Warn when a template is outdated
Reported by john.mccallum (at plantandfood) | May 30th, 2011 @ 11:02 PM | in v1.1
the process CL works fine...but
[cfljam@pgenome 40.assemble]$ source ~/.bashrc [cfljam@pgenome
40.assemble]$ moa run Warning: Removing a stale lockfile
Error: no in or output files
[cfljam@pgenome 40.assemble]$ moa clean [cfljam@pgenome
40.assemble]$ pwd /data/moa/onion/20.genomic.sequencing/40.assemble
[cfljam@pgenome 40.assemble]$ moa clean [cfljam@pgenome
40.assemble]$ moa show postcommand L awk '$2=="Singleton" {print
$1}' DHSkim/454ReadStatus.txt > singletons.lst;sed
's/contig/CUDH2122_/' DHSkim/454AllContigs.fna >
CUDH2122_contigs.fasta
precommand o (undefined)
process L runAssembly -force -o DHSkim -a 100 -minlen 45 -tr -rip
../00.raw/MID6.sff
project L DHskim
title L Newbler assembly of reads
[cfljam@pgenome 40.assemble]$ moa run Error: no in or output
files
[cfljam@pgenome 40.assemble]$
Comments and changes to this ticket
-
john.mccallum (at plantandfood) May 31st, 2011 @ 11:07 PM
- State changed from resolved to new
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/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ source ~/.bashrc [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ moa show postcommand L awk '/ssaha:SNP/ {print $2, "ssaha2SNP","SNP",$9,$9, "1",".",".","ID=$2 }' ssaha2SNP.out > ssaha2SNP.gff [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$
-
MF June 1st, 2011 @ 04:22 AM
- Tag changed from simple to template refresh
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to keeping template code in your directory) - I'll change this ticket to providing a warning if your template is outdated..
-
MF June 1st, 2011 @ 04:23 AM
- Title changed from Simple template bug? to Warn when a template is outdated
-
john.mccallum (at plantandfood) June 1st, 2011 @ 04:26 AM
Still wonky...is this permission defaults??
[cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ pwd /data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ ls -l .. total 60
drwxrwxr-x 4 cflmwf users 4096 Jun 1 10:36 00.Candidates
drwxrwxr-x 3 cflmwf users 4096 May 11 11:12 01.Candidate_BLASTdb
drwxrwxr-x 5 cflmwf users 4096 May 4 13:31 05.TBLASTN_DH2150
drwxrwxr-x 5 cflmwf users 4096 Jun 1 09:47 06.TBLASTN_USDA
drwxrwxr-x 5 cflmwf users 4096 May 11 12:54 07.BLASTX_DH2150
drwxrwxr-x 5 cfljam users 4096 Jun 1 10:27 08.TBLASTN_USDA_5225
drwxrwxr-x 5 cfljam users 4096 Jun 1 10:22 09.TBLASTN_USDA_OH1
drwxrwxr-x 4 cflmwf users 4096 May 11 12:47 10.gsMapper_Nasik
drwxrwxr-x 4 cflmwf users 4096 May 11 12:15 11.gsMapper_NasikToUSDACGs
drwxrwxr-x 4 cflmwf users 4096 May 11 12:26 12.gsMapper_DH2150ToUSDACGs
drwxrwxr-x 3 cflmwf users 4096 May 4 10:06 20.primersearch
drwxrwxr-x 3 cflmwf users 4096 May 11 13:35 21.USDA_CG_primersearch
drwxrwxr-x 3 cflmwf users 4096 May 4 14:16 30.primerDesign
drwxrwxr-x 3 cflmwf users 4096 May 5 09:05 35.primersearchSQL
drwxrwxr-x 3 cfljam users 4096 Jun 1 11:05 40.OH1onto5225_ssahaSNP
[cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ moa refresh Warning: Encountered a run error?
Traceback (most recent call last):
File "/opt/moa10/bin/moa", line 318, inrun_1()
File "/opt/moa10/bin/moa", line 292, in run_1
run_2()
File "/opt/moa10/bin/moa", line 246, in run_2
run_3(wd)
File "/opt/moa10/bin/moa", line 191, in run_3
pluginHandler.runCallback(job, command)
File "/opt/moa10/lib/python/moa/plugin/init.py", line 85, in runCallback
commandInfo['call'](job)
File "/opt/moa10/lib/python/moa/plugin/template.py", line 73, in refresh
job.refreshTemplate()
File "/opt/moa10/lib/python/moa/job.py", line 310, in refreshTemplate
moa.template.refresh(self.wd)
File "/opt/moa10/lib/python/moa/template/init.py", line 114, in refresh
provider=meta.get('provider', None))
File "/opt/moa10/lib/python/moa/template/init.py", line 57, in installTemplate
PROVIDERS.installTemplate(wd, tName, provider)
File "/opt/moa10/lib/python/moa/template/provider/init.py", line 101, in installTemplate
p.installTemplate(wd, tName)
File "/opt/moa10/lib/python/moa/template/provider/core.py", line 67, in installTemplate
shutil.rmtree(extraFileDir)
File "/usr/lib64/python2.6/shutil.py", line 221, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/usr/lib64/python2.6/shutil.py", line 219, in rmtree
os.remove(fullname)
OSError: [Errno 13] Permission denied: '/data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP/.moa/template.d/meta'
[cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ -
MF June 1st, 2011 @ 05:51 AM
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 the right to edit it, possibly even look at it..I've restored the permissions..
cheers
Mark
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