Galaxy

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