User contributions for David da Silva Pires

3 June 2015

• 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.