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.
Line 13: Line 13:
  
 
== Support ==  
 
== Support ==  
UAB galaxy-users list-serv: [http://vo.uabgrid.uab.edu/sympa/subscribe/galaxy-user subscribe] [https://vo.uabgrid.uab.edu/sympa/arc/galaxy-user search].  
+
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@vo.uabgrid.uab.edu] to contact admins of the UAB galaxy instance.
+
UAB galaxy-help list-serv: [mailto:galaxy-help@listserv.uab.edu] to contact admins of the UAB galaxy instance.
  
 
== Privacy ==
 
== 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.  
+
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 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].
 
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].
Line 38: Line 41:
 
! 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
Line 44: Line 53:
 
! 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)
 +
|-
 +
|sacCer2 || S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
 
|-
 
|-
 
|ce10 || C. elegans Oct. 2010 (WS220/ce10) (ce10)
 
|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)
 
|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)
Line 104: Line 118:
  
 
=== 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 ===
  
Staphylococcus_aureus_aureus_USA300_FPR3757
+
* Staphylococcus_aureus_aureus_USA300_FPR3757
Xanthomonas_oryzae_PXO99A
+
* Xanthomonas_oryzae_PXO99A
acidBact_ELLIN345
+
* acidBact_ELLIN345
acidCell_11B
+
* acidCell_11B
acidCryp_JF_5
+
* acidCryp_JF_5
acidJS42
+
* acidJS42
acinSp_ADP1
+
* acinSp_ADP1
actiPleu_L20
+
* actiPleu_L20
aerPer1
+
* aerPer1
aeroHydr_ATCC7966
+
* aeroHydr_ATCC7966
alcaBork_SK2
+
* alcaBork_SK2
alkaEhrl_MLHE_1
+
* alkaEhrl_MLHE_1
anabVari_ATCC29413
+
* anabVari_ATCC29413
anaeDeha_2CP_C
+
* anaeDeha_2CP_C
anapMarg_ST_MARIES
+
* anapMarg_ST_MARIES
aquiAeol
+
* aquiAeol
archFulg1
+
* archFulg1
arthFB24
+
* arthFB24
azoaSp_EBN1
+
* azoaSp_EBN1
azorCaul2
+
* azorCaul2
baciAnth_AMES
+
* baciAnth_AMES
baciHalo
+
* baciHalo
baciSubt
+
* baciSubt
bactThet_VPI_5482
+
* bactThet_VPI_5482
bartHens_HOUSTON_1
+
* bartHens_HOUSTON_1
baumCica_HOMALODISCA
+
* baumCica_HOMALODISCA
bdelBact
+
* bdelBact
bifiLong
+
* bifiLong
blocFlor
+
* blocFlor
bordBron
+
* bordBron
borrBurg
+
* borrBurg
bradJapo
+
* bradJapo
brucMeli
+
* brucMeli
buchSp
+
* buchSp
burk383
+
* burk383
burkCeno_AU_1054
+
* burkCeno_AU_1054
burkCeno_HI2424
+
* burkCeno_HI2424
burkCepa_AMMD
+
* burkCepa_AMMD
burkMall_ATCC23344
+
* burkMall_ATCC23344
burkPseu_1106A
+
* burkPseu_1106A
burkThai_E264
+
* burkThai_E264
burkViet_G4
+
* burkViet_G4
burkXeno_LB400
+
* burkXeno_LB400
caldMaqu1
+
* caldMaqu1
caldSacc_DSM8903
+
* caldSacc_DSM8903
campFetu_82_40
+
* campFetu_82_40
campJeju
+
* campJeju
campJeju_81_176
+
* campJeju_81_176
campJeju_RM1221
+
* campJeju_RM1221
candCars_RUDDII
+
* candCars_RUDDII
candPela_UBIQUE_HTCC1
+
* candPela_UBIQUE_HTCC1
carbHydr_Z_2901
+
* carbHydr_Z_2901
caulCres
+
* caulCres
chlaPneu_CWL029
+
* chlaPneu_CWL029
chlaTrac
+
* chlaTrac
chloChlo_CAD3
+
* chloChlo_CAD3
chloTepi_TLS
+
* chloTepi_TLS
chroSale_DSM3043
+
* chroSale_DSM3043
chroViol
+
* chroViol
clavMich_NCPPB_382
+
* clavMich_NCPPB_382
colwPsyc_34H
+
* colwPsyc_34H
coryEffi_YS_314
+
* coryEffi_YS_314
coxiBurn
+
* coxiBurn
cytoHutc_ATCC33406
+
* cytoHutc_ATCC33406
dechArom_RCB
+
* dechArom_RCB
dehaEthe_195
+
* dehaEthe_195
deinGeot_DSM11300
+
* deinGeot_DSM11300
deinRadi
+
* deinRadi
desuHafn_Y51
+
* desuHafn_Y51
desuPsyc_LSV54
+
* desuPsyc_LSV54
desuRedu_MI_1
+
* desuRedu_MI_1
desuVulg_HILDENBOROUG
+
* desuVulg_HILDENBOROUG
dichNodo_VCS1703A
+
* dichNodo_VCS1703A
ehrlRumi_WELGEVONDEN
+
* ehrlRumi_WELGEVONDEN
ente638
+
* ente638
enteFaec_V583
+
* enteFaec_V583
erwiCaro_ATROSEPTICA
+
* erwiCaro_ATROSEPTICA
erytLito_HTCC2594
+
* erytLito_HTCC2594
eschColi_APEC_O1
+
* eschColi_APEC_O1
eschColi_CFT073
+
* eschColi_CFT073
eschColi_EC4115
+
* eschColi_EC4115
eschColi_EDL933
+
* eschColi_EDL933
eschColi_K12
+
* eschColi_K12
eschColi_MG1655
+
* eschColi_MG1655
eschColi_O157H7
+
* eschColi_O157H7
eschColi_TW14359
+
* eschColi_TW14359
flavJohn_UW101
+
* flavJohn_UW101
franCcI3
+
* franCcI3
franTula_TULARENSIS
+
* franTula_TULARENSIS
fusoNucl
+
* fusoNucl
geobKaus_HTA426
+
* geobKaus_HTA426
geobMeta_GS15
+
* geobMeta_GS15
geobSulf
+
* geobSulf
geobTher_NG80_2
+
* geobTher_NG80_2
geobUran_RF4
+
* geobUran_RF4
gloeViol
+
* gloeViol
glucOxyd_621H
+
* glucOxyd_621H
gramFors_KT0803
+
* gramFors_KT0803
granBeth_CGDNIH1
+
* granBeth_CGDNIH1
haemInfl_KW20
+
* haemInfl_KW20
haemSomn_129PT
+
* haemSomn_129PT
haheChej_KCTC_2396
+
* haheChej_KCTC_2396
halMar1
+
* halMar1
haloHalo1
+
* haloHalo1
haloHalo_SL1
+
* haloHalo_SL1
haloWals1
+
* haloWals1
heliAcin_SHEEBA
+
* heliAcin_SHEEBA
heliHepa
+
* heliHepa
heliPylo_26695
+
* heliPylo_26695
heliPylo_HPAG1
+
* heliPylo_HPAG1
heliPylo_J99
+
* heliPylo_J99
hermArse
+
* hermArse
hypeButy1
+
* hypeButy1
hyphNept_ATCC15444
+
* hyphNept_ATCC15444
idioLoih_L2TR
+
* idioLoih_L2TR
jannCCS1
+
* jannCCS1
lactLact
+
* lactLact
lactPlan
+
* lactPlan
lactSali_UCC118
+
* lactSali_UCC118
lawsIntr_PHE_MN1_00
+
* lawsIntr_PHE_MN1_00
legiPneu_PHILADELPHIA
+
* legiPneu_PHILADELPHIA
leifXyli_XYLI_CTCB0
+
* leifXyli_XYLI_CTCB0
leptInte
+
* leptInte
leucMese_ATCC8293
+
* leucMese_ATCC8293
listInno
+
* listInno
magnMC1
+
* magnMC1
magnMagn_AMB_1
+
* magnMagn_AMB_1
mannSucc_MBEL55E
+
* mannSucc_MBEL55E
mariAqua_VT8
+
* mariAqua_VT8
mariMari_MCS10
+
* mariMari_MCS10
mculMari1
+
* mculMari1
mesoFlor_L1
+
* mesoFlor_L1
mesoLoti
+
* mesoLoti
metAce1
+
* metAce1
metMar1
+
* metMar1
metaSedu
+
* metaSedu
methAeol1
+
* methAeol1
methBark1
+
* methBark1
methBoon1
+
* methBoon1
methBurt2
+
* methBurt2
methCaps_BATH
+
* methCaps_BATH
methFlag_KT
+
* methFlag_KT
methHung1
+
* methHung1
methJann1
+
* methJann1
methKand1
+
* methKand1
methLabrZ_1
+
* methLabrZ_1
methMari_C5_1
+
* methMari_C5_1
methMari_C7
+
* methMari_C7
methMaze1
+
* methMaze1
methPetr_PM1
+
* methPetr_PM1
methSmit1
+
* methSmit1
methStad1
+
* methStad1
methTher1
+
* methTher1
methTherPT1
+
* methTherPT1
methVann1
+
* methVann1
moorTher_ATCC39073
+
* moorTher_ATCC39073
mycoGeni
+
* mycoGeni
mycoTube_H37RV
+
* mycoTube_H37RV
myxoXant_DK_1622
+
* myxoXant_DK_1622
nanEqu1
+
* nanEqu1
natrPhar1
+
* natrPhar1
neisGono_FA1090_1
+
* neisGono_FA1090_1
neisMeni_FAM18_1
+
* neisMeni_FAM18_1
neisMeni_MC58_1
+
* neisMeni_MC58_1
neisMeni_Z2491_1
+
* neisMeni_Z2491_1
neorSenn_MIYAYAMA
+
* neorSenn_MIYAYAMA
nitrEuro
+
* nitrEuro
nitrMult_ATCC25196
+
* nitrMult_ATCC25196
nitrOcea_ATCC19707
+
* nitrOcea_ATCC19707
nitrWino_NB_255
+
* nitrWino_NB_255
nocaFarc_IFM10152
+
* nocaFarc_IFM10152
nocaJS61
+
* nocaJS61
nostSp
+
* nostSp
novoArom_DSM12444
+
* novoArom_DSM12444
oceaIhey
+
* oceaIhey
oenoOeni_PSU_1
+
* oenoOeni_PSU_1
onioYell_PHYTOPLASMA
+
* onioYell_PHYTOPLASMA
orieTsut_BORYONG
+
* orieTsut_BORYONG
paraDeni_PD1222
+
* paraDeni_PD1222
paraSp_UWE25
+
* paraSp_UWE25
pastMult
+
* pastMult
pediPent_ATCC25745
+
* pediPent_ATCC25745
peloCarb
+
* peloCarb
peloLute_DSM273
+
* peloLute_DSM273
peloTher_SI
+
* peloTher_SI
photLumi
+
* photLumi
photProf_SS9
+
* photProf_SS9
picrTorr1
+
* picrTorr1
pireSp
+
* pireSp
polaJS66
+
* polaJS66
polyQLWP
+
* polyQLWP
porpGing_W83
+
* porpGing_W83
procMari_CCMP1375
+
* procMari_CCMP1375
propAcne_KPA171202
+
* propAcne_KPA171202
pseuAeru
+
* pseuAeru
pseuHalo_TAC125
+
* pseuHalo_TAC125
psycArct_273_4
+
* psycArct_273_4
psycIngr_37
+
* psycIngr_37
pyrAby1
+
* pyrAby1
pyrAer1
+
* pyrAer1
pyrFur2
+
* pyrFur2
pyrHor1
+
* pyrHor1
pyroArse1
+
* pyroArse1
pyroCali1
+
* pyroCali1
pyroIsla1
+
* pyroIsla1
ralsEutr_JMP134
+
* ralsEutr_JMP134
ralsSola
+
* ralsSola
rhizEtli_CFN_42
+
* rhizEtli_CFN_42
rhodPalu_CGA009
+
* rhodPalu_CGA009
rhodRHA1
+
* rhodRHA1
rhodRubr_ATCC11170
+
* rhodRubr_ATCC11170
rhodSpha_2_4_1
+
* rhodSpha_2_4_1
rickBell_RML369_C
+
* rickBell_RML369_C
roseDeni_OCH_114
+
* roseDeni_OCH_114
rubrXyla_DSM9941
+
* rubrXyla_DSM9941
saccDegr_2_40
+
* saccDegr_2_40
saccEryt_NRRL_2338
+
* saccEryt_NRRL_2338
saliRube_DSM13855
+
* saliRube_DSM13855
saliTrop_CNB_440
+
* saliTrop_CNB_440
salmEnte_PARATYPI_ATC
+
* salmEnte_PARATYPI_ATC
salmTyph
+
* salmTyph
salmTyph_TY2
+
* salmTyph_TY2
shewANA3
+
* shewANA3
shewAmaz
+
* shewAmaz
shewBalt
+
* shewBalt
shewDeni
+
* shewDeni
shewFrig
+
* shewFrig
shewLoihPV4
+
* shewLoihPV4
shewMR4
+
* shewMR4
shewMR7
+
* shewMR7
shewOnei
+
* shewOnei
shewPutrCN32
+
* shewPutrCN32
shewW318
+
* shewW318
shigFlex_2A
+
* shigFlex_2A
siliPome_DSS_3
+
* siliPome_DSS_3
sinoMeli
+
* sinoMeli
sodaGlos_MORSITANS
+
* sodaGlos_MORSITANS
soliUsit_ELLIN6076
+
* soliUsit_ELLIN6076
sphiAlas_RB2256
+
* sphiAlas_RB2256
stapAure_MU50
+
* stapAure_MU50
stapMari1
+
* stapMari1
streCoel
+
* streCoel
strePyog_M1_GAS
+
* strePyog_M1_GAS
sulSol1
+
* sulSol1
sulfAcid1
+
* sulfAcid1
sulfToko1
+
* sulfToko1
symbTher_IAM14863
+
* symbTher_IAM14863
synePCC6
+
* synePCC6
syneSp_WH8102
+
* syneSp_WH8102
syntAcid_SB
+
* syntAcid_SB
syntFuma_MPOB
+
* syntFuma_MPOB
syntWolf_GOETTINGEN
+
* syntWolf_GOETTINGEN
therAcid1
+
* therAcid1
therElon
+
* therElon
therFusc_YX
+
* therFusc_YX
therKoda1
+
* therKoda1
therMari
+
* therMari
therPend1
+
* therPend1
therPetr_RKU_1
+
* therPetr_RKU_1
therTeng
+
* therTeng
therTher_HB27
+
* therTher_HB27
therTher_HB8
+
* therTher_HB8
therVolc1
+
* therVolc1
thioCrun_XCL_2
+
* thioCrun_XCL_2
thioDeni_ATCC25259
+
* thioDeni_ATCC25259
thioDeni_ATCC33889
+
* thioDeni_ATCC33889
trepPall
+
* trepPall
tricEryt_IMS101
+
* tricEryt_IMS101
tropWhip_TW08_27
+
* tropWhip_TW08_27
uncuMeth_RCI
+
* uncuMeth_RCI
ureaUrea
+
* ureaUrea
vermEise_EF01_2
+
* vermEise_EF01_2
vibrChol1
+
* vibrChol1
vibrChol_O395_1
+
* vibrChol_O395_1
vibrFisc_ES114_1
+
* vibrFisc_ES114_1
vibrPara1
+
* vibrPara1
vibrVuln_CMCP6_1
+
* vibrVuln_CMCP6_1
vibrVuln_YJ016_1
+
* vibrVuln_YJ016_1
wiggBrev
+
* wiggBrev
wolbEndo_OF_DROSOPHIL
+
* wolbEndo_OF_DROSOPHIL
woliSucc
+
* woliSucc
xantCamp
+
* xantCamp
xyleFast
+
* xyleFast
yersPest_CO92
+
* yersPest_CO92
zymoMobi_ZM4
+
* zymoMobi_ZM4
  
  
 
[[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
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  • shewOnei
  • shewPutrCN32
  • shewW318
  • shigFlex_2A
  • siliPome_DSS_3
  • sinoMeli
  • sodaGlos_MORSITANS
  • soliUsit_ELLIN6076
  • sphiAlas_RB2256
  • stapAure_MU50
  • stapMari1
  • streCoel
  • strePyog_M1_GAS
  • sulSol1
  • sulfAcid1
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  • symbTher_IAM14863
  • synePCC6
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  • syntAcid_SB
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  • therAcid1
  • therElon
  • therFusc_YX
  • therKoda1
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  • 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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