User contributions for David da Silva Pires
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25 June 2021
- 19:3819:38, 25 June 2021 diff hist +142 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Changing from eboVir3 to tryCru32-CLBrenerEsmeraldoLike. current
18 June 2021
- 20:3020:30, 18 June 2021 diff hist +466 GBiB: From download to BLAT at assembly hubs →Preparing the data: Changing from eboVir3 to tryCru32-CLBrenerEsmeraldoLike.
11 June 2021
- 18:1618:16, 11 June 2021 diff hist +381 GBiB: From download to BLAT at assembly hubs →Creating a basic genomes.txt file: Adding a lot of fields (not so basic anymore ;-) and changing from eboVir3 to Trypanosoma cruzi.
- 15:2015:20, 11 June 2021 diff hist +2 m GBiB: From download to BLAT at assembly hubs →Assembly hub configuration: Just adjusting some spacing between sections.
- 15:1515:15, 11 June 2021 diff hist +48 GBiB: From download to BLAT at assembly hubs →Creating a basic hub.txt file: Changing from a virus to a generic assembly Hub.
- 15:0415:04, 11 June 2021 diff hist +218 GBiB: From download to BLAT at assembly hubs →Downloading the raw data: Changing from Ebola virus to Trypanosoma cruzi genome.
29 January 2020
- 15:5115:51, 29 January 2020 diff hist +23 GBiB: From download to BLAT at assembly hubs →GBiB installation: Using a wget flag to pass through certification verification.
- 15:4915:49, 29 January 2020 diff hist +72 GBiB: From download to BLAT at assembly hubs Adding command to set right permissions to access /usr/local/src/gbib
27 January 2020
- 19:2219:22, 27 January 2020 diff hist 0 m GBiB: From download to BLAT at assembly hubs →Introduction: Updating the tested Linux distribution.
2 December 2019
- 13:3713:37, 2 December 2019 diff hist +6 m GBiB: From download to BLAT at assembly hubs →Introduction: Updating the tested Linux distribution.
4 September 2018
- 19:2219:22, 4 September 2018 diff hist +47 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Including a warning about the presence of a '.' (dot) at a track name, which causes problems at mysql tables when configuring searchTrix.
20 June 2017
- 15:5315:53, 20 June 2017 diff hist −1 GBiB: From download to BLAT at assembly hubs →Introduction: Updating the Kubuntu version.
22 April 2017
- 22:0222:02, 22 April 2017 diff hist +1 m GBiB: From download to BLAT at assembly hubs →Basic HTML page: Tip: closing point.
- 22:0122:01, 22 April 2017 diff hist +141 GBiB: From download to BLAT at assembly hubs →Gap track: New subsection explaining how to create a basic HTML page for the description of the assembly hub.
20 April 2017
- 10:1810:18, 20 April 2017 diff hist +362 GBiB: From download to BLAT at assembly hubs →Gap track: Writing the trackDb.txt files.
10 April 2017
- 14:0314:03, 10 April 2017 diff hist +250 GBiB: From download to BLAT at assembly hubs →Gap track: Adapting the gap track input and output files to the new location of AGP file.
- 13:5013:50, 10 April 2017 diff hist +98 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Fixing the path for the sorted AGP file.
- 13:3713:37, 10 April 2017 diff hist −229 GBiB: From download to BLAT at assembly hubs Since the AGP file is used to construct both assembly and gap tracks, it is better to keep it in just one directory. I chose the genome directory.
- 13:0313:03, 10 April 2017 diff hist +366 GBiB: From download to BLAT at assembly hubs →Additional configuration: Initial configuration of the gap track.
- 12:4412:44, 10 April 2017 diff hist −410 GBiB: From download to BLAT at assembly hubs →Additional configuration: Removing data refering an incomplete description of a BIGBED track.
- 12:3712:37, 10 April 2017 diff hist −15 GBiB: From download to BLAT at assembly hubs Making a double check with hubCheck: file and URL.
- 12:1712:17, 10 April 2017 diff hist −304 GBiB: From download to BLAT at assembly hubs Removing a call for the hubCheck command and placing the explanation in a better place.
- 12:0112:01, 10 April 2017 diff hist −70 GBiB: From download to BLAT at assembly hubs Dealing with genomes that have chromosomes names too long.
- 10:2310:23, 10 April 2017 diff hist +160 GBiB: From download to BLAT at assembly hubs Dealing with genomes that have all nucleotides as lowecase letters.
7 April 2017
- 16:5316:53, 7 April 2017 diff hist +375 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Including the assembly track configuration in the main trackDb.txt.
- 16:4616:46, 7 April 2017 diff hist +122 GBiB: From download to BLAT at assembly hubs Checking AGP and FASTA file in the right place.
- 16:2816:28, 7 April 2017 diff hist +6 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: Fixing the path after organizing the assembly track inside the group map.
- 13:5213:52, 7 April 2017 diff hist −48 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Changing the order of presentation, creating all the directories in just one command, separating the assembly track at map grouping and making use of input and output.
- 13:3413:34, 7 April 2017 diff hist −2 m GBiB: From download to BLAT at assembly hubs →GBiB installation: Typo.
6 April 2017
- 17:4817:48, 6 April 2017 diff hist +51 GBiB: From download to BLAT at assembly hubs →Blat configuration: Fixing the working directory and warning about the capital 'B' in "transBlat".
- 17:0617:06, 6 April 2017 diff hist +76 GBiB: From download to BLAT at assembly hubs →Blat configuration: Creating a log directory and fixing gfServer commands.
- 13:0713:07, 6 April 2017 diff hist +35 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: A better bedToBigBed command.
- 13:0513:05, 6 April 2017 diff hist +7 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: Fixing the filename.
- 13:0313:03, 6 April 2017 diff hist +100 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: Making a symbolic link for the eboVir3-chromSizes.txt file.
- 12:5812:58, 6 April 2017 diff hist +7 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: Now eboVir3.agp file is in the output/ directory.
- 12:5712:57, 6 April 2017 diff hist +7 m GBiB: From download to BLAT at assembly hubs →Track hub configuration: The assembly.bed file should also go to the output/ directory.
- 12:5512:55, 6 April 2017 diff hist +160 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Organizing the files in subdirectories.
- 12:4912:49, 6 April 2017 diff hist −90 GBiB: From download to BLAT at assembly hubs →Preparing the data: Simplifying the build of the chromSizes-sorted file.
- 12:4312:43, 6 April 2017 diff hist +11 GBiB: From download to BLAT at assembly hubs →Preparing the data: Simplifying the build of the .2bit file.
- 12:1112:11, 6 April 2017 diff hist −11 GBiB: From download to BLAT at assembly hubs Removing one pipe since awk can do the comparison and the printing in just one command. Simplifying the output filename.
- 11:5911:59, 6 April 2017 diff hist +395 GBiB: From download to BLAT at assembly hubs Building the AGP file only when needed: at assembly track configuration.
- 11:4111:41, 6 April 2017 diff hist 0 m GBiB: From download to BLAT at assembly hubs Changing to a better order the lines in the initial genomes.txt
21 July 2015
- 12:0212:02, 21 July 2015 diff hist +728 GBiB: From download to BLAT at assembly hubs Setting locale environment variables in order to provide a case-sensitive sort.
4 June 2015
- 01:0301:03, 4 June 2015 diff hist +115 GBiB: From download to BLAT at assembly hubs →Additional configuration: Incrementing the HTML description of a track.
- 00:4200:42, 4 June 2015 diff hist +107 GBiB: From download to BLAT at assembly hubs More additional configuration to genomes.txt.
- 00:3000:30, 4 June 2015 diff hist +60 GBiB: From download to BLAT at assembly hubs →Additional configuration: Additional configuration to genomes.txt.
- 00:2000:20, 4 June 2015 diff hist +66 GBiB: From download to BLAT at assembly hubs →Additional configuration: Additional configuration to hub.txt.
3 June 2015
- 13:4213:42, 3 June 2015 diff hist +295 GBiB: From download to BLAT at assembly hubs →Additional configuration: Adding an assembly hub through its URL.
- 11:1411:14, 3 June 2015 diff hist +3 GBiB: From download to BLAT at assembly hubs Moving "Custom track configuration" to "Additional configuration".
- 10:4610:46, 3 June 2015 diff hist +755 GBiB: From download to BLAT at assembly hubs →Additional configuration: Moving some additional configuration to Blat to the right place.
