User contributions for Rhead
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17 August 2012
- 23:1423:14, 17 August 2012 diff hist +159 Conservation Track QA →Make a list of all organisms for which there are nets & chains and put them in phylogenetic order: more wikipedia links
- 23:0423:04, 17 August 2012 diff hist +108 Conservation Track QA →Make a list of all organisms for which there are nets & chains and put them in phylogenetic order: added taxonomy browser back. It's not useless. :)
- 22:5722:57, 17 August 2012 diff hist +169 Conservation Track QA →Make a list of all organisms for which there are nets & chains and put them in phylogenetic order: added links to relevant wikipedia pages
- 19:4719:47, 17 August 2012 diff hist +111 Details pages -- conventions added note that SOE links should use ".soe." instead of ".cse." (per Jorge)
- 00:1800:18, 17 August 2012 diff hist +6 Conservation Track QA took out reference to NCBI taxonomy browser after having trouble with it (e.g., human, chimp, and gorilla all appear to be at same level but shouldn't be)
16 August 2012
- 22:4722:47, 16 August 2012 diff hist +132 GenBank QA →Tracks: added location of genbank counts file
- 19:1119:11, 16 August 2012 diff hist +37 Conservation Track QA moved instruction to check the maf file annotation types agains the display to "things we used to do"
- 02:4002:40, 16 August 2012 diff hist +220 GenBank QA added note to compare current tracks to those on a previous assembly, if available
15 August 2012
- 21:4721:47, 15 August 2012 diff hist −3 Genbank updates changed make command, per braney current
26 July 2012
- 18:3318:33, 26 July 2012 diff hist +80 Static Page Protocol →Files Destined for the Round Robin and Mirrors (Public Documents): added note about gitu
- 03:0203:02, 26 July 2012 diff hist +335 Static Page Protocol →Files Destined for the Round Robin and Mirrors (Public Documents): added note about using FIND=find, noted in redmine #8410
2 July 2012
- 22:3322:33, 2 July 2012 diff hist −155 Genbank updates Removed instructions to delete from /cluster/data/genbank/data/ftp (per Braney). Made the instructions generic for enabling and disabling.
13 June 2012
- 19:3119:31, 13 June 2012 diff hist −20 Outdated instructions for releasing an assembly →Push the database and tables from hgwdev to hgwbeta: removed another instruction to leave out tableDescriptions table when pushing from dev to beta
- 19:2819:28, 13 June 2012 diff hist −18 Outdated instructions for releasing an assembly →Push the database and tables from hgwdev to hgwbeta: took out instruction to remove tableDescriptions
7 June 2012
- 02:3602:36, 7 June 2012 diff hist +147 CGI Testing added Cricket's suggestion for using the CSHL Long RNA Seq track as a stress test track
25 May 2012
- 21:2521:25, 25 May 2012 diff hist +18 Post-Release-Checklist →UniProtKB: changed the bit about running makeUniProtFile.csh in a specific directory. RM#7308.
14 May 2012
- 23:1223:12, 14 May 2012 diff hist +3 Outdated instructions for releasing an assembly →Push image file to hgwbeta and rr: changed to specify push from beta to rr, not dev
10 May 2012
- 21:2621:26, 10 May 2012 diff hist +305 Updating blat servers added note to notify mirrors
23 April 2012
- 20:4320:43, 23 April 2012 diff hist −10 Outdated instructions for releasing an assembly moved pressing the done button in the push queue to the end
- 20:1920:19, 23 April 2012 diff hist 0 Outdated instructions for releasing an assembly moved check for phylogenetic order to staging section
13 March 2012
- 18:0618:06, 13 March 2012 diff hist +361 Post-Release-Checklist →UniProtKB: updated with info from Benoit Bely at UniProt
24 February 2012
- 04:1604:16, 24 February 2012 diff hist +348 QAing UCSC Genes →QAing the many related tables: example loop for getting table row counts
- 04:0604:06, 24 February 2012 diff hist +165 QAing UCSC Genes →QAing the Gene Set: one more note from Jim about checking kgXref
- 04:0204:02, 24 February 2012 diff hist +244 UCSC Genes Staging Process added section for unused tables
- 03:5903:59, 24 February 2012 diff hist +458 QAing UCSC Genes Added FASTA Alignments section
- 03:3503:35, 24 February 2012 diff hist +44 UCSC Genes Staging Process →Download page: push the cds fasta files
- 03:3303:33, 24 February 2012 diff hist −34 UCSC Genes Staging Process →Databases: removed redundant link to ucsc genes tables
- 03:1503:15, 24 February 2012 diff hist +225 QAing UCSC Genes →QAing the Gene Set: Added featureBits note.
- 03:1403:14, 24 February 2012 diff hist −2 m QAing UCSC Genes →QAing the uniProt and proteome databases
- 03:1303:13, 24 February 2012 diff hist +186 QAing UCSC Genes →QAing the uniProt and proteome databases: formatting; adding note about symlinks
- 02:2202:22, 24 February 2012 diff hist +57 UCSC Genes Staging Process →uniProt and Proteome databases: added note to push the READMEs
- 02:2002:20, 24 February 2012 diff hist +7 m UCSC Genes Staging Process →Update the hgcentral database
- 02:1602:16, 24 February 2012 diff hist +225 QAing UCSC Genes →QAing the many related tables: list of tables that should have same counts
- 02:0902:09, 24 February 2012 diff hist −2 UCSC Genes Staging Process →update isPcr: changed header name
- 01:5801:58, 24 February 2012 diff hist +711 UCSC Genes Staging Process split pcr target into hgwbeta and RR sections
- 01:2001:20, 24 February 2012 diff hist +786 QAing UCSC Genes added PCR Target section
- 00:5000:50, 24 February 2012 diff hist −412 UCSC Genes Staging Process Moved intro information from here to the QAing page
- 00:4600:46, 24 February 2012 diff hist −64 QAing UCSC Genes →Tables Related to UCSC Genes That are Separate tracks: noted that exoniphy will no longer be built
- 00:4200:42, 24 February 2012 diff hist −133 QAing UCSC Genes removed links to other ucsc genes pages from bottom of page
- 00:4100:41, 24 February 2012 diff hist +274 QAing UCSC Genes Moved intro information here from the Staging page
- 00:3200:32, 24 February 2012 diff hist −209 UCSC Genes Staging Process →Post-Release: Removed section now that all ucsc genes wiki pages are linked on every page
- 00:3100:31, 24 February 2012 diff hist +151 Post-Release-Checklist added "wiki pages about known genes" section
- 00:3000:30, 24 February 2012 diff hist +147 UCSC Genes Staging Process added "wiki pages about known genes" section
- 00:2900:29, 24 February 2012 diff hist +149 UCSC Genes tables added "wiki pages about known genes" section
- 00:2600:26, 24 February 2012 diff hist +66 QAing UCSC Genes →wiki pages about known genes: reordered links, added note about staging link
- 00:1100:11, 24 February 2012 diff hist −509 Post-Release-Checklist removed details about hgcentral, otherOrgs.ra and uniProt (they're in the QAing and Staging pages now), and added announcement section
23 February 2012
- 22:3522:35, 23 February 2012 diff hist −221 Post-Release-Checklist →Exoniphy: removed this section per Ann and Hiram.
- 21:0421:04, 23 February 2012 diff hist +1,106 QAing UCSC Genes Added a section for QAing uniProt and proteome databases
- 20:1120:11, 23 February 2012 diff hist +232 QAing UCSC Genes →QAing the many related tables: Added note to check Old UCSC Genes, Alt Events and blastTab tables.
- 20:0620:06, 23 February 2012 diff hist 0 UCSC Genes Staging Process →Files for Searching: changed hg18 to <db>
- 20:0320:03, 23 February 2012 diff hist +103 UCSC Genes Staging Process →Databases and Tables: added hgNearOk=1 note
- 20:0220:02, 23 February 2012 diff hist +33 UCSC Genes Staging Process →Searching: clarified that this was for human and mouse
- 19:4819:48, 23 February 2012 diff hist +67 UCSC Genes Staging Process →Releasing to the public website: added headers, moved push of search files up
- 19:4119:41, 23 February 2012 diff hist +26 UCSC Genes Staging Process →Staging on hgwbeta: added headers
- 19:4019:40, 23 February 2012 diff hist +41 UCSC Genes Staging Process →Data Involved: added headers; added note about alt events only being on human and mouse
- 19:2919:29, 23 February 2012 diff hist −172 QAing UCSC Genes →wiki pages about known genes: turned links into wiki links
- 06:5806:58, 23 February 2012 diff hist +855 UCSC Genes Staging Process →Releasing to the public website: added notes about symlinks, pushing the tables, isPcr
- 06:3906:39, 23 February 2012 diff hist 0 m QAing UCSC Genes No edit summary
- 06:3806:38, 23 February 2012 diff hist +23 QAing UCSC Genes →Links to Other UCSC Genes Genomewiki Pages: added ucsc genes tables link
- 06:3706:37, 23 February 2012 diff hist −17 QAing UCSC Genes collapsted the re-build problem section into the QAing the related tables section
- 06:3306:33, 23 February 2012 diff hist +337 QAing UCSC Genes added suggestions for dealing with redmine tickets
- 06:2806:28, 23 February 2012 diff hist +781 QAing UCSC Genes Added sections for a common rebuild pitfall and for QAing the many related tables
- 06:1306:13, 23 February 2012 diff hist +252 QAing UCSC Genes Made "Comparison to previous build" section specifically about human and mouse; added instruction to get help from developer/jim
- 06:0406:04, 23 February 2012 diff hist −41 QAing UCSC Genes →Determining the tables involved: fixed link
- 06:0206:02, 23 February 2012 diff hist −1,224 QAing UCSC Genes Removed HGGeneCheck instructions. This takes a week and failed to find errors in many runs, including several real errors for rn4.
- 06:0006:00, 23 February 2012 diff hist +23 Post-Release-Checklist →Add the link to the protein database /goldenPath/proteinDB/proteinsYYMMDD/database/: clarified downloads.html link, changed title of section
- 05:5405:54, 23 February 2012 diff hist +44 m Post-Release-Checklist →Update the metadata in hgcentral: clarified what hgNearOk does
- 05:5305:53, 23 February 2012 diff hist +2 Post-Release-Checklist →Update the metadata in hgcentral: removed hgPbOk and defaultDb instructions
- 05:4005:40, 23 February 2012 diff hist +21 Post-Release-Checklist →Exon Primer Links: clarified that exonPrimer is only for human and mouse
- 03:0503:05, 23 February 2012 diff hist −3 Post-Release-Checklist →HGNC Links to us: Elspeth Bruford at HNGC informed me that Michael Lush is no longer with the project.
14 February 2012
- 00:4400:44, 14 February 2012 diff hist +248 UCSC Genes tables added blastTabs section
- 00:3700:37, 14 February 2012 diff hist −1,827 UCSC Genes Staging Process removed list of assembly tables; added link to new UCSC Genes tables page
- 00:3200:32, 14 February 2012 diff hist +6 m UCSC Genes tables made headers slightly smaller
- 00:3100:31, 14 February 2012 diff hist +14 UCSC Genes tables Added "__FORCETOC__" to force a table of contents to show up at the beginning of the page
- 00:2400:24, 14 February 2012 diff hist +64 QAing UCSC Genes →wiki pages about known genes: added new ucsc genes tables page
- 00:2300:23, 14 February 2012 diff hist +322 UCSC Genes tables Added more titles, a link, and categories
- 00:0700:07, 14 February 2012 diff hist +839 UCSC Genes tables added proteins and sp tables
13 February 2012
- 23:4423:44, 13 February 2012 diff hist +979 N UCSC Genes tables Created page with "These are the lists of tables that were pushed with the latest UCSC Genes tracks. Please keep this page up to date! ;hg19 (January 2012 :bioCycMapDesc :bioCycPathway :ccdsKgMa..."
9 February 2012
- 00:3600:36, 9 February 2012 diff hist 0 m Post-Release-Checklist →Exoniphy: fixed misspelling
- 00:1900:19, 9 February 2012 diff hist +78 Post-Release-Checklist →UniProtKB: updated file locations
- 00:1500:15, 9 February 2012 diff hist −104 Post-Release-Checklist →Alert Ensembl: updated with emails and info supplied by Paul Flicek.
- 00:1000:10, 9 February 2012 diff hist +26 Post-Release-Checklist →Exoniphy: added Adam's email address
24 January 2012
- 23:2623:26, 24 January 2012 diff hist +222 BlastTabs →How to QA blastTabs: a loop for checking the hgBlastTab counts in the other dbs
- 23:1323:13, 24 January 2012 diff hist 0 BlastTabs →How to QA blastTabs: changed sacCer2 to sacCer3 in list of joiner identifiers
- 22:5622:56, 24 January 2012 diff hist +2 m BlastTabs →How to QA blastTabs: don't need headers in loop output
- 21:4821:48, 24 January 2012 diff hist +295 BlastTabs →How to QA blastTabs: added a loop for checking counts
- 05:4905:49, 24 January 2012 diff hist 0 QAing UCSC Genes →Comparison to previous build: updated second table with stats after rebuild of ucsc genes
- 05:4905:49, 24 January 2012 diff hist 0 QAing UCSC Genes →Comparison to previous build: updated table with stats after rebuild of ucsc genes
29 December 2011
- 01:0401:04, 29 December 2011 diff hist +78 UCSC Genes Staging Process clarified the organisms for which we build ucsc genes
15 November 2011
- 19:0519:05, 15 November 2011 diff hist +689 New track checklist →Searching (pre-QA): totally revamped this section to make it easier for pre-QA
10 November 2011
- 18:4418:44, 10 November 2011 diff hist +88 Pre-QA →Find track in browser & go to hgTrackUi: added link to assemblies list
4 November 2011
- 23:2323:23, 4 November 2011 diff hist −91 New track checklist →Searching (pre-QA): took out instructions to run checkHgFindSpec alone, since it depends on hgFindSpec_user if a trackDb_user is specified in .hg.conf
- 23:1823:18, 4 November 2011 diff hist +78 QAing UCSC Genes →Comparison to previous build: added note to check counts in knownCanonical, too
- 22:0122:01, 4 November 2011 diff hist +113 QAing UCSC Genes →HGGeneCheck: lots of small clarifications
- 21:2321:23, 4 November 2011 diff hist +1,987 QAing UCSC Genes added "comparison to previous build" section based on notes from Jim
- 20:4520:45, 4 November 2011 diff hist +70 QAing UCSC Genes →Other random notes: changed the header, clarified sentence.
- 19:2019:20, 4 November 2011 diff hist +307 QAing UCSC Genes →Actual steps: reformatting; took out instructions to run knownGene.csh; added Jim's joinerCheck instructions
- 18:4918:49, 4 November 2011 diff hist −1,641 QAing UCSC Genes →Background: stop spinning wheels looking for the right tables to push
- 00:5200:52, 4 November 2011 diff hist +16 Details pages -- conventions added degree symbols to list of things that should use html names
- 00:2300:23, 4 November 2011 diff hist +57 Details pages -- conventions added note about american spellings