GBiB: From download to BLAT at assembly hubs: Revision history

25 June 2021

• curprev 19:3819:38, 25 June 2021‎ David da Silva Pires talk contribs‎ 23,306 bytes +142‎ →‎Track hub configuration: Changing from eboVir3 to tryCru32-CLBrenerEsmeraldoLike.

18 June 2021

• curprev 20:3020:30, 18 June 2021‎ David da Silva Pires talk contribs‎ 23,164 bytes +466‎ →‎Preparing the data: Changing from eboVir3 to tryCru32-CLBrenerEsmeraldoLike.

11 June 2021

• curprev 18:1618:16, 11 June 2021‎ David da Silva Pires talk contribs‎ 22,698 bytes +381‎ →‎Creating a basic genomes.txt file: Adding a lot of fields (not so basic anymore ;-) and changing from eboVir3 to Trypanosoma cruzi.
• curprev 15:2015:20, 11 June 2021‎ David da Silva Pires talk contribs‎ m 22,317 bytes +2‎ →‎Assembly hub configuration: Just adjusting some spacing between sections.
• curprev 15:1515:15, 11 June 2021‎ David da Silva Pires talk contribs‎ 22,315 bytes +48‎ →‎Creating a basic hub.txt file: Changing from a virus to a generic assembly Hub.
• curprev 15:0415:04, 11 June 2021‎ David da Silva Pires talk contribs‎ 22,267 bytes +218‎ →‎Downloading the raw data: Changing from Ebola virus to Trypanosoma cruzi genome.

29 January 2020

• curprev 15:5115:51, 29 January 2020‎ David da Silva Pires talk contribs‎ 22,049 bytes +23‎ →‎GBiB installation: Using a wget flag to pass through certification verification.
• curprev 15:4915:49, 29 January 2020‎ David da Silva Pires talk contribs‎ 22,026 bytes +72‎ Adding command to set right permissions to access /usr/local/src/gbib

27 January 2020

• curprev 19:2219:22, 27 January 2020‎ David da Silva Pires talk contribs‎ m 21,954 bytes 0‎ →‎Introduction: Updating the tested Linux distribution.

2 December 2019

• curprev 13:3713:37, 2 December 2019‎ David da Silva Pires talk contribs‎ m 21,954 bytes +6‎ →‎Introduction: Updating the tested Linux distribution.

4 September 2018

• curprev 19:2219:22, 4 September 2018‎ David da Silva Pires talk contribs‎ 21,948 bytes +47‎ →‎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.

1 September 2018

• curprev 08:0208:02, 1 September 2018‎ Galt talk contribs‎ 21,901 bytes 0‎ changed cse to soe

20 June 2017

• curprev 15:5315:53, 20 June 2017‎ David da Silva Pires talk contribs‎ 21,901 bytes −1‎ →‎Introduction: Updating the Kubuntu version.

22 April 2017

• curprev 22:0222:02, 22 April 2017‎ David da Silva Pires talk contribs‎ m 21,902 bytes +1‎ →‎Basic HTML page: Tip: closing point.
• curprev 22:0122:01, 22 April 2017‎ David da Silva Pires talk contribs‎ 21,901 bytes +141‎ →‎Gap track: New subsection explaining how to create a basic HTML page for the description of the assembly hub.

20 April 2017

• curprev 10:1810:18, 20 April 2017‎ David da Silva Pires talk contribs‎ 21,760 bytes +362‎ →‎Gap track: Writing the trackDb.txt files.

10 April 2017

• curprev 14:0314:03, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,398 bytes +250‎ →‎Gap track: Adapting the gap track input and output files to the new location of AGP file.
• curprev 13:5013:50, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,148 bytes +98‎ →‎Track hub configuration: Fixing the path for the sorted AGP file.
• curprev 13:3713:37, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,050 bytes −229‎ 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.
• curprev 13:0313:03, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,279 bytes +366‎ →‎Additional configuration: Initial configuration of the gap track.
• curprev 12:4412:44, 10 April 2017‎ David da Silva Pires talk contribs‎ 20,913 bytes −410‎ →‎Additional configuration: Removing data refering an incomplete description of a BIGBED track.
• curprev 12:3712:37, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,323 bytes −15‎ Making a double check with hubCheck: file and URL.
• curprev 12:1712:17, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,338 bytes −304‎ Removing a call for the hubCheck command and placing the explanation in a better place.
• curprev 12:0112:01, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,642 bytes −70‎ Dealing with genomes that have chromosomes names too long.
• curprev 10:2310:23, 10 April 2017‎ David da Silva Pires talk contribs‎ 21,712 bytes +160‎ Dealing with genomes that have all nucleotides as lowecase letters.

7 April 2017

• curprev 16:5316:53, 7 April 2017‎ David da Silva Pires talk contribs‎ 21,552 bytes +375‎ →‎Track hub configuration: Including the assembly track configuration in the main trackDb.txt.
• curprev 16:4616:46, 7 April 2017‎ David da Silva Pires talk contribs‎ 21,177 bytes +122‎ Checking AGP and FASTA file in the right place.
• curprev 16:2816:28, 7 April 2017‎ David da Silva Pires talk contribs‎ m 21,055 bytes +6‎ →‎Track hub configuration: Fixing the path after organizing the assembly track inside the group map.
• curprev 13:5213:52, 7 April 2017‎ David da Silva Pires talk contribs‎ 21,049 bytes −48‎ →‎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.
• curprev 13:3413:34, 7 April 2017‎ David da Silva Pires talk contribs‎ m 21,097 bytes −2‎ →‎GBiB installation: Typo.

6 April 2017

• curprev 17:4817:48, 6 April 2017‎ David da Silva Pires talk contribs‎ 21,099 bytes +51‎ →‎Blat configuration: Fixing the working directory and warning about the capital 'B' in "transBlat".
• curprev 17:0617:06, 6 April 2017‎ David da Silva Pires talk contribs‎ 21,048 bytes +76‎ →‎Blat configuration: Creating a log directory and fixing gfServer commands.
• curprev 13:0713:07, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,972 bytes +35‎ →‎Track hub configuration: A better bedToBigBed command.
• curprev 13:0513:05, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,937 bytes +7‎ →‎Track hub configuration: Fixing the filename.
• curprev 13:0313:03, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,930 bytes +100‎ →‎Track hub configuration: Making a symbolic link for the eboVir3-chromSizes.txt file.
• curprev 12:5812:58, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,830 bytes +7‎ →‎Track hub configuration: Now eboVir3.agp file is in the output/ directory.
• curprev 12:5712:57, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,823 bytes +7‎ →‎Track hub configuration: The assembly.bed file should also go to the output/ directory.
• curprev 12:5512:55, 6 April 2017‎ David da Silva Pires talk contribs‎ 20,816 bytes +160‎ →‎Track hub configuration: Organizing the files in subdirectories.
• curprev 12:4912:49, 6 April 2017‎ David da Silva Pires talk contribs‎ 20,656 bytes −90‎ →‎Preparing the data: Simplifying the build of the chromSizes-sorted file.
• curprev 12:4312:43, 6 April 2017‎ David da Silva Pires talk contribs‎ 20,746 bytes +11‎ →‎Preparing the data: Simplifying the build of the .2bit file.
• curprev 12:1112:11, 6 April 2017‎ David da Silva Pires talk contribs‎ 20,735 bytes −11‎ Removing one pipe since awk can do the comparison and the printing in just one command. Simplifying the output filename.
• curprev 11:5911:59, 6 April 2017‎ David da Silva Pires talk contribs‎ 20,746 bytes +395‎ Building the AGP file only when needed: at assembly track configuration.
• curprev 11:4111:41, 6 April 2017‎ David da Silva Pires talk contribs‎ m 20,351 bytes 0‎ Changing to a better order the lines in the initial genomes.txt

21 July 2015

• curprev 12:0212:02, 21 July 2015‎ David da Silva Pires talk contribs‎ 20,351 bytes +728‎ Setting locale environment variables in order to provide a case-sensitive sort.

4 June 2015

• curprev 01:0301:03, 4 June 2015‎ David da Silva Pires talk contribs‎ 19,623 bytes +115‎ →‎Additional configuration: Incrementing the HTML description of a track.
• curprev 00:4200:42, 4 June 2015‎ David da Silva Pires talk contribs‎ 19,508 bytes +107‎ More additional configuration to genomes.txt.
• curprev 00:3000:30, 4 June 2015‎ David da Silva Pires talk contribs‎ 19,401 bytes +60‎ →‎Additional configuration: Additional configuration to genomes.txt.
• curprev 00:2000:20, 4 June 2015‎ David da Silva Pires talk contribs‎ 19,341 bytes +66‎ →‎Additional configuration: Additional configuration to hub.txt.

3 June 2015

• curprev 13:4213:42, 3 June 2015‎ David da Silva Pires talk contribs‎ 19,275 bytes +295‎ →‎Additional configuration: Adding an assembly hub through its URL.
• curprev 11:1411:14, 3 June 2015‎ David da Silva Pires talk contribs‎ 18,980 bytes +3‎ Moving "Custom track configuration" to "Additional configuration".
• curprev 10:4610:46, 3 June 2015‎ David da Silva Pires talk contribs‎ 18,977 bytes +755‎ →‎Additional configuration: Moving some additional configuration to Blat to the right place.
• curprev 10:4410:44, 3 June 2015‎ David da Silva Pires talk contribs‎ 18,222 bytes −574‎ →‎Blat configuration: Letting just the minimal configuration.

2 June 2015

• curprev 09:3609:36, 2 June 2015‎ David da Silva Pires talk contribs‎ 18,796 bytes +51‎ Constructing only the assembly track and moving additional configuration to the right place.
• curprev 09:2509:25, 2 June 2015‎ David da Silva Pires talk contribs‎ 18,745 bytes 0‎ Moving the construction of the AGP file to the subsession "Preparing the data".
• curprev 09:2009:20, 2 June 2015‎ David da Silva Pires talk contribs‎ 18,745 bytes 0‎ Simplifying the session "Track hub configuration".
• curprev 09:1609:16, 2 June 2015‎ David da Silva Pires talk contribs‎ 18,745 bytes +2‎ Simplifying the session "Preparing the data".
• curprev 09:1209:12, 2 June 2015‎ David da Silva Pires talk contribs‎ 18,743 bytes 0‎ Using only 4 cores of the laptop.

1 June 2015

• curprev 23:3823:38, 1 June 2015‎ David da Silva Pires talk contribs‎ 18,743 bytes +358‎ →‎Preparing the data: Changing from relative to absolute path.
• curprev 23:3323:33, 1 June 2015‎ David da Silva Pires talk contribs‎ 18,385 bytes +154‎ Adapting the session "Preparing the data" to ebola data.
• curprev 23:2223:22, 1 June 2015‎ David da Silva Pires talk contribs‎ m 18,231 bytes +43‎ New session: "Creating a basic genomes.txt file".

29 May 2015

• curprev 22:2722:27, 29 May 2015‎ David da Silva Pires talk contribs‎ 18,188 bytes +43‎ Creating a subsession for hub.txt file.
• curprev 22:2222:22, 29 May 2015‎ David da Silva Pires talk contribs‎ 18,145 bytes +48‎ →‎Downloading the raw data: Fixing user, host and extension.
• curprev 22:1622:16, 29 May 2015‎ David da Silva Pires talk contribs‎ 18,097 bytes +34‎ Fixing color at ssh command.
• curprev 10:1310:13, 29 May 2015‎ David da Silva Pires talk contribs‎ 18,063 bytes +1‎ Moving the subsection "Dowloading the raw data" to the section "Assembly hub configuration".
• curprev 09:2309:23, 29 May 2015‎ David da Silva Pires talk contribs‎ 18,062 bytes 0‎ Preparing earlier the .2bit file in order to obtain the assembly track.

28 May 2015

• curprev 23:2723:27, 28 May 2015‎ David da Silva Pires talk contribs‎ 18,062 bytes 0‎ →‎Track hub configuration: Moving information about assembly track to the correct place.
• curprev 23:2223:22, 28 May 2015‎ David da Silva Pires talk contribs‎ 18,062 bytes +7‎ →‎Track hub configuration: Inclusion of "EOI" at trackDb.txt.
• curprev 23:2123:21, 28 May 2015‎ David da Silva Pires talk contribs‎ 18,055 bytes 0‎ Moving down information about the construction of an HTML page.

27 May 2015

• curprev 00:3900:39, 27 May 2015‎ David da Silva Pires talk contribs‎ 18,055 bytes −129‎ →‎Track hub configuration: A simpler version of trackDb.txt
• curprev 00:3500:35, 27 May 2015‎ David da Silva Pires talk contribs‎ 18,184 bytes −222‎ →‎Preparing the raw data: Simpler versions of hub.txt and genomes.txt.

26 May 2015

• curprev 23:3123:31, 26 May 2015‎ David da Silva Pires talk contribs‎ 18,406 bytes −264‎ →‎Preparing the raw data: We don't need to extract a fasta file from .2bit file anymore.
• curprev 23:1423:14, 26 May 2015‎ David da Silva Pires talk contribs‎ 18,670 bytes +16‎ →‎GBiB maintenance: It seems that even if we do an updateBrowser, a subsequent gbibAddTools still install some updates.
• curprev 23:1023:10, 26 May 2015‎ David da Silva Pires talk contribs‎ 18,654 bytes −100‎ →‎GBiB configuration: Eliminating "hub" as a shared folder.
• curprev 23:0423:04, 26 May 2015‎ David da Silva Pires talk contribs‎ 18,754 bytes −297‎ Simplifying the "Download the raw data" instructions.

22 May 2015

• curprev 18:5518:55, 22 May 2015‎ David da Silva Pires talk contribs‎ 19,051 bytes +37‎ Simplifying the configuration of the first track.
• curprev 17:0517:05, 22 May 2015‎ David da Silva Pires talk contribs‎ 19,014 bytes +145‎ We don't need to download the .2bit. Downloading fasta directly.
• curprev 16:4416:44, 22 May 2015‎ David da Silva Pires talk contribs‎ 18,869 bytes +11‎ Replacing S. mansoni with Ebola virus at genomes.txt.
• curprev 16:2816:28, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,858 bytes +155‎ Checking hub state with the command hubCheck.
• curprev 16:1516:15, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,703 bytes −3‎ Typo fix.
• curprev 16:1416:14, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,706 bytes +15‎ Removing unnecessary html extension.
• curprev 16:0716:07, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,691 bytes +91‎ Rearranging some paragraphs.
• curprev 15:4415:44, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,600 bytes +18‎ Typo fix. Another estimation to update time.
• curprev 15:2615:26, 22 May 2015‎ David da Silva Pires talk contribs‎ 18,582 bytes +83‎ Including command to install VirtualBox package.
• curprev 15:0715:07, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,499 bytes 0‎ Changing the place relative to GBiB box on download.
• curprev 15:0315:03, 22 May 2015‎ David da Silva Pires talk contribs‎ 18,499 bytes +36‎ Separating the download and the preparation of the raw data.
• curprev 13:5213:52, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,463 bytes +116‎ Fixing some folders names.
• curprev 13:3913:39, 22 May 2015‎ David da Silva Pires talk contribs‎ m 18,347 bytes +13‎ Replacing Gene Network by Virus Network.

19 May 2015

• curprev 18:1518:15, 19 May 2015‎ David da Silva Pires talk contribs‎ 18,334 bytes +11‎ Including "-verbose=1" option to bedToBigBed.
• curprev 15:3115:31, 19 May 2015‎ David da Silva Pires talk contribs‎ 18,323 bytes +730‎ Construction of the GC percent track.
• curprev 13:3013:30, 19 May 2015‎ David da Silva Pires talk contribs‎ 17,593 bytes +1,212‎ Construction of assembly and gap tracks.
• curprev 12:5012:50, 19 May 2015‎ David da Silva Pires talk contribs‎ 16,381 bytes +456‎ Building an AGP file from fasta using the hgFakeAgp command.
• curprev 09:2409:24, 19 May 2015‎ David da Silva Pires talk contribs‎ 15,925 bytes +165‎ Extracting fasta sequence from .2bit file.
• curprev 00:5800:58, 19 May 2015‎ David da Silva Pires talk contribs‎ 15,760 bytes +690‎ Using colors to show *who* should type *where*. Just the two first sections done.
• curprev 00:4400:44, 19 May 2015‎ David da Silva Pires talk contribs‎ 15,070 bytes +74‎ Warning about the uniqueness of a track name at trackDb.txt.

17 May 2015

• curprev 15:0215:02, 17 May 2015‎ David da Silva Pires talk contribs‎ 14,996 bytes +52‎ Adding the option "group" to trackDb.txt.
• curprev 14:0814:08, 17 May 2015‎ David da Silva Pires talk contribs‎ 14,944 bytes +156‎ Suggesting the inclusion of an image of the organism.
• curprev 13:4013:40, 17 May 2015‎ David da Silva Pires talk contribs‎ 14,788 bytes +113‎ Adding the new option "negateValues on" at trackDb.txt.
• curprev 12:4912:49, 17 May 2015‎ David da Silva Pires talk contribs‎ 14,675 bytes +572‎ A better custom track configuration and limitations to some values.
• curprev 11:0711:07, 17 May 2015‎ David da Silva Pires talk contribs‎ 14,103 bytes +803‎ Adding a track description page.
• curprev 01:3601:36, 17 May 2015‎ David da Silva Pires talk contribs‎ 13,300 bytes +171‎ A better custom track configuration

12 May 2015

• curprev 10:1710:17, 12 May 2015‎ David da Silva Pires talk contribs‎ 13,129 bytes +583‎ Setting gfServer for blat and transBlat at cron (/etc/rc.local) and switching from schMan2 to eboVir3.

11 May 2015

• curprev 23:0223:02, 11 May 2015‎ David da Silva Pires talk contribs‎ 12,546 bytes −60‎ Fixing the page description of the hub.
• curprev 14:3514:35, 11 May 2015‎ David da Silva Pires talk contribs‎ 12,606 bytes +1,328‎ Using the hubCheck command at other steps and creating an HTML page for the organism.
• curprev 13:1413:14, 11 May 2015‎ David da Silva Pires talk contribs‎ m 11,278 bytes 0‎ Tipo fix: firts ---> first.
• curprev 13:1213:12, 11 May 2015‎ David da Silva Pires talk contribs‎ 11,278 bytes −134‎ Changing hubPublicCheck to hubCheck, since we will not need to work with databases.
• curprev 00:5200:52, 11 May 2015‎ David da Silva Pires talk contribs‎ 11,412 bytes +367‎ Creating the HTML page description for the hub.
• curprev 00:1800:18, 11 May 2015‎ David da Silva Pires talk contribs‎ m 11,045 bytes 0‎ Tipo fix: longlabel ---> longLabel.
• curprev 00:0600:06, 11 May 2015‎ David da Silva Pires talk contribs‎ m 11,045 bytes 0‎ Tipo fix: shortlabel ---> shortLabel.
• curprev 00:0000:00, 11 May 2015‎ David da Silva Pires talk contribs‎ m 11,045 bytes −246‎ Changing the way we show "here documents" (<<) such that one can copy and paste them.

10 May 2015

• curprev 23:5523:55, 10 May 2015‎ David da Silva Pires talk contribs‎ m 11,291 bytes −49‎ Moving creation of folders to "Preparing raw data" section.
• curprev 22:0122:01, 10 May 2015‎ David da Silva Pires talk contribs‎ 11,340 bytes +542‎ First version of "Preparing the raw data" subsection. Using eboVir3. Minor corrections at "GBiB configuration" section.
• curprev 21:1221:12, 10 May 2015‎ David da Silva Pires talk contribs‎ 10,798 bytes −58‎ Removing the "Bidirectional" option on "Drag'n'Drop" because GBiB does not come with a CD-ROM drive in order to install guest additions.
• curprev 20:4520:45, 10 May 2015‎ David da Silva Pires talk contribs‎ m 10,856 bytes −259‎ Changing the way we show command lines: from " $>" to " $>".
• curprev 20:3420:34, 10 May 2015‎ David da Silva Pires talk contribs‎ 11,115 bytes +658‎ Refining information on section "GBiB installation".
• curprev 14:1214:12, 10 May 2015‎ David da Silva Pires talk contribs‎ m 10,457 bytes +5‎ Emphasizing a little more.
• curprev 14:0914:09, 10 May 2015‎ David da Silva Pires talk contribs‎ m 10,452 bytes +51‎ Augmenting one of the advantages.
• curprev 14:0314:03, 10 May 2015‎ David da Silva Pires talk contribs‎ 10,401 bytes +1,105‎ First version of "Introduction" section.

8 May 2015

• curprev 19:0319:03, 8 May 2015‎ David da Silva Pires talk contribs‎ m 9,296 bytes −2‎ should ---> must
• curprev 19:0219:02, 8 May 2015‎ David da Silva Pires talk contribs‎ 9,298 bytes +102‎ Inclusion of rules for hub.txt fields.

7 May 2015

• curprev 17:1417:14, 7 May 2015‎ Brian Lee talk contribs‎ 9,196 bytes +1‎ typo fix
• curprev 17:1317:13, 7 May 2015‎ Brian Lee talk contribs‎ 9,195 bytes +668‎ Adding some references links
• curprev 16:5516:55, 7 May 2015‎ Ann talk contribs‎ 8,527 bytes −134‎ →‎GBiB installation
• curprev 12:5912:59, 7 May 2015‎ David da Silva Pires talk contribs‎ m 8,661 bytes −1‎ Typo correction: whith ---> with.

6 May 2015

• curprev 21:1421:14, 6 May 2015‎ Malcook talk contribs‎ m 8,662 bytes +1‎ No edit summary
• curprev 21:1421:14, 6 May 2015‎ Malcook talk contribs‎ 8,661 bytes +29‎ →‎GBiB installation
• curprev 20:2420:24, 6 May 2015‎ David da Silva Pires talk contribs‎ 8,632 bytes +93‎ First version of "GBiB maintenance" section.
• curprev 20:1420:14, 6 May 2015‎ David da Silva Pires talk contribs‎ 8,539 bytes +192‎ First version of "Custom track configuration" section.
• curprev 20:1320:13, 6 May 2015‎ Malcook talk contribs‎ 8,347 bytes −4‎ No edit summary
• curprev 20:0120:01, 6 May 2015‎ David da Silva Pires talk contribs‎ 8,351 bytes +422‎ First version of "Blat configuration" section.
• curprev 19:4019:40, 6 May 2015‎ David da Silva Pires talk contribs‎ 7,929 bytes +5,183‎ First version of "Track hub configuration" section.
• curprev 14:0714:07, 6 May 2015‎ David da Silva Pires talk contribs‎ 2,746 bytes +1,087‎ Fisrt version of "GBiB Configuration" section.
• curprev 13:4513:45, 6 May 2015‎ David da Silva Pires talk contribs‎ 1,659 bytes +359‎ No edit summary
• curprev 11:1111:11, 6 May 2015‎ David da Silva Pires talk contribs‎ 1,300 bytes +331‎ No edit summary

• curprev 01:5001:50, 6 May 2015‎ David da Silva Pires talk contribs‎ 969 bytes +969‎ 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..."