Galaxy
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Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
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