Question: Using Ensembl gene annotation with Galaxy
0
matt.chambers42 • 50 wrote:
I'm trying to use ensembl gene annotations for my tool* but I don't understand how to map them to the UCSC dbkeys. There are multiple ensembl releases for each UCSC dbkey. My loc file has the latest ensembl release for each genome assembly/patch and I've tried to map it to the corresponding UCSC dbkey with this loc file:
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| ce11_WBcel235 ce11 C.elegans (Ensembl 89 celegans) (ce11/WBcel235) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/celegans-may2017 | |
| ce10_WBcel215 ce10 C.elegans (Ensembl 67 celegans) (ce10/WBcel215) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/celegans-may2012 | |
| ce6_WS190 ce6 C.elegans (Ensembl 54 celegans) (ce6/WS190) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/celegans-may2009 | |
| cintestinalis_KH cintestinalis_KH C.intestinalis (Ensembl 89 cintestinalis) (KH) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cintestinalis-may2017 | |
| ci2_JGI 2 ci2 C.intestinalis (Ensembl 54 cintestinalis) (ci2/JGI 2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cintestinalis-may2009 | |
| dm6_BDGP6 dm6 Fly (Ensembl 89 dmelanogaster) (dm6/BDGP6) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dmelanogaster-may2017 | |
| dm3_BDGP 5 dm3 Fly (Ensembl 78 dmelanogaster) (dm3/BDGP 5) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dmelanogaster-dec2014 | |
| dm2_BDGP 5.4 dm2 Fly (Ensembl 54 dmelanogaster) (dm2/BDGP 5.4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dmelanogaster-may2009 | |
| hg38_GRCh38.p10 hg38 Human (Ensembl 89 hsapiens) (hg38/GRCh38.p10) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-may2017 | |
| hg38_GRCh38.p5 hg38 Human (Ensembl 84 hsapiens) (hg38/GRCh38.p5) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-mar2016 | |
| hg38_GRCh38.p3 hg38 Human (Ensembl 82 hsapiens) (hg38/GRCh38.p3) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-sep2015 | |
| hg38_GRCh38.p2 hg38 Human (Ensembl 80 hsapiens) (hg38/GRCh38.p2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-may2015 | |
| hg38_GRCh38 hg38 Human (Ensembl 78 hsapiens) (hg38/GRCh38) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-dec2014 | |
| hg19_GRCh37.p13 hg19 Human (Ensembl 75 hsapiens) (hg19/GRCh37.p13) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-feb2014 | |
| hg19_GRCh37.p7 hg19 Human (Ensembl 67 hsapiens) (hg19/GRCh37.p7) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-may2012 | |
| hg18_NCBI 36 hg18 Human (Ensembl 54 hsapiens) (hg18/NCBI 36) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/hsapiens-may2009 | |
| mm10_GRCm38.p5 mm10 Mouse (Ensembl 89 mmusculus) (mm10/GRCm38.p5) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmusculus-may2017 | |
| mm10_GRCm38.p4 mm10 Mouse (Ensembl 86 mmusculus) (mm10/GRCm38.p4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmusculus-oct2016 | |
| mm10_GRCm38.p3 mm10 Mouse (Ensembl 80 mmusculus) (mm10/GRCm38.p3) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmusculus-may2015 | |
| mm10_GRCm38.p2 mm10 Mouse (Ensembl 77 mmusculus) (mm10/GRCm38.p2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmusculus-oct2014 | |
| mm9_NCBI m37 mm9 Mouse (Ensembl 67 mmusculus) (mm9/NCBI m37) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmusculus-may2012 | |
| rn6_Rnor_6.0 rn6 Rat (Ensembl 89 rnorvegicus) (rn6/Rnor_6.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/rnorvegicus-may2017 | |
| rn5_Rnor_5.0 rn5 Rat (Ensembl 79 rnorvegicus) (rn5/Rnor_5.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/rnorvegicus-mar2015 | |
| rn4_RGSC 3.4 rn4 Rat (Ensembl 67 rnorvegicus) (rn4/RGSC 3.4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/rnorvegicus-may2012 | |
| ailMel1_ailMel1 ailMel1 Panda (Ensembl 89 amelanoleuca) (ailMel1/ailMel1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/amelanoleuca-may2017 | |
| aplatyrhynchos_BGI_duck_1.0 aplatyrhynchos_BGI_duck_1.0 Duck (Ensembl 89 aplatyrhynchos) (BGI_duck_1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/aplatyrhynchos-may2017 | |
| anoCar2_AnoCar2.0 anoCar2 Anole lizard (Ensembl 89 acarolinensis) (anoCar2/AnoCar2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/acarolinensis-may2017 | |
| anoCar1_AnoCar1.0 anoCar1 Anole lizard (Ensembl 54 acarolinensis) (anoCar1/AnoCar1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/acarolinensis-may2009 | |
| amexicanus_AstMex102 amexicanus_AstMex102 Cave fish (Ensembl 89 amexicanus) (AstMex102) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/amexicanus-may2017 | |
| bosTau6_UMD3.1 bosTau6 Cow (Ensembl 89 btaurus) (bosTau6/UMD3.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/btaurus-may2017 | |
| bosTau4_Btau_4.0 bosTau4 Cow (Ensembl 54 btaurus) (bosTau4/Btau_4.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/btaurus-may2009 | |
| calJac3_C_jacchus3.2.1 calJac3 Marmoset (Ensembl 89 cjacchus) (calJac3/C_jacchus3.2.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cjacchus-may2017 | |
| canFam3_CanFam3.1 canFam3 Dog (Ensembl 89 cfamiliaris) (canFam3/CanFam3.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cfamiliaris-may2017 | |
| canFam2_CanFam 2.0 canFam2 Dog (Ensembl 67 cfamiliaris) (canFam2/CanFam 2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cfamiliaris-may2012 | |
| cavPor3_cavPor3 cavPor3 Guinea Pig (Ensembl 89 cporcellus) (cavPor3/cavPor3) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/cporcellus-may2017 | |
| chlSab2_ChlSab1.1 chlSab2 Vervet-AGM (Ensembl 89 csabaeus) (chlSab2/ChlSab1.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/csabaeus-may2017 | |
| choHof1_choHof1 choHof1 Sloth (Ensembl 89 choffmanni) (choHof1/choHof1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/choffmanni-may2017 | |
| csavignyi_CSAV 2.0 csavignyi_CSAV 2.0 C.savignyi (Ensembl 89 csavignyi) (CSAV 2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/csavignyi-may2017 | |
| danRer6_Zv8 danRer6 Zebrafish (Ensembl 54 drerio) (danRer6/Zv8) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/drerio-may2009 | |
| danRer10_GRCz10 danRer10 Zebrafish (Ensembl 89 drerio) (danRer10/GRCz10) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/drerio-may2017 | |
| danRer9_Zv9 danRer9 Zebrafish (Ensembl 79 drerio) (danRer9/Zv9) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/drerio-mar2015 | |
| dasNov3_Dasnov3.0 dasNov3 Armadillo (Ensembl 89 dnovemcinctus) (dasNov3/Dasnov3.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dnovemcinctus-may2017 | |
| dnovemcinctus_ARMA dnovemcinctus_ARMA Armadillo (Ensembl 54 dnovemcinctus) (ARMA) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dnovemcinctus-may2009 | |
| dnovemcinctus_dasNov2 dnovemcinctus_dasNov2 Armadillo (Ensembl 67 dnovemcinctus) (dasNov2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dnovemcinctus-may2012 | |
| dipOrd1_dipOrd1 dipOrd1 Kangaroo rat (Ensembl 89 dordii) (dipOrd1/dipOrd1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/dordii-may2017 | |
| echTel2_TENREC echTel2 Tenrec (Ensembl 89 etelfairi) (echTel2/TENREC) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/etelfairi-may2017 | |
| equCab2_Equ Cab 2 equCab2 Horse (Ensembl 89 ecaballus) (equCab2/Equ Cab 2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ecaballus-may2017 | |
| eriEur1_eriEur1 eriEur1 Hedgehog (Ensembl 89 eeuropaeus) (eriEur1/eriEur1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/eeuropaeus-may2017 | |
| felCat5_Felis_catus_6.2 felCat5 Cat (Ensembl 89 fcatus) (felCat5/Felis_catus_6.2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/fcatus-may2017 | |
| felCat4_CAT felCat4 Cat (Ensembl 67 fcatus) (felCat4/CAT) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/fcatus-may2012 | |
| falbicollis_FicAlb_1.4 falbicollis_FicAlb_1.4 Collared flycatcher (Ensembl 89 falbicollis) (FicAlb_1.4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/falbicollis-may2017 | |
| gadMor1_gadMor1 gadMor1 Cod (Ensembl 89 gmorhua) (gadMor1/gadMor1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/gmorhua-may2017 | |
| galGal3_WASHUC2 galGal3 Chicken (Ensembl 67 ggallus) (galGal3/WASHUC2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ggallus-may2012 | |
| galGal4_Galgal4 galGal4 Chicken (Ensembl 85 ggallus) (galGal4/Galgal4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ggallus-jul2016 | |
| galGal5_Gallus_gallus-5.0 galGal5 Chicken (Ensembl 89 ggallus) (galGal5/Gallus_gallus-5.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ggallus-may2017 | |
| gasAcu1_BROAD S1 gasAcu1 Stickleback (Ensembl 89 gaculeatus) (gasAcu1/BROAD S1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/gaculeatus-may2017 | |
| gorGor5_gorGor1 gorGor5 Gorilla (Ensembl 54 ggorilla) (gorGor5/gorGor1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ggorilla-may2009 | |
| ggorilla_gorGor3.1 ggorilla_gorGor3.1 Gorilla (Ensembl 89 ggorilla) (gorGor3.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ggorilla-may2017 | |
| speTri2_spetri2 speTri2 Squirrel (Ensembl 89 itridecemlineatus) (speTri2/spetri2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/itridecemlineatus-may2017 | |
| latCha1_LatCha1 latCha1 Coelacanth (Ensembl 89 lchalumnae) (latCha1/LatCha1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/lchalumnae-may2017 | |
| loculatus_LepOcu1 loculatus_LepOcu1 Spotted gar (Ensembl 89 loculatus) (LepOcu1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/loculatus-may2017 | |
| lafricana_BROAD E1 lafricana_BROAD E1 Elephant (Ensembl 54 lafricana) (BROAD E1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/lafricana-may2009 | |
| loxAfr3_Loxafr3.0 loxAfr3 Elephant (Ensembl 89 lafricana) (loxAfr3/Loxafr3.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/lafricana-may2017 | |
| mmulatta_Mmul_8.0.1 mmulatta_Mmul_8.0.1 Macaque (Ensembl 89 mmulatta) (Mmul_8.0.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmulatta-may2017 | |
| mmulatta_MMUL 1.0 mmulatta_MMUL 1.0 Macaque (Ensembl 85 mmulatta) (MMUL 1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmulatta-jul2016 | |
| melGal1_Turkey_2.01 melGal1 Turkey (Ensembl 89 mgallopavo) (melGal1/Turkey_2.01) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mgallopavo-may2017 | |
| micMur1_micMur1 micMur1 Mouse lemur (Ensembl 85 mmurinus) (micMur1/micMur1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmurinus-jul2016 | |
| micMur2_Mmur_2.0 micMur2 Mouse lemur (Ensembl 89 mmurinus) (micMur2/Mmur_2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mmurinus-may2017 | |
| monDom5_monDom5 monDom5 Opossum (Ensembl 89 mdomestica) (monDom5/monDom5) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mdomestica-may2017 | |
| myoLuc2_Myoluc2.0 myoLuc2 Microbat (Ensembl 89 mlucifugus) (myoLuc2/Myoluc2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mlucifugus-may2017 | |
| mlucifugus_myoLuc1 mlucifugus_myoLuc1 Microbat (Ensembl 54 mlucifugus) (myoLuc1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/mlucifugus-may2009 | |
| nomLeu1_Nleu1.0 nomLeu1 Gibbon (Ensembl 89 nleucogenys) (nomLeu1/Nleu1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/nleucogenys-may2017 | |
| ochPri2_OchPri2.0 ochPri2 Pika (Ensembl 88 oprinceps) (ochPri2/OchPri2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/oprinceps-mar2017 | |
| ochPri2_OchPri2.0-Ens ochPri2 Pika (Ensembl 89 oprinceps) (ochPri2/OchPri2.0-Ens) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/oprinceps-may2017 | |
| oreNil2_Orenil1.0 oreNil2 Tilapia (Ensembl 89 oniloticus) (oreNil2/Orenil1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/oniloticus-may2017 | |
| ornAna1_OANA5 ornAna1 Platypus (Ensembl 89 oanatinus) (ornAna1/OANA5) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/oanatinus-may2017 | |
| ocuniculus_RABBIT ocuniculus_RABBIT Rabbit (Ensembl 54 ocuniculus) (RABBIT) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ocuniculus-may2009 | |
| oryCun2_OryCun2.0 oryCun2 Rabbit (Ensembl 89 ocuniculus) (oryCun2/OryCun2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ocuniculus-may2017 | |
| oryLat2_HdrR oryLat2 Medaka (Ensembl 89 olatipes) (oryLat2/HdrR) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/olatipes-may2017 | |
| ogarnettii_otoGar1 ogarnettii_otoGar1 Bushbaby (Ensembl 54 ogarnettii) (otoGar1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ogarnettii-may2009 | |
| otoGar3_OtoGar3 otoGar3 Bushbaby (Ensembl 89 ogarnettii) (otoGar3/OtoGar3) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ogarnettii-may2017 | |
| oviAri3_Oar_v3.1 oviAri3 Sheep (Ensembl 89 oaries) (oviAri3/Oar_v3.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/oaries-may2017 | |
| panTro2_CHIMP2.1 panTro2 Chimp (Ensembl 54 ptroglodytes) (panTro2/CHIMP2.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ptroglodytes-may2009 | |
| panTro1_CHIMP2.1.4 panTro1 Chimp (Ensembl 89 ptroglodytes) (panTro1/CHIMP2.1.4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ptroglodytes-may2017 | |
| papAnu2_PapAnu2.0 papAnu2 Olive Baboon (Ensembl 89 panubis) (papAnu2/PapAnu2.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/panubis-may2017 | |
| psinensis_PelSin_1.0 psinensis_PelSin_1.0 Chinese softshell turtle (Ensembl 89 psinensis) (PelSin_1.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/psinensis-may2017 | |
| petMar2_Pmarinus_7.0 petMar2 Lamprey (Ensembl 89 pmarinus) (petMar2/Pmarinus_7.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/pmarinus-may2017 | |
| pformosa_Poecilia_formosa-5.1.2 pformosa_Poecilia_formosa-5.1.2 Amazon molly (Ensembl 89 pformosa) (Poecilia_formosa-5.1.2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/pformosa-may2017 | |
| ponAbe2_PPYG2 ponAbe2 Orangutan (Ensembl 89 pabelii) (ponAbe2/PPYG2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/pabelii-may2017 | |
| proCap1_proCap1 proCap1 Rock hyrax (Ensembl 89 pcapensis) (proCap1/proCap1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/pcapensis-may2017 | |
| pteVam1_pteVam1 pteVam1 Megabat (Ensembl 89 pvampyrus) (pteVam1/pteVam1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/pvampyrus-may2017 | |
| sacCer3_R64-1-1 sacCer3 S.cerevisiae (Ensembl 89 scerevisiae) (sacCer3/R64-1-1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/scerevisiae-may2017 | |
| sacCer1_SGD1.01 sacCer1 S.cerevisiae (Ensembl 54 scerevisiae) (sacCer1/SGD1.01) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/scerevisiae-may2009 | |
| sacCer2_EF 4 sacCer2 S.cerevisiae (Ensembl 74 scerevisiae) (sacCer2/EF 4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/scerevisiae-dec2013 | |
| sarHar1_Devil_ref v7.0 sarHar1 Tasmanian Devil (Ensembl 89 sharrisii) (sarHar1/Devil_ref v7.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/sharrisii-may2017 | |
| sorAra1_sorAra1 sorAra1 Shrew (Ensembl 89 saraneus) (sorAra1/sorAra1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/saraneus-may2017 | |
| susScr3_Sscrofa10.2 susScr3 Pig (Ensembl 89 sscrofa) (susScr3/Sscrofa10.2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/sscrofa-may2017 | |
| taeGut1_taeGut3.2.4 taeGut1 Zebra finch (Ensembl 89 tguttata) (taeGut1/taeGut3.2.4) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/tguttata-may2017 | |
| fr2_FUGU 4.0 fr2 Fugu (Ensembl 89 trubripes) (fr2/FUGU 4.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/trubripes-may2017 | |
| tetNig2_TETRAODON 8.0 tetNig2 Tetraodon (Ensembl 89 tnigroviridis) (tetNig2/TETRAODON 8.0) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/tnigroviridis-may2017 | |
| tupBel1_tupBel1 tupBel1 Tree Shrew (Ensembl 89 tbelangeri) (tupBel1/tupBel1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/tbelangeri-may2017 | |
| turTru2_turTru1 turTru2 Dolphin (Ensembl 89 ttruncatus) (turTru2/turTru1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/ttruncatus-may2017 | |
| vicPac1_vicPac1 vicPac1 Alpaca (Ensembl 89 vpacos) (vicPac1/vicPac1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/vpacos-may2017 | |
| xenTro3_JGI 4.2 xenTro3 Xenopus (Ensembl 89 xtropicalis) (xenTro3/JGI 4.2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/xtropicalis-may2017 | |
| xenTro2_JGI 4.1 xenTro2 Xenopus (Ensembl 54 xtropicalis) (xenTro2/JGI 4.1) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/xtropicalis-may2009 | |
| xmaculatus_Xipmac4.4.2 xmaculatus_Xipmac4.4.2 Platyfish (Ensembl 89 xmaculatus) (Xipmac4.4.2) /cvmfs/omicron-data.duckdns.org/customProDB/ensembl/xmaculatus-may2017 |
When I try to run my tool with it, I see the full list from the loc file, but I get an error when executing:
An invalid option was selected for builtin, 'GRCh37.p13', please verify.
I don't understand where it even gets that value from.
*because building an ensembl annotation by release # is reproducible, unlike UCSC which always returns the latest gene annotations