Galaxy

Overview

The UAB Galaxy platform for experimental biology and comparative genomics is 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
tophat	1.4.0	Align transcriptome short reads to a reference genome
cufflinks, cuffdiff, cuffcompare	1.3.0	Reconstruct and quantify transcript levels from tophat alignments.
samtools	0.1.12a	Alignment (SAM/BAM file) manipulations
velvet	1.1.03	Denovo Assembly
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
hg19	Human Feb. 2009 (GRCh37/hg19) (hg19)
hg18	Human Mar. 2006 (NCBI36/hg18) (hg18)
hg17	Human May 2004 (NCBI35/hg17) (hg17)
hg16	Human July 2003 (NCBI34/hg16) (hg16)
mm10	Mouse Dec. 2011 (GRCm38/mm10) (mm10)
mm9	Mouse July 2007 (NCBI37/mm9) (mm9)
mm8	Mouse Feb. 2006 (NCBI36/mm8) (mm8)
mm7	Mouse Aug. 2005 (NCBI35/mm7) (mm7)
mm6
mm5
sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
sacCer2	S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
ce10	C. elegans Oct. 2010 (WS220/ce10) (ce10)
rn5	Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
rn4	Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
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