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reorganizing to accomodate stage. initial commit of staging files.
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Chris Childers committed Jul 13, 2021
1 parent 0dddc2e commit e58b052
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21 changes: 21 additions & 0 deletions move_back_scripts/stage/README
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#create the list of endllpoints:
# from the command line
select common_name, directory from organism ORDER by common_name;
#get a list of all the organisms
psql-U postgres -d webapollo_2 -c 'select common_name,directory from organism ORDER by common_name;'>organism_list.txt

#makeaworkingfile
cporganism_list.txtorganism_list.txt2



#removetheleadingandtrailinglines
nanoorganism_list.txt2

#removeextrawhitespacefromthefile
perl-pi-e"s/+//g"organism_list.txt2

# the perl script needs ALL spaces removed
perl -pi -e "s/ //g" organism_list.txt2


11 changes: 11 additions & 0 deletions move_back_scripts/stage/make_copy_commands.pl
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#!/usr/bin/perl -w

use strict;

while (<>){
$_ =~ m/(\S*)\|(\S*)/;
# print "mkdir $1; cd $1; cp ./$1/* $2/trackList.json; cd .. \n";
print "cp ../../working/$1/* $2/; \n";
print "cp ../../css/custom.css $2/; \n";
}

256 changes: 256 additions & 0 deletions move_back_scripts/stage/move_conf_files_back.sh
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132 changes: 132 additions & 0 deletions move_back_scripts/stage/organism_list.txt
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common_name | directory
------------------------------------+--------------------------------------------------------------
10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
Aethina_tumida | /app/data/other_species/aettum/jbrowse/data
Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data
Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data
Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data
Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/
Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data
Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data
Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data
Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data
Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data
Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data
Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data
Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data
Bradysia_coprophila | /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data
Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data
Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data
Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/
Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data
Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data
Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data
Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data
Diabrotica_virgifera_training | /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data
Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data
Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data
Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data
Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data
Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data
Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data
Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data
Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data
Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data
Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data
Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data
Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data
Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data
Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data
Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data
Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data
Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data
Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data
Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data
Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/
Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data
Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data
Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data
Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data
Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data
Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data
Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data
Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/
Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
Manduca_sexta | /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data
Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data
Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data
Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data
Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data
Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data
Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data
Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data
Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data
Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data
Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data
Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data
Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data
Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data
Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data
Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data
Photinus_pyralis | /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data
Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data
Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
Saccharomyces eubayanus | /app/data/other_species/saceub/SEUB3.0/jbrowse/data
Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data
Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data
Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data
Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data
Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data
(128 rows)

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