Merge branch 'moa.0.11' of ssh.github.com:mfiers/Moa into moa.0.11

README

@@ -1,10 +1,13 @@
 Moa - lightweight workflows in bioinformatics.
 
-For information on how to install and operate Moa, please refer to
-http://mfiers.github.com/Moa/
-f
-or try:
+For information on how to install and operate Moa, please read the documentation at:
 
-moa --help
+http://moa.readthedocs.org/en/latest/index.html
+
+check the source code at:
 
+https://github.com/mfiers/Moa
 
+or run:
+
+moa --help

lib/python/moa/plugin/job/smw/__init__.py

@@ -63,6 +63,9 @@ def _savePage2(page, txt):
         #moa.ui.message("saved change message to SMW")
     except mwclient.errors.LoginError:
         moa.ui.error("Invalid login for smw - cannot save change message")
+    except:
+        moa.ui.error("Cannot save to SMW - uncertain why")
+        return
 
 def _savePage(page, txt):
     background = sysConf.plugins.job.smw.get('background', False)
@@ -155,11 +158,12 @@ def hook_finish(job):
     message = moa.ui._textFormattedMessage(
         [sysConf.args.changeMessage,
          sysConf.doc.changeMessage] )
-        
+
     if sysConf.commands[sysConf.args.command]['logJob']:
         if sysConf.args.command != 'smw_save_job':
             _saveJobToSmw(job)
         _saveChangeMessage(job, message)
+
     sys.exit(0)
 
 def _checkJobInSmw(job):

lib/python/moa/plugin/system/evernote.py

@@ -0,0 +1,116 @@
+# Copyright 2009-2011 Mark Fiers
+# The New Zealand Institute for Plant & Food Research
+# 
+# This file is part of Moa - http://github.com/mfiers/Moa
+# 
+# Licensed under the GPL license (see 'COPYING')
+# 
+"""
+**evernote** - Use evernote to store job results
+------------------------------------------------
+
+Use evernote to store a small message on job completion
+
+Depends on an authenticated geeknote installation in the path. Moa
+expects it to be aliased as `geeknote`
+
+see:
+http://www.geeknote.me/
+
+"""
+
+import os
+import sys
+import time
+import socket
+from datetime import datetime, timedelta
+import subprocess as sp
+
+import moa.logger 
+l = moa.logger.getLogger(__name__)
+import moa.ui
+
+from moa.sysConf import sysConf
+
+def niceRunTime(d):
+    """
+    Nice representation of the run time
+    d is time duration string    
+    """
+    d = str(d)
+    if ',' in d:
+        days, time = d.split(',')
+    else:
+        days = 0
+        time = d
+
+    hours, minutes, seconds = time.split(':')
+    hours, minutes = int(hours), int(minutes)
+    seconds, miliseconds = seconds.split('.')
+    seconds = int(seconds)
+    miliseconds = int(miliseconds)
+
+    if days > 0:
+        if days == 1:            
+            return "1 day, %d hrs" % hours
+        else:
+            return "%d days, %d hrs" % (days, hours)
+
+    if hours == 0 and minutes == 0 and seconds == 0:
+        return "<1 sec"
+    if hours > 0:
+        return "%d:%02d hrs" % (hours, minutes)
+    elif minutes > 0:
+        return "%d:%02d min" % (minutes, seconds)
+    else:
+        return "%d sec" % seconds
+
+def hook_postRun():
+    """
+    Send a tweet out upon completing the default run
+    """
+    runtime =  datetime.today() - sysConf.logger.start_time    
+    #print runtime
+    #print timedelta(seconds=1)
+    if timedelta(seconds=1) > runtime:
+        # do not return anythin unless it ran for at least a certain
+        # amount of time
+        return 
+
+    short_title = '%s/%s finished' % (
+        socket.gethostname().split('.')[0],
+        sysConf.job.wd.rsplit('/', 1)[-1])
+
+    content = ['Moa job finished\n']
+    content.append("    Run time: %s\n" % niceRunTime(runtime))
+    content.append("    Host: %s\n" % socket.gethostname())
+    content.append("    Wd: %s\n" % sysConf.job.wd)
+
+    #fork - don't wait for this!
+    pid = os.fork()
+    if pid != 0: 
+        return
+    print short_title
+    print "\n".join(content)
+    #start geeknote process
+    moa.ui.message('Sending message to evernote', store=False)
+    cl = '%s create --title "%s" --content - --notebook Moa' % (
+        sysConf.plugins.system.evernote.geeknote, short_title)
+    print cl
+    P = sp.Popen(cl, stdin=sp.PIPE, stdout=sp.PIPE, stderr=sp.PIPE, shell=True)
+
+    o,e = P.communicate("\n".join(content))
+    o = o.strip()
+    e = e.strip()
+
+    if o or e:
+        with open('.moa/geeknote.log', 'a') as F:
+            F.write("------\n%s\n%s\n" % (short_title, "\n".join(content)))
+            if o:
+                F.write('\n\nSTDOUT:\n')
+                F.write(o)
+            if e:
+                F.write('\n\nSTDERR:\n')
+                F.write(e)
+    sys.exit(0)
+

lib/python/moa/plugin/system/info.py

@@ -26,6 +26,7 @@
 
 @moa.args.argument('filter', nargs='?', help='show only directories that match this filter')
 @moa.args.addFlag('-a', '--all')
+@moa.args.doNotLog
 @moa.args.command
 def tree(job, args):
     """
@@ -102,6 +103,7 @@ def tree(job, args):
         #    ("%%s %%-%ds | %%s"  % maxTemplateLen) % (s,t,p), f='jinja')
 
 @moa.args.needsJob
+@moa.args.doNotLog
 @moa.args.command
 def out(job, args):
     """
@@ -114,6 +116,7 @@ def out(job, args):
         print out
 
 @moa.args.needsJob
+@moa.args.doNotLog
 @moa.args.command
 def err(job, args):
     """
@@ -125,6 +128,7 @@ def err(job, args):
     else:
         print err
 
+@moa.args.doNotLog
 @moa.args.command
 def version(job, args):
     """

lib/python/moa/template/local_templates/autohagfish.jinja2

@@ -0,0 +1,57 @@
+### prepare
+
+if [[ ! -f "db.1.ebwt" ]]
+then
+    echo "Building index for {{ fasta }}"
+    bowtie-build {{ fasta }} db
+else
+    echo "Skip bowtie build - files exists"
+fi
+
+### run
+
+DEBUG=""
+
+mkdir -p touch
+[[ -f "{{ outbase }}.unsorted" ]] || (
+    echo "Running bowtie for"
+    echo "  forward: {{ fw_fq }}"
+    echo "  reverse: {{ rev_fq }}"
+    if [[ $DEBUG == 'echo' ]]
+    then
+        echo bowtie -I 1 -X 10000 -p {{ threads }} --fr  -S \
+            db -1 {{ fw_fq }} -2 {{ rev_fq }}  \
+            \| samtools view -f 2 -bS - \> {{ outbase }}.unsorted
+    else
+        bowtie -I 1 -X 10000 -p {{ threads }} --fr  -S \
+            db -1 {{ fw_fq }} -2 {{ rev_fq }}  \
+            | samtools view -f 2 -bS - > {{ outbase }}.unsorted
+    fi
+)
+
+[[ -f "{{ outbase }}.bam" ]] || (
+    echo "Sorting {{ outbase }}.bam"
+    $DEBUG samtools sort {{ outbase }}.unsorted {{ outbase }}
+)
+
+[[ -f "{{ outbase }}.bai" ]] || (
+    echo "Indexing {{ outbase }}"
+    $DEBUG samtools index {{ outbase }}.bam
+)
+
+[[ -d "readpairs/{{ outbase }}" ]] || (
+    echo "running hagfish_extract for {{ outbase }}"
+    $DEBUG hagfish_extract -v {{ outbase }}.bam 
+)
+
+### finish
+
+hagfish_gapfinder -v -f {{ fasta }}
+hagfish_coverage_combine -v
+hagfish_report -v
+
+### clean
+
+rm -rf `dirname {{ output }}`
+rm -rf bins combined coverage  readpairs  report  seqInfo  stats 
+

lib/python/moa/template/local_templates/autohagfish.moa

@@ -0,0 +1,62 @@
+author: Mark Fiers
+backend: ruff
+commands:
+  run:
+    help: 'Run hagfish'
+    mode: map
+  clean:
+    mode: simple
+    help: remove all Hagfish files
+  finish:
+    help: finish up - find gaps - combine plots - create a report
+    mode: simple
+creation_date: Tue Mar 29 16:34:19 2011
+description: Run the preparatory steps for hagfish
+filesets:
+  fasta:
+    category: prerequisite
+    help: fasta sequence of the reference 
+    type: single
+    optional: false
+  fw_fq:
+    category: input
+    help: 'forward fq input'
+    optional: false
+    pattern: '*/*1.fq'
+    type: set
+  rev_fq:
+    category: input
+    help: 'reverse fq input'
+    optional: true
+    pattern: '*/*2.fq'
+    type: map
+    source: fw_fq
+  outbase:
+    category: output
+    help: 'basename for output files'
+    optional: true
+    pattern: './*'
+    type: map
+    source: fw_fq
+parameters:
+  threads:
+    default: 8
+    help: 'no threads to use'
+    optional: true
+    type: integer
+  min_ok:
+    default: 0
+    help: Minimal acceptable insert size for an aligned pair. If omitted,
+      hagfish will make an estimate
+    optional: true
+    type: int
+  max_ok:
+    default: 0
+    help: Maximal acceptable insert size for an aligned pair. If omitted,
+      hagfish will make an estimate
+    optional: true
+    type: int
+moa_id: autohagfish
+modification_date: Thu, 19 May 2011 20:49:04 +1200
+name: autohagfish
+title: Automatically run bowtie & hagfish combined