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 manipulation)
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
*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 .