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.
- 10:4410:44, 3 June 2015 diff hist −574 GBiB: From download to BLAT at assembly hubs →Blat configuration: Letting just the minimal configuration.
2 June 2015
- 09:3609:36, 2 June 2015 diff hist +51 GBiB: From download to BLAT at assembly hubs Constructing only the assembly track and moving additional configuration to the right place.
- 09:2509:25, 2 June 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs Moving the construction of the AGP file to the subsession "Preparing the data".
- 09:2009:20, 2 June 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs Simplifying the session "Track hub configuration".
- 09:1609:16, 2 June 2015 diff hist +2 GBiB: From download to BLAT at assembly hubs Simplifying the session "Preparing the data".
- 09:1209:12, 2 June 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs Using only 4 cores of the laptop.
1 June 2015
- 23:3823:38, 1 June 2015 diff hist +358 GBiB: From download to BLAT at assembly hubs →Preparing the data: Changing from relative to absolute path.
- 23:3323:33, 1 June 2015 diff hist +154 GBiB: From download to BLAT at assembly hubs Adapting the session "Preparing the data" to ebola data.
- 23:2223:22, 1 June 2015 diff hist +43 m GBiB: From download to BLAT at assembly hubs New session: "Creating a basic genomes.txt file".
29 May 2015
- 22:2722:27, 29 May 2015 diff hist +43 GBiB: From download to BLAT at assembly hubs Creating a subsession for hub.txt file.
- 22:2222:22, 29 May 2015 diff hist +48 GBiB: From download to BLAT at assembly hubs →Downloading the raw data: Fixing user, host and extension.
- 22:1622:16, 29 May 2015 diff hist +34 GBiB: From download to BLAT at assembly hubs Fixing color at ssh command.
- 10:1310:13, 29 May 2015 diff hist +1 GBiB: From download to BLAT at assembly hubs Moving the subsection "Dowloading the raw data" to the section "Assembly hub configuration".
- 09:2309:23, 29 May 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs Preparing earlier the .2bit file in order to obtain the assembly track.
28 May 2015
- 23:2723:27, 28 May 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Moving information about assembly track to the correct place.
- 23:2223:22, 28 May 2015 diff hist +7 GBiB: From download to BLAT at assembly hubs →Track hub configuration: Inclusion of "EOI" at trackDb.txt.
- 23:2123:21, 28 May 2015 diff hist 0 GBiB: From download to BLAT at assembly hubs Moving down information about the construction of an HTML page.
27 May 2015
- 00:3900:39, 27 May 2015 diff hist −129 GBiB: From download to BLAT at assembly hubs →Track hub configuration: A simpler version of trackDb.txt
- 00:3500:35, 27 May 2015 diff hist −222 GBiB: From download to BLAT at assembly hubs →Preparing the raw data: Simpler versions of hub.txt and genomes.txt.
26 May 2015
- 23:3123:31, 26 May 2015 diff hist −264 GBiB: From download to BLAT at assembly hubs →Preparing the raw data: We don't need to extract a fasta file from .2bit file anymore.
- 23:1423:14, 26 May 2015 diff hist +16 GBiB: From download to BLAT at assembly hubs →GBiB maintenance: It seems that even if we do an updateBrowser, a subsequent gbibAddTools still install some updates.
- 23:1023:10, 26 May 2015 diff hist −100 GBiB: From download to BLAT at assembly hubs →GBiB configuration: Eliminating "hub" as a shared folder.
- 23:0423:04, 26 May 2015 diff hist −297 GBiB: From download to BLAT at assembly hubs Simplifying the "Download the raw data" instructions.
22 May 2015
- 18:5518:55, 22 May 2015 diff hist +37 GBiB: From download to BLAT at assembly hubs Simplifying the configuration of the first track.
- 17:0517:05, 22 May 2015 diff hist +145 GBiB: From download to BLAT at assembly hubs We don't need to download the .2bit. Downloading fasta directly.
- 16:4416:44, 22 May 2015 diff hist +11 GBiB: From download to BLAT at assembly hubs Replacing S. mansoni with Ebola virus at genomes.txt.
- 16:2816:28, 22 May 2015 diff hist +155 m GBiB: From download to BLAT at assembly hubs Checking hub state with the command hubCheck.
- 16:1516:15, 22 May 2015 diff hist −3 m GBiB: From download to BLAT at assembly hubs Typo fix.
- 16:1416:14, 22 May 2015 diff hist +15 m GBiB: From download to BLAT at assembly hubs Removing unnecessary html extension.
- 16:0716:07, 22 May 2015 diff hist +91 m GBiB: From download to BLAT at assembly hubs Rearranging some paragraphs.
- 15:4415:44, 22 May 2015 diff hist +18 m GBiB: From download to BLAT at assembly hubs Typo fix. Another estimation to update time.
- 15:2615:26, 22 May 2015 diff hist +83 GBiB: From download to BLAT at assembly hubs Including command to install VirtualBox package.
- 15:0715:07, 22 May 2015 diff hist 0 m GBiB: From download to BLAT at assembly hubs Changing the place relative to GBiB box on download.
- 15:0315:03, 22 May 2015 diff hist +36 GBiB: From download to BLAT at assembly hubs Separating the download and the preparation of the raw data.
- 13:5213:52, 22 May 2015 diff hist +116 m GBiB: From download to BLAT at assembly hubs Fixing some folders names.
- 13:3913:39, 22 May 2015 diff hist +13 m GBiB: From download to BLAT at assembly hubs Replacing Gene Network by Virus Network.
19 May 2015
- 18:1518:15, 19 May 2015 diff hist +11 GBiB: From download to BLAT at assembly hubs Including "-verbose=1" option to bedToBigBed.
- 15:3115:31, 19 May 2015 diff hist +730 GBiB: From download to BLAT at assembly hubs Construction of the GC percent track.
- 13:3013:30, 19 May 2015 diff hist +1,212 GBiB: From download to BLAT at assembly hubs Construction of assembly and gap tracks.
- 12:5012:50, 19 May 2015 diff hist +456 GBiB: From download to BLAT at assembly hubs Building an AGP file from fasta using the hgFakeAgp command.
- 09:2409:24, 19 May 2015 diff hist +165 GBiB: From download to BLAT at assembly hubs Extracting fasta sequence from .2bit file.
- 00:5800:58, 19 May 2015 diff hist +690 GBiB: From download to BLAT at assembly hubs Using colors to show *who* should type *where*. Just the two first sections done.
- 00:4400:44, 19 May 2015 diff hist +74 GBiB: From download to BLAT at assembly hubs Warning about the uniqueness of a track name at trackDb.txt.
17 May 2015
- 15:0215:02, 17 May 2015 diff hist +52 GBiB: From download to BLAT at assembly hubs Adding the option "group" to trackDb.txt.
- 14:0814:08, 17 May 2015 diff hist +156 GBiB: From download to BLAT at assembly hubs Suggesting the inclusion of an image of the organism.
- 13:4013:40, 17 May 2015 diff hist +113 GBiB: From download to BLAT at assembly hubs Adding the new option "negateValues on" at trackDb.txt.
- 12:4912:49, 17 May 2015 diff hist +572 GBiB: From download to BLAT at assembly hubs A better custom track configuration and limitations to some values.
- 11:0711:07, 17 May 2015 diff hist +803 GBiB: From download to BLAT at assembly hubs Adding a track description page.
- 01:3601:36, 17 May 2015 diff hist +171 GBiB: From download to BLAT at assembly hubs A better custom track configuration
12 May 2015
- 10:1710:17, 12 May 2015 diff hist +583 GBiB: From download to BLAT at assembly hubs Setting gfServer for blat and transBlat at cron (/etc/rc.local) and switching from schMan2 to eboVir3.
11 May 2015
- 23:0223:02, 11 May 2015 diff hist −60 GBiB: From download to BLAT at assembly hubs Fixing the page description of the hub.
- 14:3514:35, 11 May 2015 diff hist +1,328 GBiB: From download to BLAT at assembly hubs Using the hubCheck command at other steps and creating an HTML page for the organism.
- 13:1413:14, 11 May 2015 diff hist 0 m GBiB: From download to BLAT at assembly hubs Tipo fix: firts ---> first.
- 13:1213:12, 11 May 2015 diff hist −134 GBiB: From download to BLAT at assembly hubs Changing hubPublicCheck to hubCheck, since we will not need to work with databases.
- 00:5200:52, 11 May 2015 diff hist +367 GBiB: From download to BLAT at assembly hubs Creating the HTML page description for the hub.
- 00:1800:18, 11 May 2015 diff hist 0 m GBiB: From download to BLAT at assembly hubs Tipo fix: longlabel ---> longLabel.
- 00:0600:06, 11 May 2015 diff hist 0 m GBiB: From download to BLAT at assembly hubs Tipo fix: shortlabel ---> shortLabel.
- 00:0000:00, 11 May 2015 diff hist −246 m GBiB: From download to BLAT at assembly hubs Changing the way we show "here documents" (<<) such that one can copy and paste them.
10 May 2015
- 23:5523:55, 10 May 2015 diff hist −49 m GBiB: From download to BLAT at assembly hubs Moving creation of folders to "Preparing raw data" section.
- 22:0122:01, 10 May 2015 diff hist +542 GBiB: From download to BLAT at assembly hubs First version of "Preparing the raw data" subsection. Using eboVir3. Minor corrections at "GBiB configuration" section.
- 21:1221:12, 10 May 2015 diff hist −58 GBiB: From download to BLAT at assembly hubs Removing the "Bidirectional" option on "Drag'n'Drop" because GBiB does not come with a CD-ROM drive in order to install guest additions.
- 20:4520:45, 10 May 2015 diff hist −259 m GBiB: From download to BLAT at assembly hubs Changing the way we show command lines: from " $>" to " $>".
- 20:3420:34, 10 May 2015 diff hist +658 GBiB: From download to BLAT at assembly hubs Refining information on section "GBiB installation".
- 14:1214:12, 10 May 2015 diff hist +5 m GBiB: From download to BLAT at assembly hubs Emphasizing a little more.
- 14:0914:09, 10 May 2015 diff hist +51 m GBiB: From download to BLAT at assembly hubs Augmenting one of the advantages.
- 14:0314:03, 10 May 2015 diff hist +1,105 GBiB: From download to BLAT at assembly hubs First version of "Introduction" section.
8 May 2015
- 19:0319:03, 8 May 2015 diff hist −2 m GBiB: From download to BLAT at assembly hubs should ---> must
- 19:0219:02, 8 May 2015 diff hist +102 GBiB: From download to BLAT at assembly hubs Inclusion of rules for hub.txt fields.
7 May 2015
- 12:5912:59, 7 May 2015 diff hist −1 m GBiB: From download to BLAT at assembly hubs Typo correction: whith ---> with.
6 May 2015
- 20:2420:24, 6 May 2015 diff hist +93 GBiB: From download to BLAT at assembly hubs First version of "GBiB maintenance" section.
- 20:1420:14, 6 May 2015 diff hist +192 GBiB: From download to BLAT at assembly hubs First version of "Custom track configuration" section.
- 20:0120:01, 6 May 2015 diff hist +422 GBiB: From download to BLAT at assembly hubs First version of "Blat configuration" section.
- 19:4019:40, 6 May 2015 diff hist +5,183 GBiB: From download to BLAT at assembly hubs First version of "Track hub configuration" section.
- 14:0714:07, 6 May 2015 diff hist +1,087 GBiB: From download to BLAT at assembly hubs Fisrt version of "GBiB Configuration" section.
- 13:4513:45, 6 May 2015 diff hist +359 GBiB: From download to BLAT at assembly hubs No edit summary
- 11:1111:11, 6 May 2015 diff hist +331 GBiB: From download to BLAT at assembly hubs No edit summary
- 01:5501:55, 6 May 2015 diff hist +102 N Category:GBiB Created page with "Information relative to installation, configuration and maintenance of GBiB (Genome Browser in a Box)." current
- 01:5001:50, 6 May 2015 diff hist +969 N GBiB: From download to BLAT at assembly hubs Created page with "== GBiB installation == * Create a folder at your machine to place the installation files: $> sudo mkdir /usr/local/src/gbib == GBiB Configuration == * Click at "Setting..."
- 01:1201:12, 6 May 2015 diff hist +89 Main Page No edit summary
