User contributions
From UABgrid Documentation
(Latest | Earliest) View (newer 250 | older 250) (20 | 50 | 100 | 250 | 500)
- 14:03, 28 August 2020 (diff | hist) . . (+861) . . Jupyter (More information on custom building conda environments on cheahea)
- 11:41, 21 April 2020 (diff | hist) . . (+20) . . m UAB Openstack Tutorial (→Create Application Credentials) (top)
- 12:29, 28 February 2020 (diff | hist) . . (+526) . . m UAB Openstack Tutorial (Add info on getting creds)
- 12:17, 28 February 2020 (diff | hist) . . (+3,373) . . N UAB Openstack Tutorial (Initial Page Creation)
- 20:19, 7 February 2020 (diff | hist) . . (+141) . . m Jupyter (→Build your conda environment: How to update)
- 21:33, 6 February 2020 (diff | hist) . . (+12) . . m Jupyter (--no-builds option)
- 22:26, 14 January 2020 (diff | hist) . . (+64) . . Jupyter (→Build your conda environment)
- 22:25, 14 January 2020 (diff | hist) . . (+85) . . Jupyter (→Build your conda environment)
- 22:22, 14 January 2020 (diff | hist) . . (+76) . . N File:JupyterCustomEnv.jpeg (File showing what a custom conda environment looks like in Jupyter On Demand) (top)
- 22:21, 14 January 2020 (diff | hist) . . (+55) . . Jupyter (→Set up your cheaha .condarc file)
- 22:21, 14 January 2020 (diff | hist) . . (+2) . . Jupyter (→Add ipkernel to your conda environment)
- 22:20, 14 January 2020 (diff | hist) . . (+37) . . Jupyter (→Export YAML file containing your environment to cheaha)
- 22:20, 14 January 2020 (diff | hist) . . (+84) . . Jupyter (→Export YAML file containing your environment to cheaha)
- 22:19, 14 January 2020 (diff | hist) . . (+257) . . Jupyter (→Adding Custom Conda Environments to Jupyter)
- 22:17, 14 January 2020 (diff | hist) . . (+667) . . Jupyter (Added Custom Jupyter Conda Environments)
- 21:08, 27 October 2019 (diff | hist) . . (+33) . . Jupyter (→Jupyter On Demand)
- 21:07, 27 October 2019 (diff | hist) . . (+16) . . N File:LaunchJupyter.png (Button to press.) (top)
- 21:02, 27 October 2019 (diff | hist) . . (+43) . . Jupyter (Adding numbering)
- 20:57, 27 October 2019 (diff | hist) . . (+187) . . Jupyter (→Jupyter On Demand)
- 19:05, 27 October 2019 (diff | hist) . . (+60) . . Jupyter (Updated GPU instructions)
- 19:03, 27 October 2019 (diff | hist) . . (+27) . . N File:PascalNodes.png (Arguments for getting a GPU) (top)
- 19:03, 27 October 2019 (diff | hist) . . (+43) . . N File:TestPytorch.png (Shows successful pytorch run on pascalnodes) (top)
- 18:57, 27 October 2019 (diff | hist) . . (+66) . . N File:PascalNodes.pdf (Shows arguments for starting a job using PascaleNodes to get a GPU) (top)
- 18:57, 27 October 2019 (diff | hist) . . (+57) . . N File:TestPytorch.pdf (Shows success test of PyTorch on Jupter Notebook Oct 2019) (top)
- 11:19, 24 October 2019 (diff | hist) . . (+17) . . Jupyter (→Jupyter On Demand)
- 11:17, 24 October 2019 (diff | hist) . . (+104) . . Jupyter (→Jupyter by Proxy: Warning added)
- 11:16, 24 October 2019 (diff | hist) . . (+113) . . m Jupyter (→Jupyter On Demand: Cleanup)
- 11:14, 24 October 2019 (diff | hist) . . (+46) . . Jupyter (→Jupyter On Demand)
- 11:31, 22 October 2019 (diff | hist) . . (0) . . m Jupyter (→Jupyter On Demand)
- 11:26, 22 October 2019 (diff | hist) . . (+1) . . m Jupyter (→Jupyter On Demand)
- 11:15, 22 October 2019 (diff | hist) . . (+9) . . m Jupyter (Updated Anaconda environment)
- 10:31, 17 September 2019 (diff | hist) . . (+57) . . Jupyter (GPU environment description)
- 10:29, 17 September 2019 (diff | hist) . . (+24) . . N File:JupyterNotebookGPUEnvironment.png (Arguments for using GPUs) (top)
- 10:29, 17 September 2019 (diff | hist) . . (+94) . . Jupyter (→Jupyter On Demand)
- 10:24, 17 September 2019 (diff | hist) . . (+168) . . Jupyter (→Jupyter On Demand: Cleanup starting Jupyter)
- 10:15, 17 September 2019 (diff | hist) . . (+44) . . N File:JupyterNotebookStart.png (Image of starting Jupyter Notebook on cheaha) (top)
- 10:13, 17 September 2019 (diff | hist) . . (+172) . . m Jupyter (→Jupyter On Demand: - environment arguments)
- 17:21, 31 August 2019 (diff | hist) . . (+121) . . Jupyter (On Demand added)
- 12:38, 30 January 2019 (diff | hist) . . (+25) . . PheDRS (→NLP Discovered Patients) (top)
- 12:31, 30 January 2019 (diff | hist) . . (+366) . . PheDRS (→Evidence Code Ontology: Updating NLP)
- 12:19, 30 January 2019 (diff | hist) . . (+529) . . PheDRS (→Evidence Code Ontology)
- 11:59, 30 January 2019 (diff | hist) . . (+698) . . PheDRS (→Developer Guide to PheDRS Data Loading Criteria: Updating vocabulary meaning.)
- 15:39, 24 January 2019 (diff | hist) . . (+826) . . PheDRS (→Phenotype Detection Registry System (PheDRS) User Documentation: Evidence Codes)
- 15:28, 24 January 2019 (diff | hist) . . (+5) . . m PheDRS (→Installation / Setup: TODO)
- 15:19, 18 January 2019 (diff | hist) . . (-80) . . m PheDRS (→Developer Guide to PheDRS Data Loading Criteria)
- 14:54, 18 January 2019 (diff | hist) . . (+15) . . m PheDRS (→Developer Guide to PheDRS Data Loading Criteria)
- 14:51, 18 January 2019 (diff | hist) . . (-65) . . PheDRS (→Developer Guide for Registry Configuration Properties)
- 14:44, 18 January 2019 (diff | hist) . . (-153) . . m PheDRS (→Developer Guide for Registry Configuration Properties)
- 14:38, 18 January 2019 (diff | hist) . . (-84) . . PheDRS (→Developer Guide for Registry Configuration Properties)
- 14:33, 18 January 2019 (diff | hist) . . (+6,091) . . PheDRS (→Developer Guide for Registry Configuration Properties)
- 14:22, 18 January 2019 (diff | hist) . . (+107) . . PheDRS (→Phenotype Detection Registry System (PheDRS) User Documentation)
- 14:19, 18 January 2019 (diff | hist) . . (+708) . . PheDRS (→Registry Configuration: Adding developer guide for registry configuration properties)
- 12:01, 18 January 2019 (diff | hist) . . (+53) . . m PheDRS (→Phenotype Detection Registry System (PheDRS) User Documentation)
- 11:57, 18 January 2019 (diff | hist) . . (+401) . . PheDRS (→Phenotype Detection Registry System (PheDRS) User Documentation: Documentation Location)
- 11:39, 18 January 2019 (diff | hist) . . (+33) . . PheDRS (→Phenotype Detection Registry System)
- 11:48, 17 January 2019 (diff | hist) . . (+785) . . PheDRS (→Phenotype Detection Registry System: Added roles)
- 17:40, 14 January 2019 (diff | hist) . . (+187) . . PheDRS (Placeholders for Content)
- 16:25, 14 January 2019 (diff | hist) . . (+2,240) . . PheDRS (CVTERM Prop configuration added)
- 14:58, 14 January 2019 (diff | hist) . . (+338) . . N PheDRS (Creation)
- 09:55, 1 November 2018 (diff | hist) . . (-5) . . Jupyter (→3. Copy notebook settings)
- 09:54, 1 November 2018 (diff | hist) . . (+352) . . Jupyter (Detailing steps to starting Jupyter)
- 11:39, 19 October 2018 (diff | hist) . . (+26) . . Jupyter (→DeepNLP option)
- 10:31, 18 October 2018 (diff | hist) . . (+227) . . Jupyter (DeepNLP option)
- 14:55, 11 October 2018 (diff | hist) . . (+205) . . Jupyter (Additional information on Python_Virtual_Environment and Anaconda)
- 15:02, 4 October 2018 (diff | hist) . . (+164) . . Jupyter (Added memory heavy option)
- 18:03, 25 September 2018 (diff | hist) . . (+731) . . N DeepNLP (Create documentation for conda module)
- 11:16, 12 September 2018 (diff | hist) . . (+520) . . Jupyter (Adding GPU info, cleanup)
- 18:06, 4 September 2018 (diff | hist) . . (+71) . . Jupyter (putty port forward link added)
- 16:20, 4 September 2018 (diff | hist) . . (+531) . . Jupyter (Windows instructions for connecting and proxying from cheaha)
- 17:44, 2 September 2018 (diff | hist) . . (+266) . . Jupyter (IO data rate fix)
- 21:19, 1 September 2018 (diff | hist) . . (+17) . . m Jupyter (Typo fix, bolding relevant bits)
- 11:35, 29 August 2018 (diff | hist) . . (+305) . . Jupyter (→Jupyter on Cheaha)
- 11:26, 29 August 2018 (diff | hist) . . (+290) . . Jupyter (→Jupyter on Cheaha)
- 13:28, 22 August 2018 (diff | hist) . . (+68) . . m Slurm (Link to Jupyter Notebook)
- 14:41, 21 August 2018 (diff | hist) . . (+1,028) . . Jupyter (Description of how to run Jupyter Notebook interactively using Anaconda3/5.2.0)
- 16:17, 17 December 2012 (diff | hist) . . (+1,118) . . NgsCctsBuildAbyss (Notes on sucessfull compiling of abyss) (top)
- 09:19, 16 September 2011 (diff | hist) . . (+73) . . Galaxy DNA-Seq Tutorial (→Comparative Genomics) (top)
- 09:17, 16 September 2011 (diff | hist) . . (+36) . . Galaxy DNA-Seq Tutorial (→Difference from consensus)
- 09:16, 16 September 2011 (diff | hist) . . (+13) . . Galaxy DNA-Seq Tutorial (→SNPEff - Variation Summation (optional))
- 09:15, 16 September 2011 (diff | hist) . . (-3) . . Galaxy DNA-Seq Tutorial (→Comparative Genomics)
- 09:14, 16 September 2011 (diff | hist) . . (-3) . . Galaxy DNA-Seq Tutorial (→Difference from consensus)
- 09:14, 16 September 2011 (diff | hist) . . (-2) . . Galaxy DNA-Seq Tutorial (→Pileup Filter)
- 09:14, 16 September 2011 (diff | hist) . . (-2) . . Galaxy DNA-Seq Tutorial (→Finding the Relevant SNPs versus Control)
- 01:46, 16 September 2011 (diff | hist) . . (+125) . . Galaxy DNA-Seq Tutorial (→Pileup Filter)
- 01:45, 16 September 2011 (diff | hist) . . (+10) . . Galaxy DNA-Seq Tutorial (→SNPEff - Variation Summation)
- 01:44, 16 September 2011 (diff | hist) . . (+304) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 01:29, 16 September 2011 (diff | hist) . . (+207) . . Galaxy DNA-Seq Tutorial (→Results from SNPEff)
- 01:26, 16 September 2011 (diff | hist) . . (+88) . . Galaxy DNA-Seq Tutorial
- 01:22, 16 September 2011 (diff | hist) . . (+164) . . Galaxy DNA-Seq Tutorial (→FastQC Results)
- 01:19, 16 September 2011 (diff | hist) . . (+8) . . Galaxy DNA-Seq Tutorial (→FastQC Results)
- 01:17, 16 September 2011 (diff | hist) . . (0) . . N File:Fastqc summary.jpg (top)
- 01:13, 16 September 2011 (diff | hist) . . (+3) . . Galaxy DNA-Seq Tutorial (→Running FastQC)
- 01:12, 16 September 2011 (diff | hist) . . (+154) . . Galaxy DNA-Seq Tutorial (→Metadata - Formatting and Grooming Data)
- 00:55, 16 September 2011 (diff | hist) . . (+194) . . Galaxy DNA-Seq Tutorial (→Trimming Reads)
- 00:49, 16 September 2011 (diff | hist) . . (-7) . . Galaxy DNA-Seq Tutorial (→Quality Control = Formatting and Grooming Data)
- 00:47, 16 September 2011 (diff | hist) . . (+109) . . Galaxy DNA-Seq Tutorial (→Formatting and Grooming Data)
- 22:41, 15 September 2011 (diff | hist) . . (+148) . . Galaxy DNA-Seq Tutorial (→Short read alignment to reference genome using BWA)
- 21:58, 15 September 2011 (diff | hist) . . (+1) . . Galaxy (→Available datasets)
- 21:57, 15 September 2011 (diff | hist) . . (+2) . . Galaxy (→Available datasets)
- 16:53, 15 September 2011 (diff | hist) . . (+351) . . Galaxy DNA-Seq Tutorial
- 16:50, 15 September 2011 (diff | hist) . . (0) . . N File:SNPEffResultTabular.jpg (top)
- 16:43, 15 September 2011 (diff | hist) . . (+534) . . Galaxy DNA-Seq Tutorial (→Difference from consensus)
- 16:36, 15 September 2011 (diff | hist) . . (0) . . N File:CMV21950RvsVACWR CompareData.jpg (top)
- 16:31, 15 September 2011 (diff | hist) . . (+472) . . Galaxy DNA-Seq Tutorial (→Locating Relevant SNPs versus Control)
- 16:18, 15 September 2011 (diff | hist) . . (+83) . . Galaxy DNA-Seq Tutorial
- 16:15, 15 September 2011 (diff | hist) . . (+13) . . Galaxy DNA-Seq Tutorial (→Linking to data)
- 16:14, 15 September 2011 (diff | hist) . . (+41) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 16:14, 15 September 2011 (diff | hist) . . (0) . . N File:GalaxyTutorialSharedLibrary.jpg (top)
- 16:13, 15 September 2011 (diff | hist) . . (+209) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 15:56, 15 September 2011 (diff | hist) . . (+26) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 15:56, 15 September 2011 (diff | hist) . . (+44) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 15:54, 15 September 2011 (diff | hist) . . (+573) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 15:44, 15 September 2011 (diff | hist) . . (+285) . . Galaxy DNA-Seq Tutorial
- 15:32, 15 September 2011 (diff | hist) . . (+106) . . Galaxy DNA-Seq Tutorial (→Other Variant Detection Approaches)
- 15:28, 15 September 2011 (diff | hist) . . (-2) . . Galaxy DNA-Seq Tutorial (→Samtools)
- 15:28, 15 September 2011 (diff | hist) . . (+116) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 15:09, 15 September 2011 (diff | hist) . . (+75) . . Galaxy DNA-Seq Tutorial
- 15:06, 15 September 2011 (diff | hist) . . (+16) . . N File:SamBamFileFormatFlags.jpg (SAM format flags) (top)
- 15:02, 15 September 2011 (diff | hist) . . (+45) . . Galaxy DNA-Seq Tutorial
- 14:56, 15 September 2011 (diff | hist) . . (+153) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 14:51, 15 September 2011 (diff | hist) . . (+237) . . Galaxy DNA-Seq Tutorial (→Short read alignment to reference genome using BWA)
- 14:46, 15 September 2011 (diff | hist) . . (+152) . . Galaxy DNA-Seq Tutorial (→Results)
- 14:43, 15 September 2011 (diff | hist) . . (+262) . . Galaxy DNA-Seq Tutorial (→Performing cleanup)
- 14:40, 15 September 2011 (diff | hist) . . (+32) . . N File:FastQTrimmerRun.jpg (CMV 21950R being trimmed from 3') (top)
- 14:31, 15 September 2011 (diff | hist) . . (+226) . . Galaxy DNA-Seq Tutorial
- 14:27, 15 September 2011 (diff | hist) . . (+88) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 14:25, 15 September 2011 (diff | hist) . . (0) . . File:DrawQualityScoreBoxplot.jpg (uploaded a new version of "File:DrawQualityScoreBoxplot.jpg": Run box plot) (top)
- 14:22, 15 September 2011 (diff | hist) . . (+35) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 14:21, 15 September 2011 (diff | hist) . . (0) . . N File:QualityStatsResults.jpg (top)
- 14:18, 15 September 2011 (diff | hist) . . (-10) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 14:17, 15 September 2011 (diff | hist) . . (0) . . N File:RunComputeQualityStats.jpg (top)
- 14:14, 15 September 2011 (diff | hist) . . (+30) . . Galaxy DNA-Seq Tutorial
- 14:11, 15 September 2011 (diff | hist) . . (+98) . . Galaxy DNA-Seq Tutorial (→Reference Genome)
- 14:09, 15 September 2011 (diff | hist) . . (+114) . . Galaxy DNA-Seq Tutorial
- 14:04, 15 September 2011 (diff | hist) . . (+465) . . Galaxy DNA-Seq Tutorial (FastQC and Compute stats cleanup)
- 13:47, 15 September 2011 (diff | hist) . . (0) . . N File:FastQCRunSettings.jpg (top)
- 13:39, 15 September 2011 (diff | hist) . . (+127) . . Galaxy DNA-Seq Tutorial
- 13:32, 15 September 2011 (diff | hist) . . (+115) . . Galaxy DNA-Seq Tutorial (→Reference Genome)
- 13:30, 15 September 2011 (diff | hist) . . (+217) . . Galaxy (→Available datasets: Added new datasets)
- 13:21, 15 September 2011 (diff | hist) . . (+368) . . Galaxy DNA-Seq Tutorial
- 13:09, 15 September 2011 (diff | hist) . . (+66) . . Galaxy DNA-Seq Tutorial (→Linking to data)
- 13:08, 15 September 2011 (diff | hist) . . (0) . . N File:DataLibraryVacWRFastQ.jpg (top)
- 10:56, 15 September 2011 (diff | hist) . . (+38) . . Galaxy DNA-Seq Tutorial (Pileup filtering)
- 10:55, 15 September 2011 (diff | hist) . . (+35) . . N File:PileupFiltering100Reads.jpg (Pileup run settings for Vaccinia WR) (top)
- 00:13, 15 September 2011 (diff | hist) . . (+75) . . Galaxy DNA-Seq Tutorial (Filtering SNPs)
- 00:11, 15 September 2011 (diff | hist) . . (+50) . . N File:FilterRunVacWR.jpg (How to filter a SAM file for SNPs versus reference) (top)
- 23:22, 14 September 2011 (diff | hist) . . (+32) . . Galaxy DNA-Seq Tutorial
- 23:21, 14 September 2011 (diff | hist) . . (+27) . . N File:SNPEffResults.jpg (SNP Results for Vaccinia WR) (top)
- 23:20, 14 September 2011 (diff | hist) . . (+141) . . Galaxy DNA-Seq Tutorial
- 23:18, 14 September 2011 (diff | hist) . . (+17) . . N File:SNPEffCoverage.jpg (For a vaccinia WR) (top)
- 23:17, 14 September 2011 (diff | hist) . . (+214) . . Galaxy DNA-Seq Tutorial (SNPEff separate section)
- 22:47, 14 September 2011 (diff | hist) . . (+78) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 22:45, 14 September 2011 (diff | hist) . . (+19) . . N File:SNPEff.jpg (SNPEff run settings) (top)
- 22:38, 14 September 2011 (diff | hist) . . (+127) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 22:34, 14 September 2011 (diff | hist) . . (+153) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 22:09, 14 September 2011 (diff | hist) . . (+107) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 22:08, 14 September 2011 (diff | hist) . . (+44) . . N File:GeneratePileup.jpg (Generate pileup for Vaccinia, call consensus) (top)
- 22:06, 14 September 2011 (diff | hist) . . (+20) . . Galaxy DNA-Seq Tutorial (→Looking at differences with SNPEff)
- 17:36, 14 September 2011 (diff | hist) . . (+22) . . Galaxy DNA-Seq Tutorial (Flagstat)
- 17:35, 14 September 2011 (diff | hist) . . (+29) . . N File:Sam2bam.jpg (Conversion of SAM file to BAM) (top)
- 17:35, 14 September 2011 (diff | hist) . . (+44) . . Galaxy DNA-Seq Tutorial (Flagstat)
(Latest | Earliest) View (newer 250 | older 250) (20 | 50 | 100 | 250 | 500)
