock files
2) added mirror_lock

TAG: mirror_wget-5-2-0-3
DATE: 10/08/2014
STAFF: lec
CHANGES: TR11654
removed in weeklycron.csh
1) geisha.arizona.edu
2) www.zfin.org
3) weeklycron.csh - added

TAG: mirror_wget-5-2-0-2
DATE: 10/03/2014
STAFF: sc
CHANGES: TR11754 added:
* ftp.ncbi.nih.gov.gbRel 
* ftp.ncbi.nih.gov.refseqRel

TAG: mirror_wget-5-2-0-1
TAG: mirror_wget-5-1-9-1
DATE: 09/05/2014, 09/15/2014
STAFF: lec
CHANGES:TR11654 - geisha.arizona.edu
1) geisha.arizona.edu
2) www.zfin.org
3) weeklycron.csh - added

TAG: mirror_wget-tr11674-2
DATE: 08/20/2014
STAFF: sc
CHANGES:
1) www.i-dcc.org_imits - added fetch of 8 new columns for curator use only
2)  www.ebi.ac.uk - filter out 'EuroPhenome', set rows=100000, limit to just fields we want

TAG: mirror_wget-tr11674-1
DATE: 08/01/2014
STAFF: sc
CHANGES: 
1. added: www.i-dcc.org_imits and www.ebi.ac.uk
2. added above to weekly script

TAG: mirror_wget-tr11674-BP
DATE: 08/01/2014
STAFF: sc
CHANGES: tr11674 branch point tag

TAG: mirror_wget-5-1-7-4
DATE: 04/11/2014
STAFF: dbm
CHANGES:
1) TR11613/removed www.ebi.ac.uk package because the input file will now
           come from the mirror_ftp product
2) TR11613/removed monthlycron.csh since www.ebi.ac.uk was the only package
           that it was downloading

TAG: mirror_wget-5-1-7-3
DATE: 03/21/2014
STAFF: lec
CHANGES:
1) TR11615/added emnet.informatics.jax.org2

TAG: mirror_wget-5-1-7-2
DATE: 02/07/2014
STAFF: lec
CHANGES:
1) TR11515/added emnet.informatics.jax.org:48080

TAG: mirror_wget-5-1-7-1
DATE: 02/05/2014
STAFF: lec
CHANGES:
1) TR11515/added www.mousephenotype.org

TAG: mirror_wget-5-1-5-6
DATE: 11/22/2013
STAFF: dbm
CHANGES:
1) dailycron.csh, weeklycron.csh, monthlycron.csh: echo package name
2) purl.obolibrary.org, www.genenames.org,
   www.gensat.org, www.sanger.ac.uk2,
   www.sanger.ac.uk3, www.sanger.ac.uk4: send wget stdout to /dev/null

TAG: mirror_wget-5-1-5-5
DATE: 10/04/2013
STAFF: sc
CHANGES: TR11455 
1) www.i-dcc.org3 get  'escell_ikmc_project_id' instead of 'ikmc_project_id'

TAG: mirror_wget-5-1-5-4
TAG: mirror_wget-5-1-5-3
TAG: mirror_wget-5-1-5-2
DATE: 09/10/2013
STAFF: lec
CHANGES:
1) see TR11367/new version of wget installed
2) new purl.obolibrary.org version

TAG: mirror_wget-5-1-5-1
DATE: 09/03/2013
STAFF: dbm
CHANGES: TR11475
1) dailycron.csh, monthlycron.csh, weeklycron.csh: remove "-x" option

TAG: mirror_wget-5-1-4-7
TAG: mirror_wget-5-1-4-6
DATE: 08/27/2013
STAFF: lec
CHANGES:
1) TR11470/add build.berkeleybop.org

TAG: mirror_wget-5-1-4-5
DATE: 07/25/2013
STAFF: sc
CHANGES:
1) www.ncbi.nlm.nih.gov - removed per TR11433
2) mouse.brain-map.org - removed per Lori/Connie. abaload no longer available.
 
TAG: mirror_wget-5-1-4-4
DATE: 07/22/2013
STAFF: lec
CHANGES: 
1) weeklycron.csh: TR11442/remove www.europhenome.org temporarily

TAG: mirror_wget-5-1-4-3
DATE: 07/12/2013
STAFF: sc
CHANGES: TR11396 
1) www.i-dcc.org2 AND www.i-dcc.org3 - updated pipeline in the URL
2) *.csh -fx for linux

TAG: mirror_wget-5-1-4-2
DATE: 07/12/2013
STAFF: sc
CHANGES: 
1) www.sanger.ac.uk - obsolete, was replaced by www.sanger.ac.uk3
2) dailycron.csh - removed www.sanger.ac.uk

TAG: mirror_wget-5-1-4-1
DATE: 06/13/2013
STAFF: sc
CHANGES: TR.. mary will create 
1) added: purl.obolibrary1.org - purl.obolibrary5.org for mary dolan
2) dailytasks.csh added above

TAG: mirror_wget-5-1-3-2
DATE: 05/18/2013
STAFF: dbm
CHANGES: 
1) Bug fix - The URL and LOG need to be tab-separated in the package file in
   order for the dailycron script to separate them properly. This was fixed
   in www.genetrap.org, www.sanger.ac.uk, www.sequenceontology.org and
   purl.obolibrary.org

TAG: mirror_wget-5-1-3-1
DATE: 04/30/2013
STAFF: sc
CHANGES: TR11367
1) Added purl.obolibrary.org
2) add purl.obolibrary.org to dailycron.csh

TAG: mirror_wget-5-1-2-1 
DATE: 4/01/2013
STAFF: sc
CHANGES: merge tr6519 changes to trunk

TAG: mirror_wget-tr6519-3
DATE: 3/25/2013
STAFF: sc
CHANGES:
1) 1) www.i-dcc.org3 - reversed the change in tr6519-2

TAG: mirror_wget-tr6519-2
DATE: 2/15/2013
STAFF: sc
CHANGES:
1) www.i-dcc.org3 - updated <Attribute name="ikmc_project_id"> 
    to <Attribute name="targeting_vector_ikmc_project_id">

TAG: mirror_wget-tr6519-1
DATE: 1/31/2013
STAFF: sc
CHANGES: 
1) www.i-dcc.org3 - added mutation_subtype fo targetedalleleload

TAG: mirror_wget-tr6519-BP
DATE: 1/31/2013
STAFF: sc
CHANGES: Branch point tag for N2MO 
1) www.i-dcc.org3 - added mutation_subtype fo targetedalleleload

TAG: mirror_wget-5-1-1-1
DATE: 12/04/2012
STAFF: sc
CHANGES: www.i-dcc.org*
1) updated "mutation_subtype" to "mutation_type"
2) updated uniqueRows="0" to uniqueRows="1"

TAG: mirror_wget-5-0-10-7
TAG: mirror_wget-5-0-10-6
TAG: mirror_wget-5-0-10-5
DATE: 10/29/2012
STAFF: lec
CHANGES: 
1) added www.europhenome.org
download the europhenome biomart mammalian phenotype data (TR10273)

TAG: mirror_wget-5-0-10-4
TAG: mirror_wget-5-0-10-3
TAG: mirror_wget-5-0-10-2
DATE: 08/28/2012, 09/20/2012
STAFF: lec
CHANGES: 
1) added www.sanger.ac.uk5
download the sanger biomart mammalian phenotype data (TR10273)
2) remove "pipeline" from download and set 'uniqueRows="1"'

TAG: mirror_wget-5-0-10-1
DATE: 04/20/2012
STAFF: jmason
CHANGES: 
1) added www.i-dcc.org4 (download mirko data from sanger)

TAG: mirror_wget-4-4-2-2
DATE: 03/23/2012
STAFF: sc
CHANGES: TR11011
1) added www.gensat.org
2) dailycron.csh - added above

TAG: mirror_wget-4-4-2-1
DATE: 10/19/2011
STAFF: dbm
CHANGES:
1) Moved www.i-dcc.org packages from dailycron to weeklycron

TAG: mirror_wget-4-4-1-3
DATE: 04/28/2010
STAFF: jmason
CHANGES:
1) Add CSD and EUCOMM and NorCOMM clone downloads from IDCC biomart

TAG: mirror_wget-4-4-1-2
TAG: mirror_wget-4-4-1-1
DATE: 02/03/2010
STAFF: jmason
CHANGES:
1) updated the norcomm download parameters to sort the file by cassette before
   saving it

TAG: mirror_wget-4-4-0-3
DATE: 11/18/2010
STAFF: jmason
CHANGES:
1) updated the norcomm download parameters to include more columns

TAG: mirror_wget-4-4-0-2
DATE: 11/17/2010
STAFF: jmason
CHANGES:
1) added wget script to get norcomm allele data from IKMC 
   targeting repository mart (i-dcc.org)
2) added task to dailytasks cron to execute the new norcomm
   file download

TAG: mirror_wget-4-4-0-1
DATE: 10/04/2010
STAFF: dbm
CHANGES:
1) Changed www.ebi.ac.uk to reflect new path for gene_identifiers.txt

TAG: mirror_wget-4-3-4-3
TAG: mirror_wget-4-3-4-2
TAG: mirror_wget-4-3-4-1
DATE: 07/15/2010
DATE: 07/06/2010
STAFF: lec
CHANGES:
1) TR9316/cgd.jax.org

TAG: mirror_wget-4-3-3-1
DATE: 04/20/2010
STAFF: sc
CHANGES: TR6839
1) added www.sequenceontology.org
2) dailycron.csh - added above

TAG: mirror_wget-4-3-2-2
DATE: 02/19/2010
STAFF: jmason
CHANGES:
1) Do not unzip the file after downloading

TAG: mirror_wget-4-3-2-1
DATE: 02/19/2010
STAFF: jmason
CHANGES:
1) added www.sanger.ac.uk4 for Sanger allele file (TR10090)
2) updated dailycron.csh

TAG: mirror_wget-4-3-1-1
DATE: 11/06/2009
STAFF: dbm
CHANGES:
1) added www.ebi.ac.uk for Array Express (TR9097)
2) added monthlycron.csh

TAG: mirror_wget-4-2-0-1
DATE: 02/25/2009
STAFF: dbm
CHANGES:
1) TR9388 - added func.med.harvard.edu for MouseFunc

TAG: mirror_wget-4-1-2-1
DATE: 09/24/2008
STAFF: sc
CHANGES:
1) TR9278 - new komp mirror

TAG: mirror_wget-4-1-0-2
DATE: 08/20/2008
STAFF: sc
CHANGES: 
1) TR9222 - update hcop url
2) fix weeklycron.csh - abaload url file was being invoked  
   incorrectly

TAG: mirror_wget-4-1-0-1
DATE: 08/19/2008
STAFF: sc
CHANGES: TR9209
1) added www.sanger.ac.uk2 for KOMP project

TAG: mirror_wget-4-0-0-1
DATE: 03/25/2008
STAFF: lec
CHANGES: TR8769
1) added www.brain-map.org for Allen Brain Atlas
2) added to weeklycron.csh

TAG: mirror_wget-3-5-4-4
TAG: mirror_wget-3-5-4-3
TAG: mirror_wget-3-5-4-2
DATE: 09/13/2007
STAFF: sc
CHANGES: TR8494 
1) added www.sanger.ac.uk for KOMP project

TAG: mirror_wget-3-5-4-1
DATE: 08/13/2007
STAFF: sc
CHANGES: TR8441
1) added www.genetrap.org for KOMP project

TAG: mirror_wget-3-5-1-6
TAG: mirror_wget-3-5-1-5
TAG: mirror_wget-3-5-1-4
DATE: 03/02/2007
STAFF: sc
CHANGES: TR8123 
1) www.gene.acl.ac.uk not part
 of 3-5-1-4. Added revised version found in 
 Lori's home directory which sends wget
 explicit output file path
2) Configuration.default - removed DATADIR
3) replaced DATADIR with DATADOWNLOADS
4) www.gene.ucl.ac.uk - use wget param to specify
   output file - was creating output file named
   hcop_data.cgi?species=mus&lite=1&Search=Submit

DATE: 01/29/2007
STAFF: lec
CHANGES:
1) TR8123;added www.gene.ucl.ac.uk and weeklycron.csh

TAG: mirror_wget-3-5-1-3
TAG: mirror_wget-3-5-1-2
DATE: 12/14/2006
STAFF: sc
CHANGES:
1) added index.html

TAG: mirror_wget-3-5-1-1
DATE: 10/06/2006
STAFF: lec
CHANGES:
1) TR7894

TAG: mirror_wget-1-0-1
TAG: mirror_wget-1-0-0
DATE: 01/08/2004
STAFF: lec
CHANGES: