1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e112508794a8/ changeset: e112508794a8 user: inithello date: 2012-06-26 21:10:25 summary: Added missing builds.txt for Ensembl, fixed erroneous first line in output. affected #: 2 files
diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r e112508794a8585e96bc1ba15c2be1cce421393d cron/get_ensembl.py --- a/cron/get_ensembl.py +++ b/cron/get_ensembl.py @@ -17,6 +17,7 @@ for genome in genomes: builds[genome[0]] = dict( release=genome[3], species='%s (%s/%s)' % ( genome[1], genome[2], genome[0] ) ) for build in builds.items(): - lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) ) + if build[0]: + lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) )
-print '\n'.join( lines ) \ No newline at end of file +print '\n'.join( lines )
diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r e112508794a8585e96bc1ba15c2be1cce421393d tool-data/shared/ensembl/builds.txt --- /dev/null +++ b/tool-data/shared/ensembl/builds.txt @@ -0,0 +1,165 @@ + 67 Microcebus_murinus (Mouse lemur/) +MEDAKA1 67 Oryzias_latipes (Medaka/MEDAKA1) +Myoluc2.0 67 Myotis_lucifugus (Microbat/Myoluc2.0) +anoCar1 67 Anolis_carolinensis (Anole lizard/anoCar1) +WS220 67 Caenorhabditis_elegans (C.elegans/WS220) +WS180 67 Caenorhabditis_elegans (C.elegans/WS180) +MICROBAT1 67 Myotis_lucifugus (Microbat/MICROBAT1) +loxAfr3 67 Loxodonta_africana (Elephant/loxAfr3) +AgamP3 67 Anopheles_gambiae (Mosquito/AgamP3) +DROM3 67 Drosophila_melanogaster (Fly/DROM3) +LatCha1 67 Latimeria_chalumnae (Coelacanth/LatCha1) +vicPac1 67 Vicugna_pacos (Alpaca/vicPac1) +COMMON_SHREW1 67 Sorex_araneus (Shrew/COMMON_SHREW1) +MGSC3 67 Mus_musculus (Mouse/MGSC3) +MGSC1 67 Mus_musculus (Mouse/MGSC1) +JGI4.1 67 Xenopus_tropicalis (Xenopus/JGI4.1) +RGSC1 67 Rattus_norvegicus (Rat/RGSC1) +RGSC2 67 Rattus_norvegicus (Rat/RGSC2) +gadMor1 67 Gadus_morhua (Atlantic cod/gadMor1) +CSAV2.0 67 Ciona_savignyi (C.savignyi/CSAV2.0) +oryCun2 67 Oryctolagus_cuniculus (Rabbit/oryCun2) +ZFISH6 67 Danio_rerio (Zebrafish/ZFISH6) +ZFISH7 67 Danio_rerio (Zebrafish/ZFISH7) +ZFISH4 67 Danio_rerio (Zebrafish/ZFISH4) +ZFISH5 67 Danio_rerio (Zebrafish/ZFISH5) +ZFISH2 67 Danio_rerio (Zebrafish/ZFISH2) +ZFISH3 67 Danio_rerio (Zebrafish/ZFISH3) +MOZ2a 67 Anopheles_gambiae (Mosquito/MOZ2a) +EquCab2 67 Equus_caballus (Horse/EquCab2) +AMEL1.1 67 Apis_mellifera (Honeybee/AMEL1.1) +MMUL_1 67 Macaca_mulatta (Macaque/MMUL_1) +dasNov2 67 Dasypus_novemcinctus (Armadillo/dasNov2) +choHof1 67 Choloepus_hoffmanni (Sloth/choHof1) +lamPac1 50 Lama_pacos (Alpaca/lamPac1) +OANA5 67 Ornithorhynchus_anatinus (Platypus/OANA5) +CEL160 67 Caenorhabditis_elegans (C.elegans/CEL160) +WBcel215 67 Caenorhabditis_elegans (C.elegans/WBcel215) +gorGor3 67 Gorilla_gorilla (Gorilla/gorGor3) +SQUIRREL 67 Spermophilus_tridecemlineatus (Ground Squirrel/SQUIRREL) +gorGor1 67 Gorilla_gorilla (Gorilla/gorGor1) +pteVam1 67 Pteropus_vampyrus (Flying fox/pteVam1) +SGD1 67 Saccharomyces_cerevisiae (S.cerevisiae/SGD1) +micMur1 67 Microcebus_murinus (Mouse lemur/micMur1) +proCap1 67 Procavia_capensis (Rock hyrax/proCap1) +NCBIM30 67 Mus_musculus (Mouse/NCBIM30) +NCBIM33 67 Mus_musculus (Mouse/NCBIM33) +NCBIM32 67 Mus_musculus (Mouse/NCBIM32) +NCBIM35 67 Mus_musculus (Mouse/NCBIM35) +AaegL1 67 Aedes_aegypti (A.aegypti/AaegL1) +NCBIM37 67 Mus_musculus (Mouse/NCBIM37) +NCBIM36 67 Mus_musculus (Mouse/NCBIM36) +EF2 67 Saccharomyces_cerevisiae (S.cerevisiae/EF2) +EF3 67 Saccharomyces_cerevisiae (S.cerevisiae/EF3) +EF4 67 Saccharomyces_cerevisiae (S.cerevisiae/EF4) +BDGP5.4 67 Drosophila_melanogaster (Fly/BDGP5.4) +PPYG2 67 Pongo_abelii (Orangutan/PPYG2) +CEL150 67 Caenorhabditis_elegans (C.elegans/CEL150) +AMEL2.0 67 Apis_mellifera (Honeybee/AMEL2.0) +WASHUC1 67 Gallus_gallus (Chicken/WASHUC1) +WASHUC2 67 Gallus_gallus (Chicken/WASHUC2) +Btau_3.1 67 Bos_taurus (Cow/Btau_3.1) +gorGor3.1 67 Gorilla_gorilla (Gorilla/gorGor3.1) +CEL130 67 Caenorhabditis_elegans (C.elegans/CEL130) +Zv9 67 Danio_rerio (Zebrafish/Zv9) +BROADS1 67 Gasterosteus_aculeatus (Stickleback/BROADS1) +BROADD2 67 Canis_familiaris (Dog/BROADD2) +BROADD1 67 Canis_familiaris (Dog/BROADD1) +pika 67 Ochotona_princeps (Pika/pika) +ZFISH08 67 Danio_rerio (Zebrafish/ZFISH08) +ZFISH06 67 Danio_rerio (Zebrafish/ZFISH06) +calJac3 67 Callithrix_jacchus (Marmoset/calJac3) +CHIMP2.1.4 67 Pan_troglodytes (Chimp/CHIMP2.1.4) +JGI2 67 Ciona_intestinalis (C.intestinalis/JGI2) +JGI3 67 Xenopus_tropicalis (Xenopus/JGI3) +UCSC 67 Homo_sapiens (Human/UCSC) +Zv8 67 Danio_rerio (Zebrafish/Zv8) +JGI4 67 Xenopus_tropicalis (Xenopus/JGI4) +CEL140 67 Caenorhabditis_elegans (C.elegans/CEL140) +HEDGEHOG 67 Erinaceus_europaeus (Hedgehog/HEDGEHOG) +callJacc3 67 Callithrix_jacchus (Marmoset/callJacc3) +WS210 67 Caenorhabditis_elegans (C.elegans/WS210) +BDGP4 67 Drosophila_melanogaster (Fly/BDGP4) +BDGP5 67 Drosophila_melanogaster (Fly/BDGP5) +CHIMP1 67 Pan_troglodytes (Chimp/CHIMP1) +OtoGar3 67 Otolemur_garnettii (Bushbaby/OtoGar3) +MOZ2 67 Anopheles_gambiae (Mosquito/MOZ2) +FUGU4 67 Takifugu_rubripes (Fugu/FUGU4) +MOZ1 67 Anopheles_gambiae (Mosquito/MOZ1) +GUINEAPIG 67 Cavia_porcellus (Guinea Pig/GUINEAPIG) +BROADE1 67 Loxodonta_africana (Elephant/BROADE1) +RABBIT 67 Oryctolagus_cuniculus (Rabbit/RABBIT) +TETRAODON7 67 Tetraodon_nigroviridis (Tetraodon/TETRAODON7) +TETRAODON8 67 Tetraodon_nigroviridis (Tetraodon/TETRAODON8) +gorGor2 67 Gorilla_gorilla (Gorilla/gorGor2) +SGD1.01 67 Saccharomyces_cerevisiae (S.cerevisiae/SGD1.01) +ailMel1 67 Ailuropoda_melanoleuca (Panda/ailMel1) +Sscrofa9 67 Sus_scrofa (Pig/Sscrofa9) +cavPor3 67 Cavia_porcellus (Guinea Pig/cavPor3) +Orenil1.0 67 Oreochromis_niloticus (Nile tilapia/Orenil1.0) +BDGP4.2 67 Drosophila_melanogaster (Fly/BDGP4.2) +BDGP4.3 67 Drosophila_melanogaster (Fly/BDGP4.3) +Petromyzon_marin 64 Petromyzon_marinus (Lamprey/Petromyzon_marin) +RGSC3.4 67 Rattus_norvegicus (Rat/RGSC3.4) +Pmarinus_7.0 67 Petromyzon_marinus (Lamprey/Pmarinus_7.0) +RGSC3.1 67 Rattus_norvegicus (Rat/RGSC3.1) +BDGP5.25 67 Drosophila_melanogaster (Fly/BDGP5.25) +ARMA 67 Dasypus_novemcinctus (Armadillo/ARMA) +CINT1.95 67 Ciona_intestinalis (C.intestinalis/CINT1.95) +Btau_1.0 67 Bos_taurus (Cow/Btau_1.0) +JGI_4.2 67 Xenopus_tropicalis (Xenopus/JGI_4.2) +CEL116 67 Caenorhabditis_elegans (C.elegans/CEL116) +BUSHBABY1 67 Otolemur_garnettii (Bushbaby/BUSHBABY1) +Sscrofa10.2 67 Sus_scrofa (Pig/Sscrofa10.2) +BDGP3.2.1 67 Drosophila_melanogaster (Fly/BDGP3.2.1) +taeGut3.2.4 67 Taeniopygia_guttata (Zebra finch/taeGut3.2.4) +KH 67 Ciona_intestinalis (C.intestinalis/KH) +JGI4_1 67 Xenopus_tropicalis (Xenopus/JGI4_1) +spetri2 67 Spermophilus_tridecemlineatus (Ground Squirrel/spetri2) +Btau_4.0 67 Bos_taurus (Cow/Btau_4.0) +UMD2 67 Meleagris_gallopavo (Turkey/UMD2) +NCBI28 67 Homo_sapiens (Human/NCBI28) +NCBI29 67 Homo_sapiens (Human/NCBI29) +Btau_2.0 67 Bos_taurus (Cow/Btau_2.0) +NCBI26 67 Homo_sapiens (Human/NCBI26) +CAT 67 Felis_catus (Cat/CAT) +TENREC 67 Echinops_telfairi (Tenrec/TENREC) +WS200 67 Caenorhabditis_elegans (C.elegans/WS200) +AnoCar1.0 67 Anolis_carolinensis (Anole lizard/AnoCar1.0) +Nleu1.0 67 Nomascus_leucogenys (Gibbon/Nleu1.0) +Meug_1.0 67 Macropus_eugenii (Wallaby/Meug_1.0) +C_jacchus3.2.1 67 Callithrix_jacchus (Marmoset/C_jacchus3.2.1) +CHIMP2.1 67 Pan_troglodytes (Chimp/CHIMP2.1) +WS190 67 Caenorhabditis_elegans (C.elegans/WS190) +dipOrd1 67 Dipodomys_ordii (Kangaroo rat/dipOrd1) +AnoCar2.0 67 Anolis_carolinensis (Anole lizard/AnoCar2.0) +ACME0.1 67 None (None/ACME0.1) +CEL95 67 Caenorhabditis_elegans (C.elegans/CEL95) +CEL93 67 Caenorhabditis_elegans (C.elegans/CEL93) +DEVIL7.0 67 Sarcophilus_harrisii (Tasmanian Devil/DEVIL7.0) +CEL98 67 Caenorhabditis_elegans (C.elegans/CEL98) +CEL102 67 Caenorhabditis_elegans (C.elegans/CEL102) +TREESHREW 67 Tupaia_belangeri (Tree Shrew/TREESHREW) +NCBI31 67 Homo_sapiens (Human/NCBI31) +NCBI30 67 Homo_sapiens (Human/NCBI30) +NCBI33 67 Homo_sapiens (Human/NCBI33) +NCBI35 67 Homo_sapiens (Human/NCBI35) +NCBI34 67 Homo_sapiens (Human/NCBI34) +turTru1 67 Tursiops_truncatus (Bottlenose dolphin/turTru1) +NCBI36 67 Homo_sapiens (Human/NCBI36) +UMD3.1 67 Bos_taurus (Cow/UMD3.1) +speTri1 67 Spermophilus_tridecemlineatus (Ground Squirrel/speTri1) +GRCh37 67 Homo_sapiens (Human/GRCh37) +CHIMP1A 67 Pan_troglodytes (Chimp/CHIMP1A) +WB170 67 Caenorhabditis_elegans (C.elegans/WB170) +FUGU1 67 Takifugu_rubripes (Fugu/FUGU1) +FUGU2 67 Takifugu_rubripes (Fugu/FUGU2) +NCBIM34 67 Mus_musculus (Mouse/NCBIM34) +DROM3A 67 Drosophila_melanogaster (Fly/DROM3A) +tarSyr1 67 Tarsius_syrichta (Tarsier/tarSyr1) +CBR25 67 Caenorhabditis_briggsae (C.briggsae/CBR25) +BROADO5 67 Monodelphis_domestica (Opossum/BROADO5) +BROADO2 67 Monodelphis_domestica (Opossum/BROADO2) +BROADO3 67 Monodelphis_domestica (Opossum/BROADO3) +BDGP5.13 67 Drosophila_melanogaster (Fly/BDGP5.13) +MMUL_0_1 67 Macaca_mulatta (Macaque/MMUL_0_1)
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