Galaxy: Difference between revisions
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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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== Support == | == Support == | ||
UAB galaxy-users list-serv: [ | 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@ | 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]. | ||
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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 | ||
| Line 44: | Line 53: | ||
! velvet | ! velvet | ||
| 1.1.03 || Denovo Assembly | | 1.1.03 || Denovo Assembly | ||
|- | |- | ||
! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS] | ! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS] | ||
| Line 55: | Line 58: | ||
|- | |- | ||
|} | |} | ||
== Installed Genome Indexes == | == Installed Genome Indexes == | ||
| Line 63: | Line 65: | ||
|+ | |+ | ||
! dbkey !! Genome !! Accessions | ! 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) | | 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) | |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) | ||
|- | |||
|rn5 || Rat Mar. 2012 (RGSC 5.0/rn5) (rn5) | |||
|- | |- | ||
|rn4 || Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) | |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 === | ||
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 14:48, 13 December 2017
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.
Loading Data
See Galaxy_File_Uploads.
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