we've just upgraded our Galaxy server (Galaxy revision
7148:17d57db9a7c0, upgraded to revision 10422:a886bc3ae924 ), and
have found that an NGS training workflow that one of us set up and
published is no longer accessible - we now get a stack trace
when we try to run it (screenshot attached) ; if we try to save to
file, we "get page not found" from the browser, but no errors
reported in web logs, or Galaxy log as far as we can see
Is there any way we can recover the workflow ?
How to avoid this happening in future upgrades ? This time it is not
a major problem, however we would not want this to happen to
production workflows. Should we save-to-file on all workflows as a
precaution before an upgrade ? (Would that help ? )
The workflow included steps as below.
Grateful for any suggestions.
First Part : checking GC content
.Upload the sampling.fasta file or get it from the shared data in Galaxy.
.Use geecee from EMBOSS
.Remove beginning (Text manipulation), first line
.Convert as tabular (Text manipulation) or cut (Text manipulation)
.Histogram (Graph/Display Data)on col2
.Compute data (Text manipulation) (data4 convert; col2>0.2)
.Count data (statistics on col3) If it is worth it we can remove the
sequences which have a too low GC content
Second part : sequence length
.Compute Sequence length (FASTA manipulation)
.Summary Statistics (Statistics)on col2
.Filter by length(FASTA manipulation) ; 800
.Line/world/character count(Text manipulation)
.Blastn against fungi db : yeast, only one hit to show (advanced options )
.Count the lines to know how many sequences have a hit . (Text
Bonus track : removing sequences with low GC content
.Select (filter and sort) on data 6 where matching = True
.FASTA-to-Tabular (FASTA manipulation) the input file sampling.fasta
(2 col for the title)
.Join two datasets(Join, Subtract and Group) on the columns c1
.Tabular-to-FASTA (fasta manipulation) of the previous results.
.You can see how many sequences you took away (click on the dataset
name in History) and it should correspond to the number of True in Count .
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