Difference between revisions of "Update Matrix WS205"
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| Are the correct ontology files in /u/l/w/databases? | | Are the correct ontology files in /u/l/w/databases? | ||
− | | <br> | + | | <br> yes |
| Mirror Ontology from Sanger | | Mirror Ontology from Sanger | ||
|- | |- | ||
| Were the additional ontology files generated? | | Were the additional ontology files generated? | ||
− | | <br> | + | | <br> yes |
| Compile Ontology Resources | | Compile Ontology Resources | ||
|- | |- | ||
| Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search | | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search | ||
− | | <br> | + | | <br> yes |
| Compile Ontology Resources | | Compile Ontology Resources | ||
|- | |- | ||
|Are the Ontology related summary pages working? | |Are the Ontology related summary pages working? | ||
− | | <br> | + | | <br> yes |
|Compile Ontology Resources | |Compile Ontology Resources | ||
|- | |- | ||
|Can you do a blast searches on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | |Can you do a blast searches on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | ||
− | | <br> | + | | <br> yes |
| Create Blast DBs | | Create Blast DBs | ||
|- | |- | ||
|Can you do a blat search on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | |Can you do a blat search on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | ||
− | | <br> | + | | <br> yes |
|Create Blat DBs | |Create Blat DBs | ||
|- | |- | ||
|Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | |Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | ||
− | | <br> | + | | <br> yes |
|Create ePRC DBs | |Create ePRC DBs | ||
|- | |- | ||
|Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence | |Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence | ||
− | | <br> | + | | <br> yes |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner | |Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner | ||
− | | <br> | + | | <br> yes |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Is the Gene Details Page working? <br>http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 | |Is the Gene Details Page working? <br>http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 | ||
− | | <br> | + | | <br> yes |
| Load GFF DBs | | Load GFF DBs | ||
+ | |||
+ | |||
+ | [[Category:Developer documentation]] | ||
|- | |- | ||
|Are the supplementary GFF tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | |Are the supplementary GFF tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | ||
− | | <br> | + | | <br> not all, update to GFF conf scheduled for WS206 |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ | |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ | ||
− | | <br> | + | | <br> yes, except mh and mi -- data loaded, updating conf files |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | |Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | ||
− | | <br> | + | | <br> yes |
| Build and Load GFF Patches | | Build and Load GFF Patches | ||
|- | |- | ||
| Are protein motifs available on the Protein page?<br>http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein | | Are protein motifs available on the Protein page?<br>http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein | ||
− | | <br> | + | | <br> yes |
| Build and Load GFF Patches | | Build and Load GFF Patches | ||
|- | |- | ||
|Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease | |Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease | ||
− | | <br> | + | | <br> yes |
| Compile orthology resources | | Compile orthology resources | ||
|- | |- | ||
|Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 | |Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 | ||
− | | <br> | + | | <br> yes |
| Compile orthology resources | | Compile orthology resources | ||
|- | |- | ||
|Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | ||
− | | <br> | + | | <br> yes |
| Compile interaction resources | | Compile interaction resources | ||
|- | |- | ||
− | |Can you list the available position matrices? | + | |Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all |
− | | <br> | + | | <br> yes |
| Compile position matrices | | Compile position matrices | ||
|- | |- | ||
|Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | |Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | ||
− | | <br> | + | | <br> yes |
| Update CLUSTAL database | | Update CLUSTAL database | ||
|- | |- | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− |
Latest revision as of 18:14, 17 August 2010
Check | Note | Related Compile Step |
---|---|---|
Have directories been created for given release in /u/l/w/databases? | yes |
Create Data Directories |
Has a wormbase_RELEASE directory been created in /u/l/w/acedb? | yes |
Mirror and Unpack AceDB files |
Is the Dev site running with the correct release number? | yes |
Mirror and Unpack AceDB files |
Is the wormbase pointer linked to the newly created acedb? | yes |
Mirror and Unpack AceDB files |
Is the database running and providing the correct version number? | yes |
Mirror and Unpack AceDB files |
Are the correct ontology files in /u/l/w/databases? | yes |
Mirror Ontology from Sanger |
Were the additional ontology files generated? | yes |
Compile Ontology Resources |
Is the Multi-Ontology Search Running? URL: http://dev.wormbase.org/db/ontology/search |
yes |
Compile Ontology Resources |
Are the Ontology related summary pages working? | yes |
Compile Ontology Resources |
Can you do a blast searches on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
yes |
Create Blast DBs |
Can you do a blat search on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
yes |
Create Blat DBs |
Does ePCR work? http://dev.wormbase.org/db/searches/epcr |
yes |
Create ePRC DBs |
Are the appropriate tracks visible on the appropriate genomes http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence |
yes |
Load GFF DBs |
Is the EST aligner working? http://dev.wormbase.org/db/seq/aligner |
yes |
Load GFF DBs |
Is the Gene Details Page working? http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 |
yes |
Load GFF DBs |
Are the supplementary GFF tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
not all, update to GFF conf scheduled for WS206 |
Load GFF DBs |
Are the GBrowsers for the various species working http://dev.wormbase.org/db/seq/gbrowse/ |
yes, except mh and mi -- data loaded, updating conf files |
Load GFF DBs |
Are the Genetic Limit Tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
yes |
Build and Load GFF Patches |
Are protein motifs available on the Protein page? http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein |
yes |
Build and Load GFF Patches |
Can you do a disease search? http://dev.wormbase.org/db/orthology/disease |
yes |
Compile orthology resources |
Can you list diseases for a gene? http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 |
yes |
Compile orthology resources |
Can you list interactions? http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 |
yes |
Compile interaction resources |
Can you list the available position matrices? http://dev.wormbase.org/db/seq/position_matrix?list=all |
yes |
Compile position matrices |
Can you run a CLUSTAL search? http://dev.wormbase.org/db/seq/show_mult_align |
yes |
Update CLUSTAL database |