v1.1

Thank you for taking time enumerating the commands that we need! It can be pretty stressful and recently I played among us: 5.6 hrs in the last 2 weeks with me ...

Python is probably my least favorite of all the programming languages out there in the market. I don’t just get the feel for the language. I would rather code a...

Thank you for the information posted about stress-test coding! While learning about the ins and outs of coding, me and my friends have been playing this game ca...

(from [82743f4fb5f5acc16daca9aa0ff744dea2d0a551]) Sort dirs so that the subdirs are executed in alphanumerical order. Fixes #23. https://github.com/mfiers/Moa/...

[cfljam@pgenome 10.Chrom_1]$ pwd /data/moa/onion/map/20.USDA_2012/10.Chrom_1 [cfljam@pgenome 10.Chrom_1]$ moa show jobid l.o Chrom_1
postcommand l.o fastaExtrac...

Wow - are there still jobs that use gnumake?? I deprecated that
probably more than a year ago...

I've fixed all jobs that were still gnumake - most of these wer...

[cfljam@pgenome 35.FT_reseq_2011]$ pwd /data/moa/onion/25.resequencing/35.FT_reseq_2011 [cfljam@pgenome 35.FT_reseq_2011]$ moa cp 70.popoolation_Tajima 69.popoo...

This needs -f force flag added (simple) or a clean method

[cfljam@pgenome 93.gsmapper_TSA_submit]$ moa show gsmap_name L Map_Nasik_to_SNP_markers_DHrefV2
jobid ...

[cfljam@pgenome 11.download_refseq_nt]$ pwd /data/moa/db/refseq_cplast/11.download_refseq_nt [cfljam@pgenome 11.download_refseq_nt]$ moa show db L nuccore
jobid...

This template doesnt respect fasta input.
Also the distinction between db and index base is rather confusing

...............................................

[cf...

fixed

John - is this still a valid concern??

Won't fix this - cannot think of an elegant way to do this properly.

fixed this quite a while ago

Fixed - splitted this on up in

lightweight -show mandatory and configured variables:
moa show

show all variables, set or not
moa show -a

show also private varia...

moa@ubuntu:~/work/10.PAG_DEMO/00.reads$ moa blog
enter your blog message (ctrl-d on an empty line to finish) ...
Importing subset of reads for demo
Moa: Error r...

Filename completion when entering commands is still broken....

(from [f79f8c568eda47290a954496fae2ca2396a773cf]) Checks if a relative link needs to be updated by parameter type [#37 state:resolved] https://github.com/mfier...

MOA strips off ./ when setting process

[cfljam@pgenome 10.bin]$ moa set process process:

./bin_FIE_data.R 00.data D049_WXT.csv binned_LTQ-mean.RData [cfljam@pg...

The problem is that IMHO..the job info browser view in SIMPLE is now quite cluttered to the point of being less informative and transparent...
as previously sug...

[cfljam@pgenome 10.search_onion_nr]$ pwd /data/moa/onion/70.CG_marker_design/80.TFs/10.search_onion_nr [cfljam@pgenome 10.search_onion_nr]$ moa show jobid L sea...

This "one-liner" used for making tbl format from gff
at
/data/moa/onion/20.genomic.sequencing/09.submission_SSR_reads_sequin wont run in process but fine in CL....

Could the order be changed so it reads precommand, process, postcommand?
Current is hard to read

[cfljam@pgenome 09.submission_SSR_reads_sequin]$ moa show input...

seem to have issues editing command when prefixed by ./

[cfljam@pgenome 09.submission_SSR_reads_sequin]$ pwd /data/moa/onion/20.genomic.sequencing/09.submission...

Yes - it is - sorry about that - i've asked ray to set them a little
less restrictive - now every time you do something you automatically
deny everybody else th...

Still wonky...is this permission defaults??

[cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ pwd /data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaS...

It is resolved - You need to run moa refresh - the template code was still old - so that needs updating...

(a downside to keeping template code in your director...

Not fixed I think

{also how about re-ordering the show command so postcommand is after process?}

[cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ pwd /data/moa/onion/7...

Seems to work now..

Think I fixed it

Yes I think solved

-----Original Message----- From: Lighthouse [mailto:no-reply@lighthouseapp.com]
Sent: Wednesday, June 01, 2011 9:11 AM
To: John McCallum
Subj...

John, is this one still valid, or was it solved by changing your python version??

whatever the case is - we need to do something about how moa/ruffus shows it's...

(from [691caf8fe33f800076701f6b22bbe910396ad71f]) Improved moa show output - show {{ var }} codes again [#30 state:resolved] https://github.com/mfiers/Moa/comm...

the process CL works fine...but

[cfljam@pgenome 40.assemble]$ source ~/.bashrc [cfljam@pgenome 40.assemble]$ moa run Warning: Removing a stale lockfile
Error: n...

I think that 'show' should reveal the {{input}} and {{output}} tags
so that moa show is more useful
ie make moa show, show "fastaExtract -l ../11.retrieve_USDA_...

[cfljam@pgenome 15.BLASTX_USDA_GH32]$ pwd /data/moa/onion/70.CG_marker_design/40.CHO/GH32/15.BLASTX_USDA_GH32 [cfljam@pgenome 15.BLASTX_USDA_GH32]$ moa show db ...

.moa/log directory was not writable - should give a reasonable error message when this happens

Note that it dies in a flurry of ruffus measages etc but moa err ...

fixed

Wow - fixing 24 broke this one - now both are ok.

cheers
Mark

[Cfljam@pgenome 21.BLAST_unfiltered]$ moa show db ../20.BLASTN_db_repeats/OnionRepeat
eval 1e-10
gff_blasthit F
gff_source BLAST
input ../01.UnfilteredGSSReads/...

Duplicate of 24

Fixed - problem with parsing through the parameters & categories of parameters.

The template field on category order is now deprecated

Fixed -