BLAST template confusion
Reported by john.mccallum (at plantandfood) | April 4th, 2011 @ 01:59 AM | in v1.0
Creating a new blast job inside a directory calling data from
NCBI leads to apparent inheritance of variables from higher level
directory...
ie (blast) db is set to NCBI db name...
[Cfljam@pgenome 20.NCBI_GSS]$ pwd
/data/moa/db/onion/20.Genbank_onion/20.NCBI_GSS [Cfljam@pgenome
20.NCBI_GSS]$ moa show db nucgss
postcommand
precommand
project
query allium cepa[organism]
sequence_name gss_out
title retrieve onion GSS sequences
[Cfljam@pgenome 20.NCBI_GSS]$ mkdir 10.BLASTvsOnionnt
[Cfljam@pgenome 20.NCBI_GSS]$ cd 10.BLASTvsOnionnt/ [Cfljam@pgenome
10.BLASTvsOnionnt]$ moa show Error: This command must be executed
in a Moa job directory
[Cfljam@pgenome 10.BLASTvsOnionnt]$ moa new blast -t 'Blast onion
GSS vs Onion nt' Created a Moa blast job
[Cfljam@pgenome 10.BLASTvsOnionnt]$ moa show db nucgss
eval 1e-10
gff_blasthit F
gff_source BLAST
input /.fasta
nohits 50
nothreads 2
outgff gff/.gff
output out/.out
postcommand
precommand
program blastn
project
query allium cepa[organism]
sequence_name gss_out
title Blast onion GSS vs Onion nt
Comments and changes to this ticket
-
MF April 4th, 2011 @ 03:40 AM
I agree - that is somewhat confusing... need to think about that one..
I would typically organize such jobs in leaf nodes:
./10.download.from.ncbi ./20.create.blastdb ./30.blast
but your approach is no less valid ...
-
MF April 6th, 2011 @ 02:48 AM
Think I have a solution - make only those vars inheritable that are either defined as being inheritable or NOT in the template definition.
Thus: 'db' would be in the template definition of blastdb and is not inherited by jobs in subdirs. Any dummy var would be inherited.
-
MF April 28th, 2011 @ 12:39 AM
- State changed from “new” to “invalid”
fixing this is weird - it makes thinks more complicated than need be -
I suggest that in templates we'll try to use better names for parameters -
and, possibly, that one should not organise a pipeline in such a way that there are many jobs in leaf directories of other jobs. ALthough this is a matter of taste.
It will be improved partly by solving ticket [19] - as that will make sure that it is clear if a parameter is inherited.
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lightweight workflows for bioinformatics
john.mccallum (at plantandfood)
MF