mojones / afterparty2 Goto Github PK

au3

or

au3.g

but

au

works

Dear all,

has anyone had any success downloading the afterparty VM ? We get the following error here trying the link on the docs.

Forbidden You don't have permission to access /bioinformatics/afterparty/afterparty_export.ova on this server.

Thanks,
Colin

probably we can just add it to the index in bootstrap.

need a filter

phobius, coils

e.g. for getting search results

Searching for

DSCAM

returns more hits in contig table than in search.

I tried adding an assembly to my project. It was a 48 Mbp fasta file with 10000 sequences (the longest ones from my project). Afterparty seems to work (the upload percentage status increases steadily to 100%, then the site waits), but then all I get is a screen that says No Data Received (latest chrome on a mac).

trying to login on firefox on mac osx 10.6
I get the standard firefox "the page isnt redirtecting properly" splash, suggesting it will never complete

i.e. we will not have to specify number of results in the search form, but just pull them back using AJAX when we want to display a contig table.

Seanna's idea

http://afterparty.bio.ed.ac.uk/compoundSample/show/666146

initially i was getting

Grails Runtime Exception

Error Details

Error 500: Executing action [searchContigSets] of controller
[afterparty.ContigSetController] caused exception: Runtime error executing
action
Servlet: grails
URI: /grails/contigSet/searchContigSets.dispatch
Exception Message: Cannot invoke method toInteger() on null object
Caused by: Cannot invoke method toInteger() on null object
Class: GrailsFragmentCachingFilter
At Line: [66]
Code Snippet:

Stack Trace

java.lang.NullPointerException: Cannot invoke method toInteger() on null
object

at

afterparty.ContigSetController$_closure11.doCall(ContigSetController.groovy:299)

at

grails.plugin.springcache.web.GrailsFragmentCachingFilter.doFilter(GrailsFragmentCachingFilter.groovy:66)

at net.sf.ehcache.constructs.web.filter.Filter.doFilter(Filter.java:86)

at

com.linkedin.grails.profiler.ProfilerFilter.doFilterInternal(ProfilerFilter.java:82)

at

java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)

at

java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)

at java.lang.Thread.run(Thread.java:679)

but now I am getting no response at all (or being bounced back to the page I started from - hard to tell)

Firefox 12.0, MacOS X 10.6.8, two finger typist

In the browse contigs table, perhaps could round the Coverage, Quality, GC to one or no decimal places, and show GC as a percentage, eg:

Coverage Quality %GC
60.0 5.6 39.4

That would give more space for the annotations column on the right.

.fastq files upload without a problem but .fastq.gz files (as they are downloaded from EBI/SRA) fail. Would be great if afterParty could take .gz files as well

see eg http://afterparty.bio.ed.ac.uk/contig/show/709903

which species/assembly/ etc is this from, and which contig is it?

It is diffcult to navigate BACK to the last page visited to revisit questions asked or gene lists...

Contig pages shopuld have their "containers" linked in (assembly, species, etc) as a minimum

question is how to enable this... i am guessing breadcrumbs would be harsh, but perhaps each dataset contig page could have a link to its home (assembly) page and each assembly to its (species) etc..,

While uploading annotations, I noticed that the BLAST xml upload expects .gz file, whereas the GFF3 upload does NOT like .gz files. My suggestion would be to keep it consistent (preferably only .gz for both as they are smaller) or else auto-detect on the server side.

Thanks!

http://stackoverflow.com/questions/2483919/how-to-save-svg-canvas-to-local-filesystem

It's easy to add new entries for each of these, and to edit them, but there doesn't seem to be a way to delete them. Deleting the name simply leaves a blank entry.

On the menu along the top (eg. the "Navigation" menu, and "Login") the small gray text on the black background means the menu isn't initially that obvious when using it for first time. Perhaps use white or yellow text, or the "Menu" word before it ?

general comment on [contig|contig set] view:
would be good to have a breadcrumb of the name of the species/dataset etc to contextualise each one

report formatting
would be good to have more measured formatting of dataset intro pages (ie at present it appears that the fact that the dataset HAS a name is more important than the name)

blast searching
permit setting of parameters on blast searches
state parameters used in blast search defaults

blast reports
tabulating blast reporting on contig overview/set page to separate out E-value and bit score into columns

must be some parsing error - they show up as large integers when they should be very small reals!

probably because we are ignoring un-annotated contigs

This may run and run

I am not able to click the search etc buttons and get a drop down menu using iPad mac iOS 5, safari browser
Likely an issue with the way the page operates...

If is looks like an inoperable disease maybe the site needs to say "I don't work on iPads".

M

Perhaps (maybe optionally) add the Afterparty id beside the ContigID column as that would be good if using that afterparty Id for other software (as the afterparty id is unique across all the assemblies whereas the same contig name can occur in several assemblies)?

Do we need to add a default whole-contig annotation item?

http://afterparty.bio.ed.ac.uk/compoundSample/show/709751

once I have clicked on blast by accident how do i return to the page with three choices without going back to the study and reselecting the contig set?

I did a blastx against uniprot_sprot.fasta (which should be a subset of uniprot, I think). When I uploaded this text blastx xml, the interface displays everything very nicely; however, the first column with linkouts to uniprot doesn't work (the uniprot id being sent to doesn't exist).

eg: http://afterparty.bio.ed.ac.uk/contig/show/37240648 - Blast Hits

http://docs.jboss.org/hibernate/core/3.6/reference/en-US/html/mapping.html#mapping-types-basictypes

http://afterparty.bio.ed.ac.uk/contig/show/712146
[but any contig will do]

the linkouts to uniprot give misformed queries at ENA

http://www.uniprot.org/uniprot/UniRef100_P49672

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