Difference between revisions of "Update Matrix WS206"

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|-
 
|-
 
| Have directories been created for given release in /u/l/w/databases?
 
| Have directories been created for given release in /u/l/w/databases?
−
| <br>
+
| ok
 
| Create Data Directories
 
| Create Data Directories
 
|-
 
|-
 
|Has a wormbase_RELEASE directory been created in  /u/l/w/acedb?  
 
|Has a wormbase_RELEASE directory been created in  /u/l/w/acedb?  
−
|<br>  
+
|ok  
 
|Mirror and Unpack AceDB files
 
|Mirror and Unpack AceDB files
 
|-
 
|-
 
|Is the Dev site running with the correct release number?  
 
|Is the Dev site running with the correct release number?  
−
|<br>
+
|ok
 
|Mirror and Unpack AceDB files
 
|Mirror and Unpack AceDB files
 
|-
 
|-
 
| Is the wormbase pointer linked to the newly created acedb?
 
| Is the wormbase pointer linked to the newly created acedb?
−
| <br>
+
| ok
 
| Mirror and Unpack AceDB files
 
| Mirror and Unpack AceDB files
 
|-
 
|-
 
| Is the database running and providing the correct version number?
 
| Is the database running and providing the correct version number?
−
| <br>
+
| ok
 
| Mirror and Unpack AceDB files
 
| Mirror and Unpack AceDB files
 
|-
 
|-
 
| Are the correct ontology files in /u/l/w/databases?
 
| Are the correct ontology files in /u/l/w/databases?
−
| <br>
+
| ok
 
| Mirror Ontology from Sanger
 
| Mirror Ontology from Sanger
 
|-
 
|-
 
| Were the additional ontology files generated?
 
| Were the additional ontology files generated?
−
| <br>
+
| ok
 
| 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>
+
| ok
 
| Compile Ontology Resources
 
| Compile Ontology Resources
 
|-
 
|-
 
|Are the Ontology related summary pages working?  
 
|Are the Ontology related summary pages working?  
−
| <br>
+
|ok
 
|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>
+
| see table below
 
| 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>
+
| see table below
 
|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>
+
| see table below
 
|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>
+
| ok
 
| 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>
+
| ok
 
| 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>
+
| ok
 
| Load GFF DBs
 
| Load GFF DBs
 
|-
 
|-
 
|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>
+
| ok
 
| 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>
+
| see table below
 
| 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>
+
| ok
 
| 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>
+
| ok
 
| 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>
+
| ok
 
| 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>
+
| ok
 
| 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>
+
| ok
 
| Compile interaction resources
 
| Compile interaction resources
 
|-
 
|-
 
|Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all
 
|Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all
−
| <br>
+
| ok
 
| 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>
+
| ok
 
| Update CLUSTAL database
 
| Update CLUSTAL database
 
|-
 
|-
Line 117: Line 117:
 
|-
 
|-
 
|<i>C elegans</i>
 
|<i>C elegans</i>
−
| <br>
+
| ok
−
| <br>
+
| troubleshooting
−
| <br>
+
| ok
−
| <br>
+
| ok
 
|-
 
|-
 
|<i>C briggsae</i>
 
|<i>C briggsae</i>
−
| <br>
+
| ok
−
| <br>
+
| troubleshooting
−
| <br>
+
| N/A
−
| <br>
+
| ok
 
|-
 
|-
 
|<i>C brenneri</i>
 
|<i>C brenneri</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| ok
 
|-
 
|-
−
|<i>C bruggia</i>
+
|<i>C remanei</i>
−
| <br>
+
| troubleshooting
−
| <br>
+
| troubleshooting
−
| <br>
+
| N/A
−
| <br>
+
| ok
 
|-
 
|-
 
|<i>C japonica</i>
 
|<i>C japonica</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| ok
 
|-
 
|-
 
|<i>M hapla</i>
 
|<i>M hapla</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| up; needs evaluation
 
|-
 
|-
 
|<i>M incognita</i>
 
|<i>M incognita</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| up; needs evaluation
 
|-
 
|-
 
|<i>B malayi</i>
 
|<i>B malayi</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| up; needs some debugging
 
|-
 
|-
 
|<i>P pacificus</i>
 
|<i>P pacificus</i>
−
| <br>
+
| ok
−
| <br>
+
| N/A
−
| <br>
+
| N/A
−
| <br>
+
| ok
 +
 
 +
 
 +
 
 +
[[Category:Developer documentation]]

Latest revision as of 18:20, 17 August 2010

Check Note Related Compile Step
Have directories been created for given release in /u/l/w/databases? ok Create Data Directories
Has a wormbase_RELEASE directory been created in /u/l/w/acedb? ok Mirror and Unpack AceDB files
Is the Dev site running with the correct release number? ok Mirror and Unpack AceDB files
Is the wormbase pointer linked to the newly created acedb? ok Mirror and Unpack AceDB files
Is the database running and providing the correct version number? ok Mirror and Unpack AceDB files
Are the correct ontology files in /u/l/w/databases? ok Mirror Ontology from Sanger
Were the additional ontology files generated? ok Compile Ontology Resources
Is the Multi-Ontology Search Running?
URL: http://dev.wormbase.org/db/ontology/search 		ok Compile Ontology Resources
Are the Ontology related summary pages working? ok Compile Ontology Resources
Can you do a blast searches on the appropriate genomes?
http://dev.wormbase.org/db/searches/blast_blat 		see table below Create Blast DBs
Can you do a blat search on the appropriate genomes?
http://dev.wormbase.org/db/searches/blast_blat 		see table below Create Blat DBs
Does ePCR work?
http://dev.wormbase.org/db/searches/epcr 		see table below Create ePRC DBs
Are the appropriate tracks visible on the appropriate genomes
http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence 		ok Load GFF DBs
Is the EST aligner working?
http://dev.wormbase.org/db/seq/aligner 		ok 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 		ok Load GFF DBs
Are the supplementary GFF tracks available
http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ 		ok Load GFF DBs
Are the GBrowsers for the various species working
http://dev.wormbase.org/db/seq/gbrowse/ 		see table below Load GFF DBs
Are the Genetic Limit Tracks available
http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ 		ok 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 		ok Build and Load GFF Patches
Can you do a disease search?
http://dev.wormbase.org/db/orthology/disease 		ok Compile orthology resources
Can you list diseases for a gene?
http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 		ok Compile orthology resources
Can you list interactions?
http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 		ok Compile interaction resources
Can you list the available position matrices?
http://dev.wormbase.org/db/seq/position_matrix?list=all 		ok Compile position matrices
Can you run a CLUSTAL search?
http://dev.wormbase.org/db/seq/show_mult_align 		ok Update CLUSTAL database
GENOME MATRIX
species Blast Blat ePCR GBrowse
C elegans ok troubleshooting ok ok
C briggsae ok troubleshooting N/A ok
C brenneri ok N/A N/A ok
C remanei troubleshooting troubleshooting N/A ok
C japonica ok N/A N/A ok
M hapla ok N/A N/A up; needs evaluation
M incognita ok N/A N/A up; needs evaluation
B malayi ok N/A N/A up; needs some debugging
P pacificus ok N/A N/A ok
Retrieved from "https://wiki.wormbase.org/index.php?title=Update_Matrix_WS206&oldid=6171"