Galaxy

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= Overview =
 
= 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 [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/  UABgrid].  
+
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 [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/  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.
 
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.
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There are also several [[UAB Galaxy Workshop Tutorial|UAB tutorials on NGS Analysis with Galaxy]], created for [[2011_HPC_Boot_Camp|HPC Boot Camp 2011]] and a nice talk by Jeremy Goecks during [[2011|Research Computing Day 2011.]]
 
There are also several [[UAB Galaxy Workshop Tutorial|UAB tutorials on NGS Analysis with Galaxy]], created for [[2011_HPC_Boot_Camp|HPC Boot Camp 2011]] and a nice talk by Jeremy Goecks during [[2011|Research Computing Day 2011.]]
 +
 +
== Support ==
 +
UAB galaxy-users list-serv: [https://listserv.uab.edu/scgi-bin/wa?SUBED1=GALAXY-HELP&A=1 subscribe] [https://listserv.uab.edu/scgi-bin/wa?SUBED1=GALAXY-HELP&A=1 search].
 +
 +
UAB galaxy-help list-serv: [mailto:galaxy-help@listserv.uab.edu] 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 =
 
= 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.  
 
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.
 
However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.
+
 
 +
== Loading Data ==
 +
See [[Galaxy_File_Uploads]].
 +
 
 
== Available Tools ==  
 
== Available Tools ==  
Following is a short list highlighting some of the important tools available:
+
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 [http://toolshed.g2.bx.psu.edu/ Galaxy ToolShed].
 +
 
  
 
{| border="1"
 
{| border="1"
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! bowtie  
 
! bowtie  
 
| 0.12.7 || Align genomic short reads to a reference genome
 
| 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
 
! samtools
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! velvet
 
! velvet
 
| 1.1.03 || Denovo Assembly
 
| 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.
 
 
|-
 
|-
 
! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS]
 
! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS]
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|-
 
|-
 
|}
 
|}
 
  
 
== Installed Genome Indexes ==
 
== Installed Genome Indexes ==
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! dbkey !! Genome !! Accessions
 
! dbkey !! Genome !! Accessions
 
|-
 
|-
| mm9 || Mouse July 2007 (NCBI37/mm9) (mm9)
+
| 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)
 
| mm10 || Mouse Dec. 2011 (GRCm38/mm10) (mm10)
 
|-
 
|-
| hg18 || Human Mar. 2006 (NCBI36/hg18) (hg18)
+
| mm9 || Mouse July 2007 (NCBI37/mm9) (mm9)
 
|-
 
|-
| hg19 || Human Feb. 2009 (GRCh37/hg19) (hg19)
+
| mm8 || Mouse Feb. 2006 (NCBI36/mm8) (mm8)
 
|-
 
|-
|sacCer2 || S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
+
| mm7 || Mouse Aug. 2005 (NCBI35/mm7) (mm7)
 +
|-
 +
| mm6
 +
|-
 +
| mm5
 
|-
 
|-
 
|sacCer3 || S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
 
|sacCer3 || S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
 
|-
 
|-
|ce10 || C. elegans Oct. 2010 (WS220/ce10) (ce10)
+
|sacCer2 || S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
 
|-
 
|-
|rn4 || Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
+
|ce10 || C. elegans Oct. 2010 (WS220/ce10) (ce10)
 
|-
 
|-
 
|rn5 || Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
 
|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)
 
|danRer7 || Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)
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|}
 
|}
  
= Public instance =
+
== Additional Genomes that can be quickly installed ==
A public instance of Galaxy maintained by Penn State University is at http://usegalaxy.org/
+
These are pre-indexed genomes we can easily download from Penn State's [http://wiki.galaxyproject.org/Admin/Data%20Integration 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 ===
  
= Support =
+
* Staphylococcus_aureus_aureus_USA300_FPR3757
In order to facilitate interaction among UAB Galaxy users, share experience, and provide peer-support we have established a galaxy-user group. To join this group and participate in email discussions please subscribe to the [http://vo.uabgrid.uab.edu/sympa/subscribe/galaxy-user galaxy-user group]. On-line archives of these discussions are available [https://vo.uabgrid.uab.edu/sympa/arc/galaxy-user here]. In addition to the  [https://vo.uabgrid.uab.edu/sympa/arc/galaxy-user galaxy-user] mailing list, we have a [https://vo.uabgrid.uab.edu/sympa/info/galaxy-annce galaxy-annce] mailing list for UAB's galaxy instance related announcements. The [https://vo.uabgrid.uab.edu/sympa/info/galaxy-annce galaxy-annce] is a low volume mailing list for announcing service status and system updates etc. Please note, the email discussions are a public forum. You are advised to only post information you are authorized to share and comfortable with being public.
+
* 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
  
= References =
 
* [http://bitbucket.org/galaxy/galaxy-central/wiki/Home Galaxy Wiki]
 
* [http://bitbucket.org/galaxy/galaxy-central/wiki/ImplementationInfo Galaxy Architecture]
 
* [http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy Get Galaxy]
 
* [http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer Galaxy Advanced Config]
 
  
 
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
 
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]

Latest revision as of 09:48, 13 December 2017

Contents


[edit] 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.

[edit] 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.

[edit] Support

UAB galaxy-users list-serv: subscribe search.

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

[edit] 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.

[edit] 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.

[edit] Loading Data

See Galaxy_File_Uploads.

[edit] 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

[edit] 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

[edit] Additional Genomes that can be quickly installed

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

[edit] 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

[edit] 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
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