Skip to content

Gramene ensembl oge6 #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
weix-cshl wants to merge 20 commits into
base: master
Choose a base branch
from
Open

Gramene ensembl oge6 #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
d1538d1
check in for release3
Apr 27, 2022
24b1388
check in for release3
Apr 27, 2022
a840353
config release 4
weix-cshl Apr 29, 2022
b514f69
checkin images
weix-cshl Oct 12, 2022
60accbf
checkin modules
weix-cshl Oct 12, 2022
39c65fc
checkin docs
weix-cshl Oct 12, 2022
53c34b8
checkin confs
weix-cshl Oct 12, 2022
158a75f
remove useless files
weix-cshl Oct 12, 2022
eb98df9
update release version
weix-cshl Oct 12, 2022
36070bc
Merge branch 'gramene-ensembl-oge5' into gramene-ensembl-oge4
ajo2995 Oct 12, 2022
7ee7d10
Merge pull request #7 from warelab/gramene-ensembl-oge4
ajo2995 Oct 12, 2022
7599fd4
for gramene-ensembl-oge6
weix-cshl Jan 9, 2023
fcbf7f4
commit changes for gramene-ensembl-oge6
weix-cshl Jan 9, 2023
b7d4cbf
commit changes for gramene-ensembl-oge6
weix-cshl Jan 9, 2023
c5d9d62
updated release6 notes
weix-cshl Jan 13, 2023
7be9749
updated release6 notes
weix-cshl Jan 13, 2023
ff37a41
check in
weix-cshl May 21, 2023
07a2b15
update ZS97 about page
weix-cshl May 23, 2023
d8e63d1
add changes for e108
weix-cshl Jul 22, 2024
b699a59
add species_stats_cshl.pl
weix-cshl Jul 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
523 changes: 0 additions & 523 deletions gramene/conf/MartDefs.pm
View file
Open in desktop

This file was deleted.

22 changes: 0 additions & 22 deletions gramene/conf/Plugins.pm
View file
Open in desktop

This file was deleted.

20 changes: 0 additions & 20 deletions gramene/conf/Plugins.pm.eg
View file
Open in desktop

This file was deleted.

232 changes: 118 additions & 114 deletions gramene/conf/SiteDefs.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,133 +1,137 @@

package EnsEMBL::Gramene::SiteDefs;
use strict;

# These are the gramene-specific edits to the main Ensembl SiteDefs.pm file
sub update_conf {
$SiteDefs::ENSEMBL_PORT = 8888;
#$SiteDefs::ENSEMBL_PROXY_PORT = 80;
$SiteDefs::ENSEMBL_SERVERNAME = 'oryza-ensembl.gramene.org';
#$SiteDefs::ENSEMBL_PROTOCOL = 'https';
$SiteDefs::ENSEMBL_BASE_URL = 'https://oryza-ensembl.gramene.org/';
$SiteDefs::SITE_RELEASE_VERSION = 7;
$SiteDefs::SITE_RELEASE_DATE = 'Jul 2023';
#'May 2022';

#$SiteDefs::ENSEMBL_SERVERNAME = 'ensembl.gramene.org';
$SiteDefs::ENSEMBL_SERVERNAME = 'ensembl-dev.gramene.org';

$SiteDefs::ENSEMBL_MAX_PROCESS_SIZE = 2000000;
$SiteDefs::ENSEMBL_BASE_URL = $SiteDefs::ENSEMBL_SERVERNAME;
$SiteDefs::SITE_RELEASE_VERSION = 58;
# $SiteDefs::SITE_RELEASE_VERSION_EG = 40;
$SiteDefs::SITE_RELEASE_DATE = 'July 2018';
$SiteDefs::SITE_NAME = 'Gramene';
$SiteDefs::ENSEMBL_SITETYPE = 'Gramene-Ensembl Plants';
$SiteDefs::SITE_FTP = 'ftp://ftp.gramene.org/pub';
$SiteDefs::PE_URL = 'http://plants.ensembl.org';
$SiteDefs::ENSEMBL_PORT = 80;
$SiteDefs::ENSEMBL_PROXY_PORT = 80; # Port used for self-referential URLs
$SiteDefs::ENSEMBL_USER = 'nobody';#getpwuid($>);
$SiteDefs::ENSEMBL_GROUP = 'nobody';#getgrgid($));
$SiteDefs::DIVISION = 'plants';
$SiteDefs::EG_DIVISION = 'plants';
$SiteDefs::SUBDOMAIN_DIR = 'plants';
$SiteDefs::ENSEMBL_SITETYPE = 'Ensembl Plants';
$SiteDefs::SITE_NAME = 'GrameneOryza';
$SiteDefs::SITE_FTP = 'http://ftp.gramene.org/oryza';
$SiteDefs::PE_URL = 'http://plants.ensembl.org';

$SiteDefs::ENSEMBL_SERVERADMIN = 'weix@cshl.edu';
$SiteDefs::ENSEMBL_MAIL_SERVER = 'localhost';
$SiteDefs::ENSEMBL_USER = 'nobody';#getpwuid($>);
$SiteDefs::ENSEMBL_GROUP = 'nobody';#getgrgid($));
$SiteDefs::ENSEMBL_SERVERADMIN = 'weix@cshl.edu';
$SiteDefs::ENSEMBL_MAIL_SERVER = 'localhost';

$SiteDefs::MAX_PROCESS_SIZE = 2000000;
$SiteDefs::GRAPHIC_TTF_PATH = "/usr/share/fonts/msttcorefonts/";
$SiteDefs::MAX_PROCESS_SIZE = 2000000;
# this is defined in default.ini
#$SiteDefs::GRAPHIC_TTF_PATH = "/usr/share/fonts/msttcorefonts/";


$SiteDefs::SAMTOOLS_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/samtools';
$SiteDefs::SAMTOOLS_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/samtools';

$SiteDefs::ENSEMBL_DEBUG_FLAGS = 0; # 24;
$SiteDefs::ENSEMBL_LONGPROCESS_MINTIME = 10;

$SiteDefs::EBEYE_REST_ENDPOINT = 'http://data.gramene.org/ebeye' . $SiteDefs::SITE_RELEASE_VERSION;

$SiteDefs::ENSEMBL_TOOLS_PERL_BIN = '/usr/local/bin/perl';
$SiteDefs::ENSEMBL_TMP_DIR_BLAST = $SiteDefs::ENSEMBL_SERVERROOT."/blastqueue";
$SiteDefs::ENSEMBL_BLASTSCRIPT = $SiteDefs::ENSEMBL_WEBROOT."/utils/runblast.pl";

# $SiteDefs::ENSEMBL_BLAT_BIN_PATH = '/usr/local/ucscblat/blat';
# $SiteDefs::ENSEMBL_BLAT_TWOBIT_DIR = '/usr/local/ucscblat/';
$SiteDefs::ENSEMBL_NCBIBLAST_BIN_PATH = '/usr/local/ncbi-blast-2.2.30+/bin'; # path to blast executables
# $SiteDefs::ENSEMBL_NCBIBLAST_MATRIX = '/path/to/ncbi-blast/data'; # path to blast matrix files
$SiteDefs::ENSEMBL_NCBIBLAST_DATA_PATH_DNA = "/usr/local/blastdb/ncbi_blast/genomic"; # path for the blast DNA index files
$SiteDefs::ENSEMBL_NCBIBLAST_DATA_PATH = "/usr/local/blastdb/ncbi_blast/genes"; # path for the blast index files (other than DNA)
$SiteDefs::ENSEMBL_REPEATMASK_BIN_PATH = '/usr/local/RepeatMasker'; # path to RepeatMasker executable
$SiteDefs::ASSEMBLY_CONVERTER_BIN_PATH = '/usr/local/bin/CrossMap.py';
$SiteDefs::ENSEMBL_CHAIN_FILE_DIR = '/usr/local/ensembl-live/tools_data/assembly_chain';

$SiteDefs::ENSEMBL_VEP_CACHE_DIR = "/usr/local/ensembl-live/tools_data/vep/";
$SiteDefs::ENSEMBL_VEP_PLUGIN_DATA_DIR = "/usr/local/ensembl-live/tools_data/vep/Plugins"; # path to vep plugin data files on the LSF host (or local machine if job running locally)


$SiteDefs::DATAFILE_ROOT = '/usr/local'; ## Base path for ro data files
$SiteDefs::DATAFILE_BASE_PATH = '/usr/local/vcf';

#$SiteDefs::EBEYE_REST_ENDPOINT = 'https://data.gramene.org/oryza-ebeye4';
$SiteDefs::EBEYE_REST_ENDPOINT = 'http://squam:21007';

# This should be set by the plugin, but not working. Need to hard code!
#@SiteDefs::ENSEMBL_PERL_DIRS =
# ( $SiteDefs::ENSEMBL_WEBROOT.'/perl',
# $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-common/perl',
# $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-plants/perl',
# );

$SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Oryza_sativa';
$SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Arabidopsis_thaliana';

# $SiteDefs::ENSEMBL_DATASETS

#$SiteDefs::PRODUCTION_NAMES = ['Oryza_sativa'];

$SiteDefs::ENSEMBL_DATASETS = [sort qw(
Oryza_aus
Oryza_barthii
Oryza_brachyantha
Oryza_carolina
Oryza_glaberrima
Oryza_glumaepatula
Oryza_indica
Oryza_indicair8
Oryza_meridionalis
Oryza_nivara
Oryza_punctata
Oryza_rufipogon
Oryza_sativa
Oryza_sativa117425
Oryza_sativa125619
Oryza_sativa125827
Oryza_sativa127518
Oryza_sativa127564
Oryza_sativa127652
Oryza_sativa127742
Oryza_sativa128077
Oryza_sativa132278
Oryza_sativa132424
Oryza_sativaazucena
Oryza_sativair64
Oryza_sativakitaake
Oryza_sativamh63
Oryza_sativazs97
Leersia_perrieri
Arabidopsis_thaliana
Chlamydomonas_reinhardtii
Drosophila_melanogaster
Selaginella_moellendorffii
Sorghum_bicolor
Vitis_vinifera
Zea_maysb73
Zea_maysb73v4
), qw(
)];

push @$SiteDefs::ENSEMBL_EXTRA_INC, '/usr/local/ensembl-live/htslib', '/usr/local/BioPerl-1.6.922', '/usr/local/ensembl-live/ensembl-io/modules', '/usr/local/ensembl-live/ensembl-funcgen/modules', '/usr/local/ensembl-live/ensembl-variation/modules';


$SiteDefs::ENSEMBL_VEP_SCRIPT_DEFAULT_OPTIONS = { # Default options for command line vep script (keys with value undef get ignored)
'host' => 'colden', # Database host (defaults to ensembldb.ensembl.org)
'user' => 'weix', # Defaults to 'anonymous'
'password' => 'warelab', # Not used by default
'port' => 3306, # Defaults to 5306
'fork' => 4, # Enable forking, using 4 forks
};

#----------
# User database
$SiteDefs::ENSEMBL_USERDB_NAME = 'ensembl_accounts'; #changed to ensembl_accounts lately
$SiteDefs::ENSEMBL_USERDB_USER = 'gramene_web';
$SiteDefs::ENSEMBL_USERDB_HOST = 'colden.cshl.edu';
$SiteDefs::ENSEMBL_USERDB_PORT = 3306;
$SiteDefs::ENSEMBL_USERDB_PASS = 'gram3n3';

#----------
# Logging
$SiteDefs::ENSEMBL_LOGDIR = $SiteDefs::ENSEMBL_SERVERROOT."/logs";
$SiteDefs::ENSEMBL_PIDFILE = "$SiteDefs::ENSEMBL_LOGDIR/httpd.pid";
$SiteDefs::ENSEMBL_ERRORLOG = "$SiteDefs::ENSEMBL_LOGDIR/error.log";
$SiteDefs::ENSEMBL_CUSTOMLOG = "$SiteDefs::ENSEMBL_LOGDIR/access.log combined";
#our $ENSEMBL_LOGDIR = defer { "$ENSEMBL_SYS_DIR/logs/$ENSEMBL_SERVER_SIGNATURE" }; # Path for log files
#our $ENSEMBL_PIDFILE = defer { "$ENSEMBL_LOGDIR/httpd.pid" }; # httpd process id
#our $ENSEMBL_ERRORLOG = defer { "$ENSEMBL_LOGDIR/error_log" }; # Error log file
#our $ENSEMBL_CUSTOMLOG = defer { "$ENSEMBL_LOGDIR/access_log ensembl_extended" };


#----------
# Mart/Blast
$SiteDefs::ENSEMBL_BLAST_ENABLED = 1; # Creates header link for blast
$SiteDefs::ENSEMBL_BLAST_BY_SEQID = 1; # blast on gene page sequence
$SiteDefs::ENSEMBL_MART_ENABLED = 1; # And mart

$SiteDefs::ENSEMBL_VEP_ENABLED = 1;
$SiteDefs::ENSEMBL_AC_ENABLED = 1;
$SiteDefs::ENSEMBL_IDM_ENABLED = 0;
$SiteDefs::ENSEMBL_FC_ENABLED = 0;
$SiteDefs::ENSEMBL_LD_ENABLED = 0;
$SiteDefs::ENSEMBL_VP_ENABLED = 0;
$SiteDefs::ENSEMBL_DS_ENABLED = 0;

push @SiteDefs::ENSEMBL_HTDOCS_DIRS, # Needed due to EG plugin
$SiteDefs::ENSEMBL_SERVERROOT.'/biomart-perl/htdocs';

#----------
# Temp files
#$SiteDefs::ENSEMBL_TMP_URL = "/ens-tmp";

#----------
#GeoLiteCity database file
$SiteDefs::GEOCITY_DAT = $SiteDefs::ENSEMBL_SERVERROOT.'/geocity/GeoLiteCity.dat';

#----------
# Paths and so on
# This should be set by the plugin, but not working. Need to hard code!
# push @SiteDefs::ENSEMBL_PERL_DIRS, $SiteDefs::ENSEMBL_SERVERROOT
# .'/gramene-live/ensembl-plugins/gramene/perl';

#----------
# Species stuff

$SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Oryza_sativa'; # Default
$SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Arabidopsis_thaliana';
#%SiteDefs::__species_aliases =
# (
# These are supplimental species to EnsemblGenomes
# %SiteDefs::__species_aliases,
# 'Zea_mays' => [('zea_mays', 'zm','maize')],
# 'Physcomitrella_patens' => [('physcomitrella_patens', 'pp','physcomitrella')],
# 'Arabidopsis_thaliana' => [('arabidopsis_thaliana')],
# );
# push(@{$SiteDefs::__species_aliases{'Populus_trichocarpa'}},'poplar');
#push @SiteDefs::ENSEMBL_HTDOCS_DIRS, $SiteDefs::ENSEMBL_SERVERROOT. '/../biomarts/plants/biomart-perl/htdocs';

#$SiteDefs::DOCSEARCH_INDEX_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-plants/data/docsearch';

#$SiteDefs::ENA_COLLECTION_ID = 224;

#$SiteDefs::ENA_SAMPLE_SEQ = "MDDCRFETSELQASVMISTPLFTDSWSSCNTANCNGSIKIHDIAGITYVAIPAVSMIQLGNLVGLPVTGDVLFPGLSSDEPLPMVDAAILKLFLQLKIKEGLELELLGKKLVVITGHSTGGALAAFTALWLLSQSSPPSFRVFCITFGSPLLGNQSLSTSISRSRLAHNFCHVVSIHDLVPRSSNEQFWPFGTYLFCSDKGGVCLDNAGSVRLMFNILNTTATQNTEEHQRYGHYVFTLSHMFLKSRSFLGGSIPDNSYQAGVALAVEALGFSNDDTSGVLVKECIETATRIVRAPILRSAELANELASVLPARLEIQWYKDRCDASEEQLGYYDFFKRYSLKRDFKVNMSRIRLAKFWDTVIKMVETNELPFDFHLGKKWIYASQFYQLLAEPLDIANFYKNRDIKTGGHYLEGNRPKRYEVIDKWQKGVKVPEECVRSRYASTTQDTCFWAKLEQAKEWLDEARKESSDPQRRSLLREKIVPFESYANTLVTKKEVSLDVKAKNSSYSVWEANLKEFKCKMGYENEIEMVVDESDAMET";

#$SiteDefs::GXA = 1;

#$SiteDefs::ENSEMBL_HMMER_ENABLED = 1;

$SiteDefs::ENSEMBL_BLAST_ENABLED = 1; # Creates header link for blast
$SiteDefs::ENSEMBL_BLAST_BY_SEQID = 1; # blast on gene page sequence

$SiteDefs::NCBIBLAST_REST_ENDPOINT = 'http://squam:2502'; #brie:5202';

$SiteDefs::ENSEMBL_TOOLS_LIST = [
'Blast' => 'BLAST/BLAT',
# 'VEP' => 'Variant Effect Predictor',
#'FileChameleon' => 'File Chameleon',
# 'AssemblyConverter' => 'Assembly Converter',
#'IDMapper' => 'ID History Converter',
#'AlleleFrequency' => 'Allele Frequency Calculator',
#'VcftoPed' => 'VCF to PED Converter',
#'DataSlicer' => 'Data Slicer',
#'VariationPattern' => 'Variation Pattern Finder',
#'LD' => 'Linkage Disequilibrium Calculator',
];

# our $VCF_LIB = $SiteDefs::ENSEMBL_SERVERROOT.'/vcftools/perl';
# push @SiteDefs::ENSEMBL_LIB_DIRS, $VCF_LIB;

}

Expand Down
67 changes: 67 additions & 0 deletions gramene/conf/ini-files.bad/Aegilops_tauschii.ini
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
[general]
SPECIES_RELEASE_VERSION=1

[databases]
DATABASE_CORE=%_core_%_%
DATABASE_OTHERFEATURES=%_otherfeatures_%_%
DATABASE_USERDATA=aegilops_tauschii_userdata

[DATABASE_USERDATA]

[ENSEMBL_STYLE]

[ENSEMBL_EXTERNAL_URLS]

[ENSEMBL_EXTERNAL_DATABASES]

[ENSEMBL_EXTERNAL_INDEXERS]

[ENSEMBL_INTERNAL_DAS_SOURCES]

[ENSEMBL_SPECIES_SITE]

[SPECIES_DISPLAY_NAME]

[ENSEMBL_INTERNAL_BAM_SOURCES]
Lastz_Wheat_D_subsequences_alignments = wheat_assembly
Lastz_Wheat_cap3_subsequences_alignments = wheat_assembly

[Lastz_Wheat_D_subsequences_alignments]
source_name = Brenchley et al. T. urartu D sequences
description = Lastz Alignments of the <i>T. aestivum</i> D sequences from Brenchley <i>et al.</i> against <i>T. urartu</i>
source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/atauschii/LastZ_Wheat_Genome_D.atauschii.bam
source_type = bam
display = off

[Lastz_Wheat_cap3_subsequences_alignments]
source_name = Brenchley et al. A. tauschii cap3 sequences
description = Lastz Alignments of the <i>T. aestivum</i> cap3 sequences from Brenchley <i>et al.</i> against <i>A. tauschii</i>
source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/atauschii/LastZ_Wheat_Genome_cap3.atauschii.bam
source_type = bam
display = off

[ENSEMBL_INTERNAL_BIGWIG_SOURCES]
DRS001323 = wheat_transcriptomics
DRS001324 = wheat_transcriptomics
SRS072843 = wheat_transcriptomics

[DRS001323]
source_name = Aegilops tauschii IG47182
description = RNASeq from seedling leaves of <i>Aegilops tauschii</i> (Study <a href="http://www.ebi.ac.uk/ena/data/view/DRP000562" target="_blank">DRP000562</a>), aligned using Star software
source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/DRS001323.bw
source_type = bigWig
display = off

[DRS001324]
source_name = Aegilops tauschii PI476874
description = RNASeq from seedling leaves of <i>Aegilops tauschii</i> (Study <a href="http://www.ebi.ac.uk/ena/data/view/DRP000562" target="_blank">DRP000562</a>), aligned using Star software
source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/DRS001324.bw
source_type = bigWig
display = off

[SRS072843]
source_name = Aegilops tauschii
description = Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors (Study <a href="http://www.ebi.ac.uk/ena/data/view/SRP002455" target="_blank">SRP002455</a>), aligned using Star software
source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/SRS072843.bw
source_type = bigWig
display = off
29 changes: 29 additions & 0 deletions gramene/conf/ini-files.bad/Amborella_trichopoda.ini
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
[general]
SPECIES_RELEASE_VERSION = 1

[databases]
DATABASE_CORE = %_core_%_%
DATABASE_USERDATA = amborella_trichopoda_userdata

[DATABASE_USERDATA]

[ENSEMBL_STYLE]

[ENSEMBL_EXTERNAL_URLS]

[ENSEMBL_SPECIES_SITE]

[ENSEMBL_INTERNAL_DAS_SOURCES]

[SPECIES_DISPLAY_NAME]

[ENSEMBL_EXTERNAL_DATABASES]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini

[ENSEMBL_EXTERNAL_INDEXERS]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini

[ENSEMBL_EXTERNAL_URLS]



Loading