User contributions for Curtish@uab.edu
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28 March 2013
- 07:3907:39, 28 March 2013 diff hist +7 NgsCctsBuildVicuna →Vicuna
- 07:3907:39, 28 March 2013 diff hist +65 m NgsCctsBuildVicuna →Note: pre-built exe for Linux 64bit!
- 07:3807:38, 28 March 2013 diff hist −24 m NgsCctsBuildVicuna →Vicuna
- 07:3807:38, 28 March 2013 diff hist −62 NgsCctsBuildVicuna →NCBI toolkit 7.0.0
- 03:5403:54, 28 March 2013 diff hist +25 m NgsCcts →in process
26 March 2013
- 15:5215:52, 26 March 2013 diff hist +121 NgsCcts →Gene Prediction
- 15:5015:50, 26 March 2013 diff hist +588 N NgsCctsGeneWise add GeneWise2.2.0 for VICUNA support current
- 15:4215:42, 26 March 2013 diff hist +147 NgsCcts →in process
- 15:2815:28, 26 March 2013 diff hist +187 NgsCctsBuildMosaik →Build MOSAIK from Source current
- 15:2415:24, 26 March 2013 diff hist +41 NgsCcts →Short Read Aligners
- 15:1415:14, 26 March 2013 diff hist +24 NgsCctsBuildMosaik →Build MOSAIK from Source
- 15:1415:14, 26 March 2013 diff hist +362 N NgsCctsBuildMosaik Created page with "= Build MOSAIK from Source = {{ cd /share/apps/ngs-ccts wget https://mosaik-aligner.googlecode.com/files/MOSAIK-2.1.73-source.tar echo "3bb0e83e64b8a102a038a263916022f231e1bb..."
- 15:0715:07, 26 March 2013 diff hist +9 m NgsCcts →Short Read Aligners
- 15:0715:07, 26 March 2013 diff hist +164 NgsCcts →Short Read Aligners
15 March 2013
- 17:4217:42, 15 March 2013 diff hist +157 NgsCcts →SNP analysis
- 17:3717:37, 15 March 2013 diff hist +4 m NgsCcts →SNP analysis
- 17:3317:33, 15 March 2013 diff hist +447 NgsCcts →Short Read (denovo) Assemblers
14 March 2013
- 18:4318:43, 14 March 2013 diff hist +356 GBS722 2013 →Denovo Protocol (2x) current
- 18:4118:41, 14 March 2013 diff hist +113 GBS722 2013 →Ref-based Protocol
- 18:3818:38, 14 March 2013 diff hist +79 GBS722 2013 →Ref-based Protocol
- 18:2718:27, 14 March 2013 diff hist +79 GBS722 2013 →Denovo Protocol (2x)
- 18:2318:23, 14 March 2013 diff hist +20 GBS722 2013 →Denovo Protocol (2x)
- 18:2118:21, 14 March 2013 diff hist +6 GBS722 2013 →Denovo Protocol (2x)
- 18:1518:15, 14 March 2013 diff hist +131 GBS722 2013 →Ref-based Protocol
- 18:1418:14, 14 March 2013 diff hist +73 GBS722 2013 →Ref-based Protocol
- 17:5617:56, 14 March 2013 diff hist −4 GBS722 2013 →Ref-based Protocol
- 17:5517:55, 14 March 2013 diff hist +51 GBS722 2013 →Ref-based Protocol
- 17:5417:54, 14 March 2013 diff hist +11 GBS722 2013 →Ref-based Protocol
- 17:5317:53, 14 March 2013 diff hist +19 GBS722 2013 →Ref-based Protocol
- 17:5217:52, 14 March 2013 diff hist +31 GBS722 2013 →Ref-based Protocol
- 17:4217:42, 14 March 2013 diff hist 0 GBS722 2013 →IGV Setup
- 17:3817:38, 14 March 2013 diff hist +2,392 N GBS722 2013 Created page with "= VACV-WR WT vs DRUG protocol in Galaxy = This is an abbreviated protocol cheat-sheet to help students through the class exercises. ==Links== UAB Galaxy - https://galaxy.ua..."
11 March 2013
- 19:0419:04, 11 March 2013 diff hist −49 Galaxy File Uploads remove chmod warning for importfs
- 18:5618:56, 11 March 2013 diff hist +82 Galaxy File Uploads add warning about permissions.
- 18:1218:12, 11 March 2013 diff hist +49 Galaxy →Galaxy@UAB
- 18:1118:11, 11 March 2013 diff hist +212 Galaxy →Installed Genome Indexes: added additional genomes hg16 hg17 mm8 mm7 mm6 mm5, mostly for liftOver support.
- 18:0518:05, 11 March 2013 diff hist +2 m Galaxy →Overview
- 18:0418:04, 11 March 2013 diff hist +78 Galaxy Importfs →Copying data to Cheaha using scp: winSCP link
- 18:0118:01, 11 March 2013 diff hist +255 Galaxy File Uploads added section headers, link to WinSCP, fixed wikipedia link for SCP
- 17:5317:53, 11 March 2013 diff hist +170 Galaxy File Uploads turn number list to table to add list of drawbacks/limits
7 March 2013
- 21:1021:10, 7 March 2013 diff hist +20 Galaxy →Available Tools
- 21:0821:08, 7 March 2013 diff hist +374 Galaxy →Organisms
- 21:0821:08, 7 March 2013 diff hist +570 Galaxy →microbes
- 20:5920:59, 7 March 2013 diff hist +4,961 Galaxy add available-genomes list from galaxy data-cache
- 20:3020:30, 7 March 2013 diff hist −4,236 Galaxy →Galaxy@UAB: add list of available genomes, update and abbreviate software list
- 19:3719:37, 7 March 2013 diff hist −2,092 UploadLargeData removed page. Left links to other related pages. It was redundent. current
- 19:2819:28, 7 March 2013 diff hist +152 Galaxy →Overview
9 January 2013
- 22:5022:50, 9 January 2013 diff hist 0 IgvFromComputeNode →Install/Start X on Desktop
- 22:5022:50, 9 January 2013 diff hist +4 IgvFromComputeNode →Install/Start X on Desktop
- 12:0212:02, 9 January 2013 diff hist +103 NgsCctsBuildVicuna →Vicuna
- 08:2108:21, 9 January 2013 diff hist +57 NgsCctsBuildVicuna →NCBI toolkit 7.0.0
- 08:1708:17, 9 January 2013 diff hist +49 NgsCctsBuildVicuna →NCBI toolkit 7.0.0
- 08:1708:17, 9 January 2013 diff hist +312 NgsCctsBuildVicuna →Vicuna
- 07:4207:42, 9 January 2013 diff hist +15 NgsCctsBuildVicuna →NCBI toolkit 7.0.0
- 05:5305:53, 9 January 2013 diff hist −6 NgsCctsBuildVicuna →NCBI toolkit 7.0.0
- 05:5305:53, 9 January 2013 diff hist +985 N NgsCctsBuildVicuna Created page with "= Build/Install Broad's Vicuna = == pre-requisites == === NCBI toolkit 7.0.0 === # download cd /share/apps/ngs-ccts/downloads wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi..."
18 December 2012
- 20:1920:19, 18 December 2012 diff hist +657 PublicDatasetsNgs No edit summary current
20 November 2012
- 21:4821:48, 20 November 2012 diff hist +530 N PublicDatasetsNgsDbNcbiTaxonomy Created page with "download and build files with a modified galaxy script. # populates /lustre/project/public_datasets/ngs/databases/ncbi_taxonomy /home/curtish/galaxy/scripts/taxonomy/uab_..." current
12 November 2012
5 November 2012
- 16:3916:39, 5 November 2012 diff hist +317 NgsCcts →Short Read Aligners
31 October 2012
- 16:4816:48, 31 October 2012 diff hist +195 NgsCcts →in process
30 October 2012
- 21:5321:53, 30 October 2012 diff hist +34 NgsCcts →Short Read (denovo) Assemblers
- 21:4921:49, 30 October 2012 diff hist +244 NgsCcts →Short Read (denovo) Assemblers
25 October 2012
- 18:2218:22, 25 October 2012 diff hist −1 PublicDatasetsNgs →Directory Structure
- 18:2118:21, 25 October 2012 diff hist −1 PublicDatasetsNgs →Public Genomes and indexes for NGS
- 18:2018:20, 25 October 2012 diff hist −1 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:1918:19, 25 October 2012 diff hist +544 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
9 October 2012
- 22:0922:09, 9 October 2012 diff hist −23 NgsCctsBuildBwa →Building BWA for /share/apps/ngs-ccts current
- 22:0822:08, 9 October 2012 diff hist +2 NgsCcts →Short Read Aligners
- 22:0722:07, 9 October 2012 diff hist +69 NgsCcts →Short Read (denovo) Assemblers
- 22:0522:05, 9 October 2012 diff hist +6 NgsCctsBuildAbyss No edit summary
- 22:0422:04, 9 October 2012 diff hist +119 NgsCctsBuildAbyss No edit summary
- 22:0322:03, 9 October 2012 diff hist +13 NgsCctsBuildAbyss No edit summary
- 21:5821:58, 9 October 2012 diff hist +58 NgsCctsBuildAbyss No edit summary
- 21:5721:57, 9 October 2012 diff hist +96 NgsCctsBuildAbyss No edit summary
- 21:5221:52, 9 October 2012 diff hist +928 N NgsCctsBuildAbyss Created page with " Based on [file:///share/apps/ngs-ccts/abyss-1.3.4/README.html#compilingabyssfromsource README.html:compiling from source] Requires [sparsehash] TARGET_VER=sparsehash-2.0.2..."
- 21:1821:18, 9 October 2012 diff hist +229 NgsCcts →Short Read (denovo) Assemblers
- 21:1621:16, 9 October 2012 diff hist −5 NgsCcts →Short Read Aligners
- 21:1521:15, 9 October 2012 diff hist −3 NgsCcts →Short Read Aligners
- 21:1521:15, 9 October 2012 diff hist −6 NgsCcts →Short Read (denovo) Assemblers
- 21:1521:15, 9 October 2012 diff hist +111 NgsCcts →Short Read (denovo) Assemblers
- 21:0321:03, 9 October 2012 diff hist +277 N NgsCctsBuildVelvet Created page with " TARGET_VER=velvet_1.2.08 wget http://www.ebi.ac.uk/~zerbino/velvet/${TARGET_VER}.tgz tar xzvf ${TARGET_VER}.tgz rm ${TARGET_VER}.tgz cd ${TARGET_VER} Edit Makefile to c..."
- 20:5220:52, 9 October 2012 diff hist +29 N NgsCctsBuildBwa build Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa current
- 20:5220:52, 9 October 2012 diff hist 0 m NgsCctsBuildBwa Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa
- 20:4720:47, 9 October 2012 diff hist +393 N NgsCctsBuildBwa Created page with "= Building BWA for /share/apps/ngs-ccts = Downloading and building BWA BWA_VER=bwa-0.6.2 wget http://downloads.sourceforge.net/project/bio-bwa/${BWA_VER}.tar.bz2?r=http%3A..."
- 20:4120:41, 9 October 2012 diff hist +2 NgsCcts →Short Read Aligners
- 20:4020:40, 9 October 2012 diff hist +221 NgsCcts →Short Read Aligners
- 20:3520:35, 9 October 2012 diff hist +6 NgsCcts →Short Read Aligners
- 20:3420:34, 9 October 2012 diff hist +20 NgsCcts →Alignment Visualization
- 20:3320:33, 9 October 2012 diff hist +554 NgsCcts No edit summary
4 October 2012
- 21:0621:06, 4 October 2012 diff hist +120 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 17:3217:32, 4 October 2012 diff hist +210 PublicDatasetsNgs →Public Genomes and indexes for NGS
- 17:2917:29, 4 October 2012 diff hist +60 NgsCcts →Shared CCTS NGS apps
3 October 2012
- 15:3515:35, 3 October 2012 diff hist +179 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
2 October 2012
- 18:5818:58, 2 October 2012 diff hist +412 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:4918:49, 2 October 2012 diff hist +283 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:2118:21, 2 October 2012 diff hist +32 PublicDatasetsNgs →Directory Structure
- 18:2018:20, 2 October 2012 diff hist +31 N NgsGenomes Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets current
- 18:2018:20, 2 October 2012 diff hist 0 m PublicDatasetsNgs Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets
1 October 2012
- 18:1318:13, 1 October 2012 diff hist +2,402 N PublicDatasetsNgs Created page with "= Public Genomes and indexes for NGS = CCTS BMI in conjunection with anyone who wishes to participate, maintains a public directory of genomic sequences and indexes built fro..."