Galaxy

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
(microbes)
(Organisms)
Line 104: Line 104:
  
 
=== Organisms ===
 
=== Organisms ===
AaegL1
+
* AaegL1
Acropora_digitifera
+
* Acropora_digitifera
AgamP3
+
* AgamP3
Arabidopsis_thaliana_TAIR10
+
* Arabidopsis_thaliana_TAIR10
Arabidopsis_thaliana_TAIR9
+
* Arabidopsis_thaliana_TAIR9
Araly1
+
* Araly1
Bombyx_mori_p50T_2.0
+
* Bombyx_mori_p50T_2.0
CpipJ1
+
* CpipJ1
Homo_sapiens_AK1
+
* Homo_sapiens_AK1
Homo_sapiens_nuHg19_mtrCRS
+
* Homo_sapiens_nuHg19_mtrCRS
Hydra_JCVI
+
* Hydra_JCVI
IscaW1
+
* IscaW1
PhumU1
+
* PhumU1
Physcomitrella_patens_patens
+
* Physcomitrella_patens_patens
Ptrichocarpa_156
+
* Ptrichocarpa_156
Saccharomyces_cerevisiae_S288C_SGD2010
+
* Saccharomyces_cerevisiae_S288C_SGD2010
Schizosaccharomyces_pombe_1.1
+
* Schizosaccharomyces_pombe_1.1
Spur_v2.6
+
* Spur_v2.6
Sscrofa9.58
+
* Sscrofa9.58
Tcacao_1.0
+
* Tcacao_1.0
Tcas_3.0
+
* Tcas_3.0
Theobroma_cocoa
+
* Theobroma_cocoa
Zea_mays_B73_RefGen_v2
+
* Zea_mays_B73_RefGen_v2
ailMel1
+
* ailMel1
anoCar1
+
* anoCar1
anoCar2
+
* anoCar2
anoGam1
+
* anoGam1
apiMel1
+
* apiMel1
apiMel2
+
* apiMel2
apiMel3
+
* apiMel3
apiMel4.5
+
* apiMel4.5
aplCal1
+
* aplCal1
bighorn_sheep
+
* bighorn_sheep
borEut13
+
* borEut13
bosTau2
+
* bosTau2
bosTau3
+
* bosTau3
bosTau4
+
* bosTau4
bosTau5
+
* bosTau5
bosTau6
+
* bosTau6
bosTau7
+
* bosTau7
bosTauMd3
+
* bosTauMd3
braFlo1
+
* braFlo1
caeJap1
+
* caeJap1
caePb1
+
* caePb1
caePb2
+
* caePb2
caeRem2
+
* caeRem2
caeRem3
+
* caeRem3
calJac1
+
* calJac1
calJac3
+
* calJac3
canFam1
+
* canFam1
canFam2
+
* canFam2
canFam3
+
* canFam3
cavPor2
+
* cavPor2
cavPor3
+
* cavPor3
cb3
+
* cb3
ce10
+
* ce10
ce2
+
* ce2
ce3
+
* ce3
ce4
+
* ce4
ce5
+
* ce5
ce6
+
* ce6
ce7
+
* ce7
ce8
+
* ce8
ce9
+
* ce9
choHof1
+
* choHof1
chrPic1
+
* chrPic1
ci2
+
* ci2
danRer2
+
* danRer2
danRer3
+
* danRer3
danRer4
+
* danRer4
danRer5
+
* danRer5
danRer6
+
* danRer6
danRer7
+
* danRer7
dasNov1
+
* dasNov1
dasNov2
+
* dasNov2
dipOrd1
+
* dipOrd1
dm1
+
* dm1
dm2
+
* dm2
dm3
+
* dm3
dp3
+
* dp3
dp4
+
* dp4
droAna1
+
* droAna1
droAna2
+
* droAna2
droAna3
+
* droAna3
droEre1
+
* droEre1
droEre2
+
* droEre2
droGri1
+
* droGri1
droGri2
+
* droGri2
droMoj1
+
* droMoj1
droMoj2
+
* droMoj2
droMoj3
+
* droMoj3
droPer1
+
* droPer1
droSec1
+
* droSec1
droSim1
+
* droSim1
droVir1
+
* droVir1
droVir2
+
* droVir2
droVir3
+
* droVir3
droWil1
+
* droWil1
droYak1
+
* droYak1
droYak2
+
* droYak2
echTel1
+
* echTel1
emf
+
* emf
equCab1
+
* equCab1
equCab2
+
* equCab2
equCab2_chrM
+
* equCab2_chrM
eriEur1
+
* eriEur1
felCat3
+
* felCat3
felCat4
+
* felCat4
fr1
+
* fr1
fr2
+
* fr2
fr3
+
* fr3
galGal2
+
* galGal2
galGal3
+
* galGal3
galGal4
+
* galGal4
gasAcu1
+
* gasAcu1
geoFor1
+
* geoFor1
gorGor1
+
* gorGor1
gorGor3
+
* gorGor3
hetGla1
+
* hetGla1
hetGla2
+
* hetGla2
hg16
+
* hg16
hg17
+
* hg17
hg18
+
* hg18
hg19
+
* hg19
hg_g1k_v37
+
* hg_g1k_v37
lMaj5
+
* lMaj5
lengths
+
* lengths
loxAfr3
+
* loxAfr3
loxAfr4
+
* loxAfr4
macEug1
+
* macEug1
melGal1
+
* melGal1
melUnd1
+
* melUnd1
micMur1
+
* micMur1
mm10
+
* mm10
mm5
+
* mm5
mm6
+
* mm6
mm7
+
* mm7
mm8
+
* mm8
mm9
+
* mm9
monDom4
+
* monDom4
monDom5
+
* monDom5
myoLuc1
+
* myoLuc1
myoLuc2
+
* myoLuc2
nomLeu1
+
* nomLeu1
nomLeu2
+
* nomLeu2
ochPri2
+
* ochPri2
ornAna1
+
* ornAna1
oryCun1
+
* oryCun1
oryCun2
+
* oryCun2
oryLat1
+
* oryLat1
oryLat2
+
* oryLat2
oryza_sativa_japonica_nipponbare_IRGSP4.0
+
* oryza_sativa_japonica_nipponbare_IRGSP4.0
otoGar1
+
* otoGar1
oviAri1
+
* oviAri1
pUC18
+
* pUC18
panTro1
+
* panTro1
panTro2
+
* panTro2
panTro3
+
* panTro3
papHam1
+
* papHam1
petMar1
+
* petMar1
phiX
+
* phiX
ponAbe2
+
* ponAbe2
priPac1
+
* priPac1
rheMac2
+
* rheMac2
rheMac3
+
* rheMac3
rn3
+
* rn3
rn4
+
* rn4
rn5
+
* rn5
sacCer1
+
* sacCer1
sacCer2
+
* sacCer2
sacCer3
+
* sacCer3
sarHar1
+
* sarHar1
sorAra1
+
* sorAra1
strPur2
+
* strPur2
strPur3
+
* strPur3
susScr2
+
* susScr2
susScr3
+
* susScr3
taeGut1
+
* taeGut1
tarSyr1
+
* tarSyr1
tetNig1
+
* tetNig1
tetNig2
+
* tetNig2
triCas2
+
* triCas2
tupBel1
+
* tupBel1
venter1
+
* venter1
xenTro1
+
* xenTro1
xenTro2
+
* xenTro2
xenTro3
+
* xenTro3
  
 
=== Microbes ===
 
=== Microbes ===

Revision as of 15:08, 7 March 2013

Contents


Overview

The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on Galaxy, backed by the Cheaha compute cluster, and powered by UABgrid.

The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.

Using Galaxy / Tutorials

There are numerous general tutorials online at the Penn State public Galaxy site that are worth looking at.

There are also several UAB tutorials on NGS Analysis with Galaxy, created for HPC Boot Camp 2011 and a nice talk by Jeremy Goecks during Research Computing Day 2011.

Support

UAB galaxy-users list-serv: subscribe search.

UAB galaxy-help list-serv: [1] to contact admins of the UAB galaxy instance.

Privacy

Note that your data will be stored on the cluster filesystem, and while not accessible to ordinary users, it can be easily accessed by any of the galaxy or cluster administrators. It is not encrypted. Do not store sensitive information in this system.

Galaxy@UAB

The UAB Galaxy instance can be accessed at https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed. However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.

Available Tools

Following is a partial list highlighting some of the important tools available. Additional tools can be installed upon request. To search for tools already integrated into the Galaxy system, see the Galaxy ToolShed.


Software Version Information
bwa 0.5.9-r26 Align genomic short reads to a reference genome
bowtie 0.12.7 Align genomic short reads to a reference genome
samtools 0.1.12a Alignment (SAM/BAM file) manipulations
velvet 1.1.03 Denovo Assembly
Top Hat 1.4.0 Align transcriptome short reads to a reference genome
Cuff Links 1.3.0 Reconstruct and quantify transcript levels from tophat alignments.
EMBOSS 6.3.1 European Molecular Biology Open Software Suite - sequence manipulation and format conversion


Installed Genome Indexes

You can always use your own genome by uploading the .fasta into your history, but alignments against installed (pre-indexed) genomes run much more quickly. If you need an additional genome installed, please contact [2].

dbkey Genome Accessions
mm9 Mouse July 2007 (NCBI37/mm9) (mm9)
mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10)
hg18 Human Mar. 2006 (NCBI36/hg18) (hg18)
hg19 Human Feb. 2009 (GRCh37/hg19) (hg19)
sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
ce10 C. elegans Oct. 2010 (WS220/ce10) (ce10)
rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
rn5 Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
danRer7 Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)
eschColi_APEC_O1 Escherichia coli APEC O1 chr=5082025
eschColi_CFT073 Escherichia coli CFT073 chr=5231428
eschColi_EC4115 Escherichia coli EC4115 chr=5572075,plasmid_pO157=94644,plasmid_pEC4115=37452
eschColi_K12 Escherichia coli K12 chr=4639675
eschColi_EDL993 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_O157H7 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_TW14359 Escherichia coli TW14359 chr=5528136,plasmid_pO157=94601

Additional Genomes that can be quickly installed

These are pre-indexed genomes we can easily download from Penn State's Galaxy Data-Cache

Organisms

  • AaegL1
  • Acropora_digitifera
  • AgamP3
  • Arabidopsis_thaliana_TAIR10
  • Arabidopsis_thaliana_TAIR9
  • Araly1
  • Bombyx_mori_p50T_2.0
  • CpipJ1
  • Homo_sapiens_AK1
  • Homo_sapiens_nuHg19_mtrCRS
  • Hydra_JCVI
  • IscaW1
  • PhumU1
  • Physcomitrella_patens_patens
  • Ptrichocarpa_156
  • Saccharomyces_cerevisiae_S288C_SGD2010
  • Schizosaccharomyces_pombe_1.1
  • Spur_v2.6
  • Sscrofa9.58
  • Tcacao_1.0
  • Tcas_3.0
  • Theobroma_cocoa
  • Zea_mays_B73_RefGen_v2
  • ailMel1
  • anoCar1
  • anoCar2
  • anoGam1
  • apiMel1
  • apiMel2
  • apiMel3
  • apiMel4.5
  • aplCal1
  • bighorn_sheep
  • borEut13
  • bosTau2
  • bosTau3
  • bosTau4
  • bosTau5
  • bosTau6
  • bosTau7
  • bosTauMd3
  • braFlo1
  • caeJap1
  • caePb1
  • caePb2
  • caeRem2
  • caeRem3
  • calJac1
  • calJac3
  • canFam1
  • canFam2
  • canFam3
  • cavPor2
  • cavPor3
  • cb3
  • ce10
  • ce2
  • ce3
  • ce4
  • ce5
  • ce6
  • ce7
  • ce8
  • ce9
  • choHof1
  • chrPic1
  • ci2
  • danRer2
  • danRer3
  • danRer4
  • danRer5
  • danRer6
  • danRer7
  • dasNov1
  • dasNov2
  • dipOrd1
  • dm1
  • dm2
  • dm3
  • dp3
  • dp4
  • droAna1
  • droAna2
  • droAna3
  • droEre1
  • droEre2
  • droGri1
  • droGri2
  • droMoj1
  • droMoj2
  • droMoj3
  • droPer1
  • droSec1
  • droSim1
  • droVir1
  • droVir2
  • droVir3
  • droWil1
  • droYak1
  • droYak2
  • echTel1
  • emf
  • equCab1
  • equCab2
  • equCab2_chrM
  • eriEur1
  • felCat3
  • felCat4
  • fr1
  • fr2
  • fr3
  • galGal2
  • galGal3
  • galGal4
  • gasAcu1
  • geoFor1
  • gorGor1
  • gorGor3
  • hetGla1
  • hetGla2
  • hg16
  • hg17
  • hg18
  • hg19
  • hg_g1k_v37
  • lMaj5
  • lengths
  • loxAfr3
  • loxAfr4
  • macEug1
  • melGal1
  • melUnd1
  • micMur1
  • mm10
  • mm5
  • mm6
  • mm7
  • mm8
  • mm9
  • monDom4
  • monDom5
  • myoLuc1
  • myoLuc2
  • nomLeu1
  • nomLeu2
  • ochPri2
  • ornAna1
  • oryCun1
  • oryCun2
  • oryLat1
  • oryLat2
  • oryza_sativa_japonica_nipponbare_IRGSP4.0
  • otoGar1
  • oviAri1
  • pUC18
  • panTro1
  • panTro2
  • panTro3
  • papHam1
  • petMar1
  • phiX
  • ponAbe2
  • priPac1
  • rheMac2
  • rheMac3
  • rn3
  • rn4
  • rn5
  • sacCer1
  • sacCer2
  • sacCer3
  • sarHar1
  • sorAra1
  • strPur2
  • strPur3
  • susScr2
  • susScr3
  • taeGut1
  • tarSyr1
  • tetNig1
  • tetNig2
  • triCas2
  • tupBel1
  • venter1
  • xenTro1
  • xenTro2
  • xenTro3

Microbes

  • Staphylococcus_aureus_aureus_USA300_FPR3757
  • Xanthomonas_oryzae_PXO99A
  • acidBact_ELLIN345
  • acidCell_11B
  • acidCryp_JF_5
  • acidJS42
  • acinSp_ADP1
  • actiPleu_L20
  • aerPer1
  • aeroHydr_ATCC7966
  • alcaBork_SK2
  • alkaEhrl_MLHE_1
  • anabVari_ATCC29413
  • anaeDeha_2CP_C
  • anapMarg_ST_MARIES
  • aquiAeol
  • archFulg1
  • arthFB24
  • azoaSp_EBN1
  • azorCaul2
  • baciAnth_AMES
  • baciHalo
  • baciSubt
  • bactThet_VPI_5482
  • bartHens_HOUSTON_1
  • baumCica_HOMALODISCA
  • bdelBact
  • bifiLong
  • blocFlor
  • bordBron
  • borrBurg
  • bradJapo
  • brucMeli
  • buchSp
  • burk383
  • burkCeno_AU_1054
  • burkCeno_HI2424
  • burkCepa_AMMD
  • burkMall_ATCC23344
  • burkPseu_1106A
  • burkThai_E264
  • burkViet_G4
  • burkXeno_LB400
  • caldMaqu1
  • caldSacc_DSM8903
  • campFetu_82_40
  • campJeju
  • campJeju_81_176
  • campJeju_RM1221
  • candCars_RUDDII
  • candPela_UBIQUE_HTCC1
  • carbHydr_Z_2901
  • caulCres
  • chlaPneu_CWL029
  • chlaTrac
  • chloChlo_CAD3
  • chloTepi_TLS
  • chroSale_DSM3043
  • chroViol
  • clavMich_NCPPB_382
  • colwPsyc_34H
  • coryEffi_YS_314
  • coxiBurn
  • cytoHutc_ATCC33406
  • dechArom_RCB
  • dehaEthe_195
  • deinGeot_DSM11300
  • deinRadi
  • desuHafn_Y51
  • desuPsyc_LSV54
  • desuRedu_MI_1
  • desuVulg_HILDENBOROUG
  • dichNodo_VCS1703A
  • ehrlRumi_WELGEVONDEN
  • ente638
  • enteFaec_V583
  • erwiCaro_ATROSEPTICA
  • erytLito_HTCC2594
  • eschColi_APEC_O1
  • eschColi_CFT073
  • eschColi_EC4115
  • eschColi_EDL933
  • eschColi_K12
  • eschColi_MG1655
  • eschColi_O157H7
  • eschColi_TW14359
  • flavJohn_UW101
  • franCcI3
  • franTula_TULARENSIS
  • fusoNucl
  • geobKaus_HTA426
  • geobMeta_GS15
  • geobSulf
  • geobTher_NG80_2
  • geobUran_RF4
  • gloeViol
  • glucOxyd_621H
  • gramFors_KT0803
  • granBeth_CGDNIH1
  • haemInfl_KW20
  • haemSomn_129PT
  • haheChej_KCTC_2396
  • halMar1
  • haloHalo1
  • haloHalo_SL1
  • haloWals1
  • heliAcin_SHEEBA
  • heliHepa
  • heliPylo_26695
  • heliPylo_HPAG1
  • heliPylo_J99
  • hermArse
  • hypeButy1
  • hyphNept_ATCC15444
  • idioLoih_L2TR
  • jannCCS1
  • lactLact
  • lactPlan
  • lactSali_UCC118
  • lawsIntr_PHE_MN1_00
  • legiPneu_PHILADELPHIA
  • leifXyli_XYLI_CTCB0
  • leptInte
  • leucMese_ATCC8293
  • listInno
  • magnMC1
  • magnMagn_AMB_1
  • mannSucc_MBEL55E
  • mariAqua_VT8
  • mariMari_MCS10
  • mculMari1
  • mesoFlor_L1
  • mesoLoti
  • metAce1
  • metMar1
  • metaSedu
  • methAeol1
  • methBark1
  • methBoon1
  • methBurt2
  • methCaps_BATH
  • methFlag_KT
  • methHung1
  • methJann1
  • methKand1
  • methLabrZ_1
  • methMari_C5_1
  • methMari_C7
  • methMaze1
  • methPetr_PM1
  • methSmit1
  • methStad1
  • methTher1
  • methTherPT1
  • methVann1
  • moorTher_ATCC39073
  • mycoGeni
  • mycoTube_H37RV
  • myxoXant_DK_1622
  • nanEqu1
  • natrPhar1
  • neisGono_FA1090_1
  • neisMeni_FAM18_1
  • neisMeni_MC58_1
  • neisMeni_Z2491_1
  • neorSenn_MIYAYAMA
  • nitrEuro
  • nitrMult_ATCC25196
  • nitrOcea_ATCC19707
  • nitrWino_NB_255
  • nocaFarc_IFM10152
  • nocaJS61
  • nostSp
  • novoArom_DSM12444
  • oceaIhey
  • oenoOeni_PSU_1
  • onioYell_PHYTOPLASMA
  • orieTsut_BORYONG
  • paraDeni_PD1222
  • paraSp_UWE25
  • pastMult
  • pediPent_ATCC25745
  • peloCarb
  • peloLute_DSM273
  • peloTher_SI
  • photLumi
  • photProf_SS9
  • picrTorr1
  • pireSp
  • polaJS66
  • polyQLWP
  • porpGing_W83
  • procMari_CCMP1375
  • propAcne_KPA171202
  • pseuAeru
  • pseuHalo_TAC125
  • psycArct_273_4
  • psycIngr_37
  • pyrAby1
  • pyrAer1
  • pyrFur2
  • pyrHor1
  • pyroArse1
  • pyroCali1
  • pyroIsla1
  • ralsEutr_JMP134
  • ralsSola
  • rhizEtli_CFN_42
  • rhodPalu_CGA009
  • rhodRHA1
  • rhodRubr_ATCC11170
  • rhodSpha_2_4_1
  • rickBell_RML369_C
  • roseDeni_OCH_114
  • rubrXyla_DSM9941
  • saccDegr_2_40
  • saccEryt_NRRL_2338
  • saliRube_DSM13855
  • saliTrop_CNB_440
  • salmEnte_PARATYPI_ATC
  • salmTyph
  • salmTyph_TY2
  • shewANA3
  • shewAmaz
  • shewBalt
  • shewDeni
  • shewFrig
  • shewLoihPV4
  • shewMR4
  • shewMR7
  • shewOnei
  • shewPutrCN32
  • shewW318
  • shigFlex_2A
  • siliPome_DSS_3
  • sinoMeli
  • sodaGlos_MORSITANS
  • soliUsit_ELLIN6076
  • sphiAlas_RB2256
  • stapAure_MU50
  • stapMari1
  • streCoel
  • strePyog_M1_GAS
  • sulSol1
  • sulfAcid1
  • sulfToko1
  • symbTher_IAM14863
  • synePCC6
  • syneSp_WH8102
  • syntAcid_SB
  • syntFuma_MPOB
  • syntWolf_GOETTINGEN
  • therAcid1
  • therElon
  • therFusc_YX
  • therKoda1
  • therMari
  • therPend1
  • therPetr_RKU_1
  • therTeng
  • therTher_HB27
  • therTher_HB8
  • therVolc1
  • thioCrun_XCL_2
  • thioDeni_ATCC25259
  • thioDeni_ATCC33889
  • trepPall
  • tricEryt_IMS101
  • tropWhip_TW08_27
  • uncuMeth_RCI
  • ureaUrea
  • vermEise_EF01_2
  • vibrChol1
  • vibrChol_O395_1
  • vibrFisc_ES114_1
  • vibrPara1
  • vibrVuln_CMCP6_1
  • vibrVuln_YJ016_1
  • wiggBrev
  • wolbEndo_OF_DROSOPHIL
  • woliSucc
  • xantCamp
  • xyleFast
  • yersPest_CO92
  • zymoMobi_ZM4
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox